#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
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34803143	34803144	+	Frame_Shift_Ins	INS	-	-	CACA			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr6:34803143_34803144insCACA	ENST00000192788.5	+	7	913_914	c.742_743insCACA	c.(742-744)tcafs	p.-248fs	UHRF1BP1_ENST00000452449.2_Frame_Shift_Ins_p.-248fs	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1								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						GCTGACTGACTCACAGCTCAAG	0.505																																					p.S248fs		Atlas-Indel	.											.	UHRF1BP1	102	.	0			c.742_743insCACA						PASS	.																																			SO:0001589	frameshift_variant	54887	exon7			.	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.743_746dupCACA	6.37:g.34803144_34803147dupCACA	ENSP00000192788:p.Ser248fs	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	120	18	0.15	NM_017754	Q9NXE0	Frame_Shift_Ins	INS	ENST00000192788.5	37	CCDS43455.1																																																																																			.	.	none		0.505	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1	NM_017754	
ERAP1	51752	hgsc.bcm.edu	37	5	96116871	96116871	+	Frame_Shift_Del	DEL	T	T	-			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:96116871delT	ENST00000443439.2	-	17	2545	c.2479delA	c.(2479-2481)atafs	p.I827fs	ERAP1_ENST00000514604.1_5'Flank|ERAP1_ENST00000296754.3_Frame_Shift_Del_p.I827fs	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	827					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)		TGAGTTTTTATTTTATCTCCC	0.373																																					p.I827fs		Pindel,Atlas-Indel	.											.	ERAP1	59	.	0			c.2480delT						PASS	.						84.0	89.0	87.0					5																	96116871		2203	4300	6503	SO:0001589	frameshift_variant	51752	exon17			.	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.2479delA	5.37:g.96116871delT	ENSP00000406304:p.Ile827fs	Somatic	87	.	.		WXS	Illumina HiSeq	Phase_I	128	31	0.242	NM_001198541	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Frame_Shift_Del	DEL	ENST00000443439.2	37	CCDS47250.1																																																																																			.	.	none		0.373	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442	
FAM157A	728262	hgsc.bcm.edu	37	3	197880131	197880139	+	lincRNA	DEL	GCAGCAGCA	GCAGCAGCA	-	rs56683636		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	GCAGCAGCA	GCAGCAGCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:197880131_197880139delGCAGCAGCA	ENST00000437428.2	+	0	11_19							C9JC47	F157A_HUMAN	family with sequence similarity 157, member A											NS(1)|skin(1)	2						ACAAGAACTGgcagcagcagcagcagcag	0.536																																					p.70_73del		Atlas-Indel	.											.	FAM157A	4	.	0			c.209_217del						PASS	.																																					728262	exon2			.			3q29	2013-01-30			ENSG00000236438	ENSG00000236438			34079	other	unknown							Standard	NM_001145248		Approved		uc011bup.1	C9JC47			3.37:g.197880140_197880148delGCAGCAGCA		Somatic	293	0	0		WXS	Illumina HiSeq	Phase_I	329	38	0.115502	NM_001145248		In_Frame_Del	DEL	ENST00000437428.2	37																																																																																				.	.	alt		0.536	FAM157A-001	KNOWN	not_best_in_genome_evidence|mRNA_end_NF|basic	lincRNA	lincRNA	OTTHUMT00000340078.2	NM_001145248	
TNFAIP3	7128	hgsc.bcm.edu	37	6	138198372	138198376	+	Frame_Shift_Del	DEL	CTCAT	CTCAT	-	rs543150550		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	CTCAT	CTCAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr6:138198372_138198376delCTCAT	ENST00000237289.4	+	6	1031_1035	c.965_969delCTCAT	c.(964-969)actcatfs	p.TH322fs	TNFAIP3_ENST00000485192.1_3'UTR	NM_001270507.1|NM_001270508.1|NM_006290.3	NP_001257436.1|NP_001257437.1|NP_006281.1	P21580	TNAP3_HUMAN	tumor necrosis factor, alpha-induced protein 3	322	2 X approximate repeats.				apoptotic process (GO:0006915)|B-1 B cell homeostasis (GO:0001922)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of B cell activation (GO:0050869)|negative regulation of bone resorption (GO:0045779)|negative regulation of CD40 signaling pathway (GO:2000349)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast proliferation (GO:0090291)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 3 signaling pathway (GO:0034140)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of protein catabolic process (GO:0045732)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked deubiquitination (GO:0070536)|protein oligomerization (GO:0051259)|regulation of defense response to virus by host (GO:0050691)|regulation of germinal center formation (GO:0002634)|regulation of vascular wound healing (GO:0061043)|response to molecule of bacterial origin (GO:0002237)|tolerance induction to lipopolysaccharide (GO:0072573)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|protease binding (GO:0002020)|protein self-association (GO:0043621)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.0?(25)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(196)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	225	Breast(32;0.135)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000849)|OV - Ovarian serous cystadenocarcinoma(155;0.00468)		CATGGCACAACTCATCTCATCAATG	0.454			"""D, N, F"""		"""marginal zone B-cell lymphomas, Hodgkin's lymphoma, primary mediastinal B cell lymphoma"""																																p.322_323del	GBM(130;153 1739 22295 28918 47987)	Pindel,Atlas-Indel	.		Rec	yes		6	6q23	7128	"""tumor necrosis factor, alpha-induced protein 3"""		L	.	TNFAIP3	340	.	25	Whole gene deletion(25)	haematopoietic_and_lymphoid_tissue(25)	c.964_968del						PASS	.																																			SO:0001589	frameshift_variant	7128	exon6			.	M59465	CCDS5187.1	6q23-q25	2013-01-21			ENSG00000118503	ENSG00000118503		"""OTU domain containing"""	11896	protein-coding gene	gene with protein product		191163				2118515	Standard	NM_006290		Approved	A20, OTUD7C	uc031spw.1	P21580	OTTHUMG00000015664	ENST00000237289.4:c.965_969delCTCAT	6.37:g.138198377_138198381delCTCAT	ENSP00000237289:p.Thr322fs	Somatic	91	.	.		WXS	Illumina HiSeq	Phase_I	70	33	0.471	NM_001270508	B2R767|E1P588|Q2HIX9|Q5VXQ7|Q9NSR6	Frame_Shift_Del	DEL	ENST00000237289.4	37	CCDS5187.1																																																																																			.	.	none		0.454	TNFAIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042414.1		
NXPE2	120406	hgsc.bcm.edu	37	11	114576570	114576571	+	Frame_Shift_Ins	INS	-	-	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:114576570_114576571insA	ENST00000389586.4	+	5	1186_1187	c.996_997insA	c.(997-999)aaafs	p.K333fs	NXPE2_ENST00000375475.5_Intron	NM_182495.5	NP_872301.2	Q96DL1	NXPE2_HUMAN	neurexophilin and PC-esterase domain family, member 2	333						integral component of membrane (GO:0016021)											GTTATACTTTGAAAAAAATGTG	0.322																																					p.L332fs		Pindel,Atlas-Indel	.											.	.	.	.	0			c.996_997insA						PASS	.																																			SO:0001589	frameshift_variant	120406	exon5			.	AK057953	CCDS44738.1	11q23.2	2012-06-14	2012-06-11	2012-06-11	ENSG00000204361	ENSG00000204361			26331	protein-coding gene	gene with protein product			"""family with sequence similarity 55, member B"""	FAM55B			Standard	NM_182495		Approved	FLJ25224	uc009yyy.2	Q96DL1	OTTHUMG00000168293	ENST00000389586.4:c.1003dupA	11.37:g.114576577_114576577dupA	ENSP00000374237:p.Lys333fs	Somatic	222	.	.		WXS	Illumina HiSeq	Phase_I	256	60	0.234	NM_182495	Q2NKI8	Frame_Shift_Ins	INS	ENST00000389586.4	37	CCDS44738.1																																																																																			.	.	none		0.322	NXPE2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399181.1	NM_182495	
IL33	90865	hgsc.bcm.edu	37	9	6254556	6254556	+	Intron	DEL	A	A	-			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr9:6254556delA	ENST00000381434.3	+	6	625				IL33_ENST00000456383.2_Intron|IL33_ENST00000417746.2_Intron	NM_033439.3	NP_254274.1	O95760	IL33_HUMAN	interleukin 33						extrinsic apoptotic signaling pathway (GO:0097191)|negative regulation of immunoglobulin secretion (GO:0051025)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of T-helper 1 type immune response (GO:0002826)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of immunoglobulin secretion (GO:0051024)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage activation (GO:0043032)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type 2 immune response (GO:0002830)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|nucleus (GO:0005634)	cytokine activity (GO:0005125)			breast(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(4)|stomach(1)|urinary_tract(1)	16		Acute lymphoblastic leukemia(23;0.158)|Prostate(43;0.167)		GBM - Glioblastoma multiforme(50;0.0161)|Lung(218;0.105)		CTGTGGAGGTAAAAAAAAAAA	0.373																																					.		Atlas-Indel	.											.	IL33	27	.	0			c.612+2A>-						PASS	.						31.0	32.0	32.0					9																	6254556		2203	4300	6503	SO:0001627	intron_variant	90865	exon7			.	AB024518	CCDS6468.1, CCDS56563.1, CCDS56564.1	9p24.1	2014-01-28	2006-11-20	2006-11-20	ENSG00000137033	ENSG00000137033		"""Interleukins and interleukin receptors"""	16028	protein-coding gene	gene with protein product	"""DVS27-related protein"", ""nuclear factor for high endothelial venules"", ""interleukin-1 family, member 11"""	608678	"""chromosome 9 open reading frame 26 (NF-HEV)"""	C9orf26		10566975, 12819012	Standard	NM_033439		Approved	DVS27, DKFZp586H0523, NF-HEV, IL1F11	uc003zjt.3	O95760	OTTHUMG00000019516	ENST00000381434.3:c.612+3A>-	9.37:g.6254556delA		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	39	11	0.282051	NM_033439	B2R8L1|B4DJ35|B4E1Q9|D3DRI5|E7EAX4|Q2YEJ5	Splice_Site	DEL	ENST00000381434.3	37	CCDS6468.1																																																																																			A|1.000;|0.000	.	weak		0.373	IL33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051655.1	NM_033439	
ATXN2L	11273	hgsc.bcm.edu	37	16	28845868	28845884	+	Frame_Shift_Del	DEL	TCAGCCCCGCCGATGAT	TCAGCCCCGCCGATGAT	-	rs147688158|rs367754572		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	TCAGCCCCGCCGATGAT	TCAGCCCCGCCGATGAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr16:28845868_28845884delTCAGCCCCGCCGATGAT	ENST00000336783.4	+	18	2454_2470	c.2287_2303delTCAGCCCCGCCGATGAT	c.(2287-2304)tcagccccgccgatgatgfs	p.SAPPMM763fs	ATXN2L_ENST00000395547.2_Frame_Shift_Del_p.SAPPMM763fs|ATXN2L_ENST00000564304.1_Frame_Shift_Del_p.SAPPMM769fs|ATXN2L_ENST00000340394.8_Frame_Shift_Del_p.SAPPMM763fs|ATXN2L_ENST00000382686.4_Frame_Shift_Del_p.SAPPMM763fs|ATXN2L_ENST00000325215.6_Frame_Shift_Del_p.SAPPMM763fs|RP11-24N18.1_ENST00000563565.1_RNA|ATXN2L_ENST00000570200.1_Frame_Shift_Del_p.SAPPMM763fs|ATXN2L_ENST00000565845.1_3'UTR	NM_007245.3	NP_009176.2	Q8WWM7	ATX2L_HUMAN	ataxin 2-like	763					regulation of cytoplasmic mRNA processing body assembly (GO:0010603)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|membrane (GO:0016020)|nuclear speck (GO:0016607)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36						CCAGCCAGCCTCAGCCCCGCCGATGATGCAGGCCGCC	0.668																																					p.762_768del		Atlas-Indel	.											.	ATXN2L	159	.	0			c.2286_2302del						PASS	.																																			SO:0001589	frameshift_variant	11273	exon18			.		CCDS10639.1, CCDS10640.1, CCDS10641.1, CCDS32423.1, CCDS45451.1, CCDS58443.1	16p11	2008-02-05			ENSG00000168488	ENSG00000168488			31326	protein-coding gene	gene with protein product		607931				11784712, 14769358	Standard	NM_007245		Approved	A2lp, A2D	uc002dqy.4	Q8WWM7	OTTHUMG00000097038	ENST00000336783.4:c.2287_2303delTCAGCCCCGCCGATGAT	16.37:g.28845868_28845884delTCAGCCCCGCCGATGAT	ENSP00000338718:p.Ser763fs	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	24	11	0.458333	NM_148416	A8K1R6|B9EGM2|E9PAR9|O95135|Q63ZY4|Q6NVJ8|Q6PJW6|Q8IU61|Q8IU95|Q8WWM3|Q8WWM4|Q8WWM5|Q8WWM6|Q99703	Frame_Shift_Del	DEL	ENST00000336783.4	37	CCDS10641.1																																																																																			.	.	none		0.668	ATXN2L-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214139.1	NM_007245	
ABCC6	368	hgsc.bcm.edu	37	16	16244433	16244438	+	Splice_Site	DEL	ACCGGG	ACCGGG	-			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	ACCGGG	ACCGGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr16:16244433_16244438delACCGGG	ENST00000205557.7	-	30	4429_4433	c.4400_4404delCCCGGT	c.(4399-4404)gcccgg>g	p.AR1467del		NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	1467	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|skin(6)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)	Cisplatin(DB00515)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Etoposide(DB00773)|Indomethacin(DB00328)|Probenecid(DB01032)|Sulfinpyrazone(DB01138)|Teniposide(DB00444)|Vinblastine(DB00570)	CGGGAGCCTTACCGGGCACAGTCCAT	0.675																																					p.1467_1468del		Atlas-Indel	.											.	ABCC6	110	.	0			c.4401_4403del						PASS	.																																			SO:0001630	splice_region_variant	368	exon30			.	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.4403+1CCCGGT>-	16.37:g.16244433_16244438delACCGGG		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	155	12	0.0774194	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	In_Frame_Del	DEL	ENST00000205557.7	37	CCDS10568.1																																																																																			.	.	none		0.675	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2		In_Frame_Del
MANSC4	100287284	hgsc.bcm.edu	37	12	27919655	27919656	+	Frame_Shift_Del	DEL	GT	GT	-			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	GT	GT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:27919655_27919656delGT	ENST00000381273.3	-	2	305_306	c.306_307delAC	c.(304-309)acactgfs	p.L103fs		NM_001146221.1	NP_001139693.1	A6NHS7	MANS4_HUMAN	MANSC domain containing 4	103	MANSC. {ECO:0000255|PROSITE- ProRule:PRU00341}.					integral component of membrane (GO:0016021)				kidney(1)	1						CAGCTCTCCAGTGTTGGGCAGT	0.426																																					p.103_103del		Atlas-Indel	.											.	MANSC4	9	.	0			c.307_308del						PASS	.																																			SO:0001589	frameshift_variant	100287284	exon2			.		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.306_307delAC	12.37:g.27919657_27919658delGT	ENSP00000370673:p.Leu103fs	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	152	28	0.184211	NM_001146221		Frame_Shift_Del	DEL	ENST00000381273.3	37	CCDS53770.1																																																																																			.	.	none		0.426	MANSC4-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000402902.1		
MANSC4	100287284	hgsc.bcm.edu	37	12	27919648	27919652	+	Frame_Shift_Del	DEL	CTCTC	CTCTC	-			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	CTCTC	CTCTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:27919648_27919652delCTCTC	ENST00000381273.3	-	2	309_313	c.310_314delGAGAG	c.(310-315)gagagcfs	p.ES104fs		NM_001146221.1	NP_001139693.1	A6NHS7	MANS4_HUMAN	MANSC domain containing 4	104	MANSC. {ECO:0000255|PROSITE- ProRule:PRU00341}.					integral component of membrane (GO:0016021)				kidney(1)	1						TAATATGCAGCTCTCCAGTGTTGGG	0.42																																					p.104_105del		Atlas-Indel	.											.	MANSC4	9	.	0			c.311_315del						PASS	.																																			SO:0001589	frameshift_variant	100287284	exon2			.		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.310_314delGAGAG	12.37:g.27919648_27919652delCTCTC	ENSP00000370673:p.Glu104fs	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	162	28	0.17284	NM_001146221		Frame_Shift_Del	DEL	ENST00000381273.3	37	CCDS53770.1																																																																																			.	.	none		0.420	MANSC4-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000402902.1		
TENM4	26011	hgsc.bcm.edu	37	11	78437206	78437208	+	In_Frame_Del	DEL	TGT	TGT	-			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	TGT	TGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:78437206_78437208delTGT	ENST00000278550.7	-	23	3928_3930	c.3466_3468delACA	c.(3466-3468)acadel	p.T1156del		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	1156					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)										CCTGCAGCACTGTTGTTCTTTTT	0.433																																					p.1156_1157del		Pindel,Atlas-Indel	.											.	.	.	.	0			c.3467_3469del						PASS	.																																			SO:0001651	inframe_deletion	26011	exon23			.	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.3466_3468delACA	11.37:g.78437209_78437211delTGT	ENSP00000278550:p.Thr1156del	Somatic	237	.	.		WXS	Illumina HiSeq	Phase_I	255	39	0.153	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	In_Frame_Del	DEL	ENST00000278550.7	37	CCDS44688.1																																																																																			.	.	none		0.433	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2		
CIITA	4261	hgsc.bcm.edu	37	16	11010310	11010310	+	Frame_Shift_Del	DEL	C	C	-			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr16:11010310delC	ENST00000324288.8	+	15	3189	c.3056delC	c.(3055-3057)accfs	p.T1019fs	CIITA_ENST00000381835.5_Frame_Shift_Del_p.T435fs	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	1019					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						TCCTTGGAAACCCTCAAGTGA	0.522			T	"""FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"""	"""PMBL, Hodgkin Lymphona, """																																p.T1019fs		Pindel,Atlas-Indel	.		Dom	yes		16	16p13	4261	"""class II, major histocompatibility complex, transactivator"""		L	.	CIITA	92	.	0			c.3055delA						PASS	.						47.0	38.0	41.0					16																	11010310		2197	4300	6497	SO:0001589	frameshift_variant	4261	exon15			.	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.3056delC	16.37:g.11010310delC	ENSP00000316328:p.Thr1019fs	Somatic	76	.	.		WXS	Illumina HiSeq	Phase_I	46	11	0.239	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Frame_Shift_Del	DEL	ENST00000324288.8	37	CCDS10544.1																																																																																			.	.	none		0.522	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246	
B2M	567	hgsc.bcm.edu	37	15	45003766	45003781	+	Frame_Shift_Del	DEL	GCTGTGCTCGCGCTAC	GCTGTGCTCGCGCTAC	-	rs11553033|rs104894481|rs11553044|rs369474839|rs552741313		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	GCTGTGCTCGCGCTAC	GCTGTGCTCGCGCTAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr15:45003766_45003781delGCTGTGCTCGCGCTAC	ENST00000558401.1	+	1	92_107	c.22_37delGCTGTGCTCGCGCTAC	c.(22-39)gctgtgctcgcgctactcfs	p.AVLALL8fs	PATL2_ENST00000558573.1_5'Flank|B2M_ENST00000544417.1_Frame_Shift_Del_p.AVLALL8fs|B2M_ENST00000559916.1_Frame_Shift_Del_p.AVLALL8fs	NM_004048.2	NP_004039.1	P61769	B2MG_HUMAN	beta-2-microglobulin	8					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein refolding (GO:0042026)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to molecule of bacterial origin (GO:0002237)|retina homeostasis (GO:0001895)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cytoplasm (GO:0005737)|early endosome lumen (GO:0031905)|early endosome membrane (GO:0031901)|endoplasmic reticulum lumen (GO:0005788)|ER to Golgi transport vesicle membrane (GO:0012507)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)	p.L15fs*41(4)|p.L13F(1)|p.A8T(1)|p.A11fs*42(1)|p.L12Q(1)		breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(30)|kidney(8)|large_intestine(6)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	59		all_cancers(109;1.88e-13)|all_epithelial(112;2.13e-11)|Lung NSC(122;2.22e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;4.16e-21)|GBM - Glioblastoma multiforme(94;8.97e-07)|COAD - Colon adenocarcinoma(120;0.0357)|Colorectal(105;0.0377)|Lung(196;0.0903)|LUSC - Lung squamous cell carcinoma(244;0.192)		CGTGGCCTTAGCTGTGCTCGCGCTACTCTCTCTTTC	0.616																																					p.7_12del		Pindel,Atlas-Indel	.											B2M,NS,lymphoid_neoplasm,+1,1	B2M	99	1	8	Deletion - Frameshift(5)|Substitution - Missense(3)	haematopoietic_and_lymphoid_tissue(4)|large_intestine(2)|kidney(1)|skin(1)	c.21_36del	GRCh37	CM060840	B2M	M	rs104894481	PASS	.																																			SO:0001589	frameshift_variant	567	exon1			.	AB021288	CCDS10113.1	15q21-q22.2	2013-01-11			ENSG00000166710	ENSG00000166710		"""Immunoglobulin superfamily / C1-set domain containing"""	914	protein-coding gene	gene with protein product		109700					Standard	NM_004048		Approved		uc001zuc.3	P61769	OTTHUMG00000131247	ENST00000558401.1:c.22_37delGCTGTGCTCGCGCTAC	15.37:g.45003766_45003781delGCTGTGCTCGCGCTAC	ENSP00000452780:p.Ala8fs	Somatic	93	.	.		WXS	Illumina HiSeq	Phase_I	68	25	0.368	NM_004048	P01884|Q540F8|Q6IAT8|Q9UCK0|Q9UD48|Q9UDF4	Frame_Shift_Del	DEL	ENST00000558401.1	37	CCDS10113.1																																																																																			.	.	none		0.616	B2M-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254007.2	NM_004048	
SLC35F5	80255	hgsc.bcm.edu	37	2	114500277	114500277	+	Frame_Shift_Del	DEL	A	A	-			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:114500277delA	ENST00000245680.2	-	7	1155	c.742delT	c.(742-744)tgcfs	p.C248fs	SLC35F5_ENST00000409342.1_Frame_Shift_Del_p.C242fs	NM_025181.2	NP_079457.2	Q8WV83	S35F5_HUMAN	solute carrier family 35, member F5	248					transport (GO:0006810)	integral component of membrane (GO:0016021)		p.C248fs*22(2)|p.?(1)		endometrium(1)|kidney(4)|large_intestine(2)|lung(7)|ovary(2)|prostate(3)|skin(1)	20						ACCACAAAGCAAAAAAAAAAG	0.343																																					p.C248fs		Pindel	.											SLC35F5,colon,carcinoma,+1,1	SLC35F5	60	1	3	Deletion - Frameshift(2)|Unknown(1)	ovary(2)|skin(1)	c.743delG						PASS	.						105.0	103.0	104.0					2																	114500277		2203	4300	6503	SO:0001589	frameshift_variant	80255	exon7			.	AF529364	CCDS2119.1	2q14.1	2013-05-22			ENSG00000115084	ENSG00000115084		"""Solute carriers"""	23617	protein-coding gene	gene with protein product							Standard	XM_005263799		Approved	FLJ22004	uc002tku.1	Q8WV83	OTTHUMG00000131361	ENST00000245680.2:c.742delT	2.37:g.114500277delA	ENSP00000245680:p.Cys248fs	Somatic	44	.	.		WXS	Illumina HiSeq	Phase_I	76	15	0.197	NM_025181	Q9H6P8|Q9H7D8	Frame_Shift_Del	DEL	ENST00000245680.2	37	CCDS2119.1																																																																																			.	.	none		0.343	SLC35F5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254150.1	NM_025181	
CBWD3	445571	hgsc.bcm.edu	37	9	70900911	70900912	+	Frame_Shift_Ins	INS	-	-	A	rs200498038|rs367958837	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr9:70900911_70900912insA	ENST00000360171.6	+	11	1322_1323	c.771_772insA	c.(772-774)aaafs	p.K258fs	CBWD3_ENST00000377342.5_Frame_Shift_Ins_p.K238fs	NM_201453.2	NP_958861.2	Q5JTY5	CBWD3_HUMAN	COBW domain containing 3	258							ATP binding (GO:0005524)			kidney(1)|large_intestine(1)|lung(2)|prostate(1)	5				all cancers(8;0.00136)|Epithelial(8;0.0288)|GBM - Glioblastoma multiforme(74;0.0402)|OV - Ovarian serous cystadenocarcinoma(323;0.18)		TTAGTTTGCAGAAAAAACTTCA	0.317													|||unknown(NO_COVERAGE)	2457	0.490615	0.4319	0.5951	5008	,	,		19815	0.4355		0.5934	False		,,,				2504	0.4468				p.Q257fs		Pindel	.											.	CBWD3	10	.	0			c.771_772insA						PASS	.			42,54		20,2,26						3.1	1.0			1	91,101		44,3,49	no	frameshift	CBWD3	NM_201453.2		64,5,75	A1A1,A1R,RR		47.3958,43.75,46.1806				133,155				SO:0001589	frameshift_variant	445571	exon11			.	BC069006	CCDS35038.1, CCDS35038.2	9q13	2014-05-06			ENSG00000196873	ENSG00000196873			18519	protein-coding gene	gene with protein product		611080				15233989, 12421752	Standard	XM_005277637		Approved	bA561O23.1	uc004aga.4	Q5JTY5	OTTHUMG00000184383	ENST00000360171.6:c.777dupA	9.37:g.70900917_70900917dupA	ENSP00000353295:p.Lys258fs	Somatic	104	.	.		WXS	Illumina HiSeq	Phase_I	128	35	0.273	NM_201453	B4DNG9|Q6VB91	Frame_Shift_Ins	INS	ENST00000360171.6	37	CCDS35038.1																																																																																			.	.	weak		0.317	CBWD3-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052526.1	NM_201453	
PI4KAP2	375133	hgsc.bcm.edu	37	22	21841122	21841126	+	RNA	DEL	TCTTA	TCTTA	-	rs200598591		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	TCTTA	TCTTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr22:21841122_21841126delTCTTA	ENST00000450651.1	-	0	866_870							A4QPH2	PI4P2_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha pseudogene 2						phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)		kinase activity (GO:0016301)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)			endometrium(3)|urinary_tract(1)	4						GTCAGGTACTTCTTATCTGAGAACA	0.537																																					.		Pindel	.											.	PI4KAP2	11	.	0			.						PASS	.																																					375133	.			.			22q11.21	2014-03-20	2007-08-14		ENSG00000183506	ENSG00000183506			33577	pseudogene	pseudogene							Standard	NR_003700		Approved		uc011aie.1	A4QPH2	OTTHUMG00000150827		22.37:g.21841122_21841126delTCTTA		Somatic	109	.	.		WXS	Illumina HiSeq	Phase_I	111	76	0.685	.	Q6ICJ0|Q6ZT68|Q8WUK7	RNA	DEL	ENST00000450651.1	37																																																																																				TCTTA|0.738;-|0.262	0.262	strong		0.537	PI4KAP2-005	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000334908.1		
CBWD6	644019	hgsc.bcm.edu	37	9	69218548	69218549	+	Frame_Shift_Ins	INS	-	-	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr9:69218548_69218549insT	ENST00000377457.5	-	11	882_883	c.777_778insA	c.(775-780)aaacttfs	p.L260fs	CBWD6_ENST00000377449.1_Frame_Shift_Ins_p.L224fs|CBWD6_ENST00000382399.4_Frame_Shift_Ins_p.L240fs|CBWD6_ENST00000468061.1_5'UTR	NM_001085457.1	NP_001078926.1	Q4V339	CBWD6_HUMAN	COBW domain containing 6	260							ATP binding (GO:0005524)			lung(4)	4						ACATGCTGAAGTTTTTTCTGCA	0.307																																					p.L260fs		Pindel	.											.	CBWD6	19	.	0			c.778_779insA						PASS	.																																			SO:0001589	frameshift_variant	644019	exon11			.		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.778dupA	9.37:g.69218554_69218554dupT	ENSP00000366677:p.Leu260fs	Somatic	141	.	.		WXS	Illumina HiSeq	Phase_I	156	35	0.224	NM_001085457		Frame_Shift_Ins	INS	ENST00000377457.5	37	CCDS43827.1																																																																																			.	.	weak		0.307	CBWD6-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143172.2	XM_928822	
AQP12A	375318	hgsc.bcm.edu	37	2	241631786	241631786	+	Frame_Shift_Del	DEL	G	G	-	rs369196482		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:241631786delG	ENST00000337801.4	+	2	488	c.419delG	c.(418-420)agcfs	p.S141fs	AC011298.2_ENST00000407635.2_lincRNA|AQP12A_ENST00000429564.1_Frame_Shift_Del_p.S153fs	NM_198998.2	NP_945349.1	Q8IXF9	AQ12A_HUMAN	aquaporin 12A	141						integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			endometrium(2)|kidney(3)|large_intestine(2)|lung(7)	14		all_epithelial(40;7.49e-12)|Breast(86;0.000148)|Renal(207;0.00571)|Ovarian(221;0.104)|all_neural(83;0.107)|all_hematologic(139;0.182)|all_lung(227;0.186)|Melanoma(123;0.238)		Epithelial(32;2.2e-31)|all cancers(36;1.08e-28)|OV - Ovarian serous cystadenocarcinoma(60;2.13e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.52e-06)|Lung(119;0.00163)|LUSC - Lung squamous cell carcinoma(224;0.008)|Colorectal(34;0.0124)|COAD - Colon adenocarcinoma(134;0.0757)		CAGAGCTGCAGCTCGGCCCTG	0.692																																					p.S140fs		Pindel	.											.	AQP12A	32	.	0			c.418delA						PASS	.			36,3516		5,26,1745	5.0	8.0	7.0			2.5	1.0	2		7	36,7602		2,32,3785	no	frameshift	AQP12A	NM_198998.1		7,58,5530	A1A1,A1R,RR		0.4713,1.0135,0.6434			241631786	72,11118	1936	4133	6069	SO:0001589	frameshift_variant	375318	exon2			.	AB040748		2q37.3	2013-06-03	2005-05-26	2005-05-26	ENSG00000184945	ENSG00000184945		"""Ion channels / Aquaporins"""	19941	protein-coding gene	gene with protein product		609789	"""aquaporin 12"""	AQP12			Standard	NM_198998		Approved		uc002vzu.3	Q8IXF9	OTTHUMG00000183906	ENST00000337801.4:c.419delG	2.37:g.241631786delG	ENSP00000337144:p.Ser141fs	Somatic	117	.	.		WXS	Illumina HiSeq	Phase_I	54	13	0.241	NM_198998		Frame_Shift_Del	DEL	ENST00000337801.4	37																																																																																				.	.	weak		0.692	AQP12A-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000257185.2	NM_198998	
MANSC4	100287284	hgsc.bcm.edu	37	12	27919649	27919656	+	Frame_Shift_Del	DEL	TCTCCAGT	TCTCCAGT	-			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	TCTCCAGT	TCTCCAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:27919649_27919656delTCTCCAGT	ENST00000381273.3	-	2	305_312	c.306_313delACTGGAGA	c.(304-315)acactggagagcfs	p.LES103fs		NM_001146221.1	NP_001139693.1	A6NHS7	MANS4_HUMAN	MANSC domain containing 4	103	MANSC. {ECO:0000255|PROSITE- ProRule:PRU00341}.					integral component of membrane (GO:0016021)				kidney(1)	1						AATATGCAGCTCTCCAGTGTTGGGCAGT	0.418																																					p.103_105del		Pindel	.											.	MANSC4	9	.	0			c.307_314del						PASS	.																																			SO:0001589	frameshift_variant	100287284	exon2			.		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.306_313delACTGGAGA	12.37:g.27919649_27919656delTCTCCAGT	ENSP00000370673:p.Leu103fs	Somatic	187	.	.		WXS	Illumina HiSeq	Phase_I	164	35	0.213	NM_001146221		Frame_Shift_Del	DEL	ENST00000381273.3	37	CCDS53770.1																																																																																			.	.	none		0.418	MANSC4-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000402902.1		
HOXA11	3207	hgsc.bcm.edu	37	7	27222462	27222462	+	Frame_Shift_Del	DEL	T	T	-			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr7:27222462delT	ENST00000006015.3	-	2	966	c.895delA	c.(895-897)attfs	p.I299fs	HOXA11-AS_ENST00000520395.1_RNA|HOXA11-AS_ENST00000522674.1_RNA|HOXA11-AS_ENST00000520360.1_RNA|RP1-170O19.20_ENST00000470747.4_5'Flank|HOXA10_ENST00000396344.4_5'Flank|HOXA11-AS_ENST00000522863.1_RNA	NM_005523.5	NP_005514.1	P31270	HXA11_HUMAN	homeobox A11	299					anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|developmental growth (GO:0048589)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal joint morphogenesis (GO:0060272)|male gonad development (GO:0008584)|mesodermal cell fate specification (GO:0007501)|metanephros development (GO:0001656)|multicellular organismal development (GO:0007275)|organ induction (GO:0001759)|positive regulation of cell development (GO:0010720)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of transcription, DNA-templated (GO:0045893)|proximal/distal pattern formation (GO:0009954)|single fertilization (GO:0007338)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)|uterus development (GO:0060065)	nucleus (GO:0005634)|protein complex (GO:0043234)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(8)|ovary(1)|skin(2)	16						TCTCTGTTAATTTTTTTTTCC	0.448			T	NUP98	CML																																p.I299fs		Pindel	.		Dom	yes		7	7p15-p14.2	3207	homeo box A11		L	.	HOXA11	29	.	0			c.896delT						PASS	.						78.0	79.0	79.0					7																	27222462		2203	4300	6503	SO:0001589	frameshift_variant	3207	exon2			.		CCDS5411.1	7p15.2	2014-09-17	2005-12-22		ENSG00000005073	ENSG00000005073		"""Homeoboxes / ANTP class : HOXL subclass"""	5101	protein-coding gene	gene with protein product		142958	"""homeo box A11"""	HOX1I, HOX1		1973146, 1358459	Standard	NM_005523		Approved		uc003syx.3	P31270	OTTHUMG00000023437	ENST00000006015.3:c.895delA	7.37:g.27222462delT	ENSP00000006015:p.Ile299fs	Somatic	86	.	.		WXS	Illumina HiSeq	Phase_I	60	17	0.283	NM_005523	A4D190	Frame_Shift_Del	DEL	ENST00000006015.3	37	CCDS5411.1																																																																																			.	.	none		0.448	HOXA11-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358754.1		
C15orf40	123207	hgsc.bcm.edu	37	15	83677271	83677271	+	Intron	DEL	A	A	-	rs373204607		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr15:83677271delA	ENST00000513601.2	-	3	374				RP11-382A20.5_ENST00000566841.1_RNA|C15orf40_ENST00000538348.2_Intron|C15orf40_ENST00000565712.1_Intron|C15orf40_ENST00000304177.5_Intron|C15orf40_ENST00000451195.3_Intron			Q8WUR7	CO040_HUMAN	chromosome 15 open reading frame 40											large_intestine(3)|lung(2)|skin(1)	6						attttgtctcaaaaaaaaaaa	0.483																																					p.L132fs		Pindel	.											.	C15orf40	18	.	0			c.396delG						PASS	.						31.0	31.0	31.0					15																	83677271		2203	4300	6503	SO:0001627	intron_variant	123207	exon3			.	BC019820	CCDS32312.1, CCDS32312.2, CCDS53968.1, CCDS53969.1	15q25.2	2012-05-30			ENSG00000169609	ENSG00000169609			28443	protein-coding gene	gene with protein product							Standard	NM_144597		Approved	MGC29937	uc010uoo.1	Q8WUR7	OTTHUMG00000160473	ENST00000513601.2:c.366+28T>-	15.37:g.83677271delA		Somatic	18	.	.		WXS	Illumina HiSeq	Phase_I	34	12	0.353	NM_001160113	A6NIC9|B2R5E7|F5GX92|F8WD31|G5EA00	Frame_Shift_Del	DEL	ENST00000513601.2	37	CCDS32312.2																																																																																			.	.	weak		0.483	C15orf40-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360737.2	NM_144597	
MFSD6	54842	hgsc.bcm.edu	37	2	191300956	191300956	+	Silent	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:191300956T>C	ENST00000392328.1	+	3	525	c.201T>C	c.(199-201)gaT>gaC	p.D67D	MFSD6_ENST00000281416.7_Silent_p.D67D	NM_017694.3	NP_060164.3	Q6ZSS7	MFSD6_HUMAN	major facilitator superfamily domain containing 6	67					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(3)|stomach(1)	23						TAAACAACGATCTTCTAATTT	0.393																																					p.D67D		Atlas-SNP	.											MFSD6,NS,carcinoma,+2,1	MFSD6	58	1	0			c.T201C						scavenged	.						94.0	99.0	98.0					2																	191300956		2203	4300	6503	SO:0001819	synonymous_variant	54842	exon3			CAACGATCTTCTA		CCDS2306.1	2q32.2	2008-10-29			ENSG00000151690	ENSG00000151690			24711	protein-coding gene	gene with protein product		613476					Standard	NM_017694		Approved	FLJ20160	uc002urz.2	Q6ZSS7	OTTHUMG00000132671	ENST00000392328.1:c.201T>C	2.37:g.191300956T>C		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	148	3	0.0202703	NM_017694	D3KSZ4|Q86TH2|Q9NXM3	Silent	SNP	ENST00000392328.1	37	CCDS2306.1																																																																																			.	.	none		0.393	MFSD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255931.1		
SOX6	55553	hgsc.bcm.edu	37	11	16010543	16010543	+	Splice_Site	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:16010543C>T	ENST00000352083.6	-	14	2043	c.1966G>A	c.(1966-1968)Gga>Aga	p.G656R	SOX6_ENST00000316399.6_Splice_Site_p.G636R|SOX6_ENST00000528252.1_Splice_Site_p.G629R|SOX6_ENST00000396356.3_Splice_Site_p.G636R|SOX6_ENST00000528429.1_Splice_Site_p.G656R|SOX6_ENST00000527619.1_Splice_Site_p.G632R			P35712	SOX6_HUMAN	SRY (sex determining region Y)-box 6	656					astrocyte differentiation (GO:0048708)|cardiac muscle cell differentiation (GO:0055007)|cartilage development (GO:0051216)|cell morphogenesis (GO:0000902)|cellular response to transforming growth factor beta stimulus (GO:0071560)|erythrocyte development (GO:0048821)|gene silencing (GO:0016458)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oligodendrocyte cell fate specification (GO:0021778)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.G632*(1)|p.G636*(1)		NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(23)|ovary(3)|pancreas(1)|prostate(2)	43						CTGCACTCACCTAAGATTTTG	0.493											OREG0020800	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G669R		Atlas-SNP	.											SOX6_ENST00000527619,NS,carcinoma,0,2	SOX6	149	2	2	Substitution - Nonsense(2)	lung(2)	c.G2005A						scavenged	.						146.0	136.0	139.0					11																	16010543		2200	4294	6494	SO:0001630	splice_region_variant	55553	exon14			ACTCACCTAAGAT	AF309034	CCDS7821.1, CCDS53604.1, CCDS53605.1	11p15.3	2008-02-05						"""SRY (sex determining region Y)-boxes"""	16421	protein-coding gene	gene with protein product		607257				11255018	Standard	NM_033326		Approved		uc001mme.3	P35712		ENST00000352083.6:c.1966+1G>A	11.37:g.16010543C>T		Somatic	138	0	0	707	WXS	Illumina HiSeq	Phase_I	185	2	0.0108108	NM_001145819	Q86VX7|Q9BXQ3|Q9BXQ4|Q9BXQ5|Q9H0I8	Missense_Mutation	SNP	ENST00000352083.6	37		.	.	.	.	.	.	.	.	.	.	C	31	5.086314	0.94100	.	.	ENSG00000110693	ENST00000316399;ENST00000352083;ENST00000396356;ENST00000528252;ENST00000527619;ENST00000528429	D;D;D;D;D;D	0.99098	-5.42;-5.42;-5.42;-5.42;-5.42;-5.42	5.72	5.72	0.89469	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	0.000000	0.85682	D	0.000000	D	0.99704	0.9887	H	0.99435	4.565	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	D	0.97133	0.9819	9	.	.	.	.	19.879	0.96888	0.0:1.0:0.0:0.0	.	636;656;632	P35712-3;P35712;P35712-2	.;SOX6_HUMAN;.	R	636;656;636;629;632;656	ENSP00000324948:G636R;ENSP00000339876:G656R;ENSP00000379644:G636R;ENSP00000432134:G629R;ENSP00000434455:G632R;ENSP00000433233:G656R	.	G	-	1	0	SOX6	15967119	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	7.818000	0.86416	2.695000	0.91970	0.655000	0.94253	GGA	.	.	none		0.493	SOX6-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000386811.1	NM_033326	Missense_Mutation
CYP11B1	1584	hgsc.bcm.edu	37	8	143958291	143958291	+	Silent	SNP	C	C	T	rs61751154		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr8:143958291C>T	ENST00000292427.4	-	4	638	c.606G>A	c.(604-606)ttG>ttA	p.L202L	CYP11B1_ENST00000517471.1_Silent_p.L202L|CYP11B1_ENST00000377675.3_Silent_p.L273L	NM_000497.3	NP_000488.3	P15538	C11B1_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 1	202					aldosterone biosynthetic process (GO:0032342)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|glucocorticoid biosynthetic process (GO:0006704)|glucose homeostasis (GO:0042593)|immune response (GO:0006955)|mineralocorticoid biosynthetic process (GO:0006705)|regulation of blood pressure (GO:0008217)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 11-beta-monooxygenase activity (GO:0004507)			central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|lung(36)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	67	all_cancers(97;4.74e-11)|all_epithelial(106;2.06e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Cimetidine(DB00501)|Clotrimazole(DB00257)|Etomidate(DB00292)|Fluconazole(DB00196)|Hydrocortisone(DB00741)|Ketoconazole(DB01026)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Miconazole(DB01110)|Mitotane(DB00648)|Phenytoin(DB00252)|Spironolactone(DB00421)	CAAAAAGAGCCAAGTTGCTGG	0.642									Familial Hyperaldosteronism type I				.|||	1	0.000199681	0.0008	0.0	5008	,	,		19690	0.0		0.0	False		,,,				2504	0.0				p.L202L		Atlas-SNP	.											CYP11B1,right_lower_lobe,carcinoma,0,1	CYP11B1	128	1	0			c.G606A						scavenged	.						37.0	38.0	38.0					8																	143958291		2203	4300	6503	SO:0001819	synonymous_variant	1584	exon4	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	AAGAGCCAAGTTG	D16153	CCDS6392.1, CCDS34953.1	8q21-q22	2013-06-19	2003-01-14		ENSG00000160882	ENSG00000160882	1.14.15.4	"""Cytochrome P450s"""	2591	protein-coding gene	gene with protein product	"""steroid 11-beta-monooxygenase"""	610613	"""cytochrome P450, subfamily XIB (steroid 11-beta-hydroxylase), polypeptide 1"""	CYP11B		1303253	Standard	XM_005250807		Approved	P450C11, FHI, CPN1	uc003yxi.3	P15538	OTTHUMG00000164637	ENST00000292427.4:c.606G>A	8.37:g.143958291C>T		Somatic	144	15	0.104167		WXS	Illumina HiSeq	Phase_I	157	24	0.152866	NM_000497	Q14095|Q4VAQ8|Q4VAQ9|Q9UML2	Silent	SNP	ENST00000292427.4	37	CCDS6392.1																																																																																			C|0.025;T|0.975	0.975	strong		0.642	CYP11B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379475.2		
MUC4	4585	hgsc.bcm.edu	37	3	195511051	195511051	+	Missense_Mutation	SNP	C	C	A	rs74867514		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:195511051C>A	ENST00000463781.3	-	2	7859	c.7400G>T	c.(7399-7401)gGc>gTc	p.G2467V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.G2467V|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.G2467V(3)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGTGTCGGTGCCAGGAAGAGG	0.582																																					p.G2467V		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,+1,5	MUC4	1505	5	3	Substitution - Missense(3)	stomach(2)|endometrium(1)	c.G7400T						scavenged	.						36.0	33.0	34.0					3																	195511051		657	1587	2244	SO:0001583	missense	4585	exon2			TCGGTGCCAGGAA	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.7400G>T	3.37:g.195511051C>A	ENSP00000417498:p.Gly2467Val	Somatic	411	13	0.0316302		WXS	Illumina HiSeq	Phase_I	417	21	0.0503597	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	A	4.251	0.045673	0.08196	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.27890	1.64;1.7	.	.	.	.	.	.	.	.	T	0.10121	0.0248	N	0.02539	-0.55	0.23765	N	0.996904	B	0.09022	0.002	B	0.01281	0.0	T	0.36237	-0.9756	7	.	.	.	.	5.8178	0.18506	0.0:0.999:0.0:0.001	.	2467	E7ESK3	.	V	2467	ENSP00000417498:G2467V;ENSP00000420243:G2467V	.	G	-	2	0	MUC4	196995446	0.001000	0.12720	0.021000	0.16686	0.000000	0.00434	-2.888000	0.00711	-0.000000	0.14550	0.000000	0.15137	GGC	C|0.500;A|0.500	0.500	weak		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SGCE	8910	hgsc.bcm.edu	37	7	94218023	94218023	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr7:94218023C>T	ENST00000265735.7	-	10	1385	c.1275G>A	c.(1273-1275)caG>caA	p.Q425Q	SGCE_ENST00000445866.2_Silent_p.Q450Q|SGCE_ENST00000428696.2_Silent_p.Q416Q|SGCE_ENST00000415788.2_Silent_p.Q461Q|SGCE_ENST00000447873.1_Silent_p.Q416Q|SGCE_ENST00000437425.2_Silent_p.Q384Q	NM_003919.2	NP_003910.1	O43556	SGCE_HUMAN	sarcoglycan, epsilon	425					cell-matrix adhesion (GO:0007160)|muscle organ development (GO:0007517)	cytoskeleton (GO:0005856)|dendrite membrane (GO:0032590)|dystrophin-associated glycoprotein complex (GO:0016010)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|skin(1)	14	all_cancers(62;8.26e-10)|all_epithelial(64;5.59e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			GTTGGGGAATCTGAGTCTGAT	0.308																																					p.Q450Q		Atlas-SNP	.											.	SGCE	68	.	0			c.G1350A						PASS	.						130.0	129.0	130.0					7																	94218023		2203	4300	6503	SO:0001819	synonymous_variant	8910	exon11			GGGAATCTGAGTC	AF036364	CCDS5637.1, CCDS47642.1, CCDS47643.1, CCDS75634.1	7q21.3	2014-09-17			ENSG00000127990	ENSG00000127990			10808	protein-coding gene	gene with protein product		604149		DYT11		9475163, 9405466	Standard	NM_001099401		Approved		uc003unn.2	O43556	OTTHUMG00000022828	ENST00000265735.7:c.1275G>A	7.37:g.94218023C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	94	4	0.0425532	NM_001099401	B2R8N2|D6W5Q8|E9PF60|G5E9K6|Q6L8P0|Q75MH8|Q8NFG8|Q8WW28	Silent	SNP	ENST00000265735.7	37	CCDS5637.1																																																																																			.	.	none		0.308	SGCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255251.2		
EYS	346007	hgsc.bcm.edu	37	6	65300359	65300359	+	Missense_Mutation	SNP	C	C	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr6:65300359C>G	ENST00000370621.3	-	26	5927	c.5401G>C	c.(5401-5403)Gca>Cca	p.A1801P	EYS_ENST00000503581.1_Missense_Mutation_p.A1801P|EYS_ENST00000370616.2_Missense_Mutation_p.A1801P			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	1801					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						ATTGAAAGTGCTGGAGTTGCT	0.388																																					p.A1801P		Atlas-SNP	.											.	EYS	527	.	0			c.G5401C						PASS	.						136.0	126.0	129.0					6																	65300359		692	1590	2282	SO:0001583	missense	346007	exon26			AAAGTGCTGGAGT		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.5401G>C	6.37:g.65300359C>G	ENSP00000359655:p.Ala1801Pro	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	168	46	0.27381	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		.	.	.	.	.	.	.	.	.	.	C	7.913	0.736998	0.15574	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	D;D;D	0.84730	-1.89;-1.87;-1.87	5.87	2.14	0.27477	.	.	.	.	.	T	0.46405	0.1391	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.001	T	0.41466	-0.9507	9	0.66056	D	0.02	.	1.4311	0.02334	0.4143:0.259:0.21:0.1168	.	1801;1801	Q5T1H1-1;Q5T1H1	.;EYS_HUMAN	P	1801	ENSP00000424243:A1801P;ENSP00000359655:A1801P;ENSP00000359650:A1801P	ENSP00000359650:A1801P	A	-	1	0	EYS	65357080	0.000000	0.05858	0.005000	0.12908	0.036000	0.12997	-0.187000	0.09656	0.132000	0.18615	-0.467000	0.05162	GCA	.	.	none		0.388	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
ZNF821	55565	hgsc.bcm.edu	37	16	71894070	71894070	+	Nonsense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr16:71894070G>A	ENST00000565601.1	-	7	1497	c.1090C>T	c.(1090-1092)Cga>Tga	p.R364*	ZNF821_ENST00000425432.1_Nonsense_Mutation_p.R364*|ATXN1L_ENST00000569119.1_Intron|ZNF821_ENST00000564134.1_3'UTR|ZNF821_ENST00000313565.6_Nonsense_Mutation_p.R322*|ZNF821_ENST00000446827.2_Nonsense_Mutation_p.R322*	NM_001201553.1	NP_001188482.1	O75541	ZN821_HUMAN	zinc finger protein 821	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)			endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|ovary(2)	13						AACTGAGCTCGCAACATCATG	0.587																																					p.R364X		Atlas-SNP	.											ZNF821,NS,carcinoma,+1,1	ZNF821	25	1	0			c.C1090T						scavenged	.						88.0	78.0	81.0					16																	71894070		2198	4300	6498	SO:0001587	stop_gained	55565	exon7			GAGCTCGCAACAT	AF070588	CCDS32481.1, CCDS56006.1, CCDS73911.1	16q22.3	2008-05-02				ENSG00000102984		"""Zinc fingers, C2H2-type"""	28043	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_017530		Approved		uc021tlb.1	O75541		ENST00000565601.1:c.1090C>T	16.37:g.71894070G>A	ENSP00000455648:p.Arg364*	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	178	2	0.011236	NM_001201553	A6NK48|B4DKK4|D3DWS3	Nonsense_Mutation	SNP	ENST00000565601.1	37	CCDS56006.1	.	.	.	.	.	.	.	.	.	.	G	37	6.075471	0.97262	.	.	ENSG00000102984	ENST00000425432;ENST00000313565;ENST00000446827	.	.	.	6.1	2.61	0.31194	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.5882	16.2453	0.82441	0.0:0.0:0.6664:0.3336	.	.	.	.	X	364;322;322	.	ENSP00000313822:R322X	R	-	1	2	ZNF821	70451571	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.100000	0.41777	0.188000	0.20168	0.650000	0.86243	CGA	.	.	none		0.587	ZNF821-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434180.1	NM_017530	
TMEM202	338949	hgsc.bcm.edu	37	15	72700069	72700069	+	Silent	SNP	G	G	A	rs35916586	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr15:72700069G>A	ENST00000341689.3	+	5	711	c.657G>A	c.(655-657)tcG>tcA	p.S219S	TMEM202_ENST00000567679.1_3'UTR	NM_001080462.1	NP_001073931.1	A6NGA9	TM202_HUMAN	transmembrane protein 202	219						integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	18						CTTCCAGATCGCCTGCCTGTG	0.453													G|||	104	0.0207668	0.0	0.0072	5008	,	,		19775	0.0685		0.0089	False		,,,				2504	0.0215				p.S219S		Atlas-SNP	.											TMEM202,NS,malignant_melanoma,+1,2	TMEM202	40	2	0			c.G657A						scavenged	.	G		16,4382	22.3+/-47.3	0,16,2183	85.0	84.0	84.0		657	-1.2	0.0	15	dbSNP_126	84	138,8456	68.7+/-131.2	1,136,4160	no	coding-synonymous	TMEM202	NM_001080462.1		1,152,6343	AA,AG,GG		1.6058,0.3638,1.1853		219/274	72700069	154,12838	2199	4297	6496	SO:0001819	synonymous_variant	338949	exon5			CAGATCGCCTGCC		CCDS32287.1	15q24.1	2007-12-18				ENSG00000187806			33733	protein-coding gene	gene with protein product							Standard	NM_001080462		Approved	FLJ27523	uc002auq.3	A6NGA9		ENST00000341689.3:c.657G>A	15.37:g.72700069G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	141	4	0.0283688	NM_001080462		Silent	SNP	ENST00000341689.3	37	CCDS32287.1																																																																																			G|0.984;A|0.016	0.016	strong		0.453	TMEM202-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435756.1	NM_001080462	
DLG4	1742	hgsc.bcm.edu	37	17	7096397	7096397	+	Missense_Mutation	SNP	C	C	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr17:7096397C>A	ENST00000399506.2	-	17	1924	c.1733G>T	c.(1732-1734)cGg>cTg	p.R578L	DLG4_ENST00000399510.2_Missense_Mutation_p.R621L|DLG4_ENST00000302955.6_Missense_Mutation_p.R575L			P78352	DLG4_HUMAN	discs, large homolog 4 (Drosophila)	578	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|axon guidance (GO:0007411)|dendritic spine morphogenesis (GO:0060997)|establishment of protein localization (GO:0045184)|learning (GO:0007612)|locomotory exploration behavior (GO:0035641)|negative regulation of receptor internalization (GO:0002091)|nervous system development (GO:0007399)|neuromuscular process controlling balance (GO:0050885)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synaptic transmission (GO:0050806)|protein complex assembly (GO:0006461)|protein localization to synapse (GO:0035418)|receptor localization to synapse (GO:0097120)|regulation of grooming behavior (GO:2000821)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|signal transduction (GO:0007165)|social behavior (GO:0035176)|synaptic transmission (GO:0007268)|synaptic vesicle maturation (GO:0016188)|vocalization behavior (GO:0071625)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|cerebellar mossy fiber (GO:0044300)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|dendrite cytoplasm (GO:0032839)|dendritic spine (GO:0043197)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|juxtaparanode region of axon (GO:0044224)|neuron projection terminus (GO:0044306)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	acetylcholine receptor binding (GO:0033130)|beta-1 adrenergic receptor binding (GO:0031697)|D1 dopamine receptor binding (GO:0031748)|ionotropic glutamate receptor binding (GO:0035255)|P2Y1 nucleotide receptor binding (GO:0031812)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein phosphatase binding (GO:0019903)|scaffold protein binding (GO:0097110)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)	18					Guanidine(DB00536)	GTGGTAATCCCGGCCATCTAT	0.547																																					p.R621L		Atlas-SNP	.											DLG4_ENST00000302955,caecum,carcinoma,0,2	DLG4	110	2	0			c.G1862T						scavenged	.						128.0	131.0	130.0					17																	7096397		1984	4166	6150	SO:0001583	missense	1742	exon19			TAATCCCGGCCAT	U83192	CCDS45599.1, CCDS45600.1	17p13.1	2008-12-15	2001-12-04		ENSG00000132535	ENSG00000132535			2903	protein-coding gene	gene with protein product		602887				9286702	Standard	NM_001128827		Approved	PSD-95, PSD95, SAP90, SAP-90	uc010cly.3	P78352	OTTHUMG00000134327	ENST00000399506.2:c.1733G>T	17.37:g.7096397C>A	ENSP00000382425:p.Arg578Leu	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	174	2	0.0114943	NM_001365	B7Z1S1|G5E939|Q92941|Q9UKK8	Missense_Mutation	SNP	ENST00000399506.2	37		.	.	.	.	.	.	.	.	.	.	C	23.8	4.463857	0.84425	.	.	ENSG00000132535	ENST00000399506;ENST00000302955;ENST00000399510;ENST00000293813;ENST00000380912;ENST00000539674	T;T;T	0.45276	0.9;0.9;0.9	4.09	4.09	0.47781	Guanylate kinase/L-type calcium channel (1);Guanylate kinase, conserved site (1);Guanylate kinase (2);	.	.	.	.	T	0.59770	0.2218	M	0.74546	2.27	0.58432	D	0.999998	D;D;D;D	0.89917	0.996;0.973;1.0;0.988	D;D;D;D	0.91635	0.948;0.919;0.999;0.994	T	0.62320	-0.6879	9	0.66056	D	0.02	.	7.6128	0.28139	0.0:0.8866:0.0:0.1134	.	618;578;575;621	B9EGL1;P78352;G5E939;P78352-2	.;DLG4_HUMAN;.;.	L	578;575;621;621;518;621	ENSP00000382425:R578L;ENSP00000307471:R575L;ENSP00000382428:R621L	ENSP00000293813:R621L	R	-	2	0	DLG4	7037121	0.986000	0.35501	1.000000	0.80357	0.999000	0.98932	2.121000	0.41977	2.118000	0.64928	0.655000	0.94253	CGG	.	.	none		0.547	DLG4-002	KNOWN	non_canonical_TEC|not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000259419.2	NM_001365	
STX18	53407	hgsc.bcm.edu	37	4	4426931	4426931	+	Nonsense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr4:4426931G>A	ENST00000306200.2	-	8	784	c.721C>T	c.(721-723)Cga>Tga	p.R241*	STX18_ENST00000505286.1_Nonsense_Mutation_p.R241*	NM_016930.2	NP_058626.1	Q9P2W9	STX18_HUMAN	syntaxin 18	241					ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.R241*(1)		large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	5				UCEC - Uterine corpus endometrioid carcinoma (64;0.0534)		CCAATTAGTCGCTGATTTTCC	0.443																																					p.R241X		Atlas-SNP	.											STX18,rectum,carcinoma,0,1	STX18	16	1	1	Substitution - Nonsense(1)	large_intestine(1)	c.C721T						scavenged	.						150.0	124.0	133.0					4																	4426931		2203	4300	6503	SO:0001587	stop_gained	53407	exon8			TTAGTCGCTGATT	AB028741	CCDS3377.1	4p16.3-p16.2	2013-09-23			ENSG00000168818	ENSG00000168818			15942	protein-coding gene	gene with protein product		606046				10788491	Standard	NM_016930		Approved	Ufe1	uc003gic.3	Q9P2W9	OTTHUMG00000090331	ENST00000306200.2:c.721C>T	4.37:g.4426931G>A	ENSP00000305810:p.Arg241*	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	146	2	0.0136986	NM_016930	Q596L3|Q5TZP5	Nonsense_Mutation	SNP	ENST00000306200.2	37	CCDS3377.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.658307	0.88154	.	.	ENSG00000168818	ENST00000505286;ENST00000306200;ENST00000512195;ENST00000507908	.	.	.	5.3	4.37	0.52481	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09590	T	0.72	-0.0885	14.9737	0.71254	0.0:0.0:0.7837:0.2163	.	.	.	.	X	241;241;160;160	.	ENSP00000305810:R241X	R	-	1	2	STX18	4477832	1.000000	0.71417	0.996000	0.52242	0.592000	0.36648	2.298000	0.43602	2.478000	0.83669	0.563000	0.77884	CGA	.	.	none		0.443	STX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206696.1		
EXTL1	2134	hgsc.bcm.edu	37	1	26349716	26349716	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:26349716C>T	ENST00000374280.3	+	1	1446	c.579C>T	c.(577-579)ggC>ggT	p.G193G	EXTL1_ENST00000484339.1_3'UTR	NM_004455.2	NP_004446.2	Q92935	EXTL1_HUMAN	exostosin-like glycosyltransferase 1	193					protein glycosylation (GO:0006486)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0050508)	p.G193G(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|stomach(1)|urinary_tract(1)	23		Colorectal(325;3.46e-05)|Lung NSC(340;6.18e-05)|all_lung(284;9.43e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;6.44e-26)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000954)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00594)|READ - Rectum adenocarcinoma(331;0.0649)		TCCGGCCCGGCTTTGATGTGG	0.697																																					p.G193G		Atlas-SNP	.											EXTL1,NS,carcinoma,0,1	EXTL1	61	1	1	Substitution - coding silent(1)	lung(1)	c.C579T						scavenged	.						25.0	27.0	27.0					1																	26349716		2202	4298	6500	SO:0001819	synonymous_variant	2134	exon1			GCCCGGCTTTGAT	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.579C>T	1.37:g.26349716C>T		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	127	2	0.015748	NM_004455	Q6GSC1	Silent	SNP	ENST00000374280.3	37	CCDS271.1																																																																																			.	.	none		0.697	EXTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019749.1	NM_004455	
PLXNB3	5365	hgsc.bcm.edu	37	X	153037066	153037066	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:153037066C>T	ENST00000361971.5	+	14	2587	c.2473C>T	c.(2473-2475)Ccg>Tcg	p.P825S	PLXNB3_ENST00000538282.1_Missense_Mutation_p.P435S|PLXNB3_ENST00000538776.1_Missense_Mutation_p.P478S|PLXNB3_ENST00000538966.1_Missense_Mutation_p.P848S|PLXNB3_ENST00000538543.1_Intron	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	825	PSI 3.				axon guidance (GO:0007411)|cell chemotaxis (GO:0060326)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|negative regulation of GTPase activity (GO:0034260)|negative regulation of lamellipodium assembly (GO:0010593)|positive chemotaxis (GO:0050918)|positive regulation of endothelial cell proliferation (GO:0001938)|semaphorin-plexin signaling pathway (GO:0071526)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)			central_nervous_system(1)|endometrium(7)|large_intestine(2)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					CTTGTGCCCGCCGGGGGCTGT	0.697																																					p.P848S		Atlas-SNP	.											.	PLXNB3	208	.	0			c.C2542T						PASS	.						19.0	20.0	20.0					X																	153037066		2183	4289	6472	SO:0001583	missense	5365	exon15			TGCCCGCCGGGGG	AF149019	CCDS14729.1, CCDS55536.1	Xq28	2008-02-05			ENSG00000198753	ENSG00000198753		"""Plexins"""	9105	protein-coding gene	gene with protein product		300214		PLXN6		10520995	Standard	NM_005393		Approved	PLEXR, PLEXB3	uc010nuk.2	Q9ULL4	OTTHUMG00000024217	ENST00000361971.5:c.2473C>T	X.37:g.153037066C>T	ENSP00000355378:p.Pro825Ser	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	79	17	0.21519	NM_001163257	B7Z3E6|F5H773|Q9HDA4	Missense_Mutation	SNP	ENST00000361971.5	37	CCDS14729.1	.	.	.	.	.	.	.	.	.	.	C	9.903	1.207288	0.22205	.	.	ENSG00000198753	ENST00000538966;ENST00000361971;ENST00000538776;ENST00000538282	T;T;T;T	0.67698	5.3;5.27;4.68;-0.28	5.11	5.11	0.69529	.	0.369273	0.25900	N	0.027580	T	0.55705	0.1937	L	0.37630	1.12	0.09310	N	0.99999	B;B;B;B	0.24132	0.004;0.098;0.071;0.001	B;B;B;B	0.28916	0.004;0.031;0.096;0.007	T	0.38457	-0.9660	10	0.07990	T	0.79	.	14.9334	0.70935	0.0:1.0:0.0:0.0	.	478;507;848;825	B7Z3H9;B7Z9A5;F5H773;Q9ULL4	.;.;.;PLXB3_HUMAN	S	848;825;478;435	ENSP00000442736:P848S;ENSP00000355378:P825S;ENSP00000445569:P478S;ENSP00000441919:P435S	ENSP00000355378:P825S	P	+	1	0	PLXNB3	152690260	0.026000	0.19158	0.068000	0.19968	0.010000	0.07245	2.416000	0.44644	2.111000	0.64477	0.529000	0.55759	CCG	.	.	none		0.697	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1		
JAK3	3718	hgsc.bcm.edu	37	19	17948006	17948006	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:17948006G>A	ENST00000527670.1	-	12	1747	c.1718C>T	c.(1717-1719)gCg>gTg	p.A573V	JAK3_ENST00000534444.1_Missense_Mutation_p.A573V|JAK3_ENST00000458235.1_Missense_Mutation_p.A573V|JAK3_ENST00000526008.1_5'Flank			P52333	JAK3_HUMAN	Janus kinase 3	573	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell differentiation (GO:0030183)|enzyme linked receptor protein signaling pathway (GO:0007167)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of dendritic cell cytokine production (GO:0002731)|negative regulation of FasL biosynthetic process (GO:0045221)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of T cell activation (GO:0050868)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|negative regulation of thymocyte apoptotic process (GO:0070244)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of T cell apoptotic process (GO:0070232)|response to interleukin-15 (GO:0070672)|response to interleukin-2 (GO:0070669)|response to interleukin-4 (GO:0070670)|response to interleukin-9 (GO:0071104)|STAT protein import into nucleus (GO:0007262)|T cell homeostasis (GO:0043029)|tyrosine phosphorylation of STAT protein (GO:0007260)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)	p.A573V(5)		breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(85)|kidney(4)|large_intestine(11)|lung(22)|ovary(3)|prostate(5)|skin(1)|stomach(2)|upper_aerodigestive_tract(5)	147					Tofacitinib(DB08895)	CATCAAGCTCGCTGCTTCCAG	0.577		2	Mis		"""acute megakaryocytic leukemia, ETP ALL"""																																p.A573V		Atlas-SNP	.		Dom	yes		19	19p13.1	3718	Janus kinase 3		L	JAK3,NS,lymphoid_neoplasm,0,5	JAK3	341	5	5	Substitution - Missense(5)	haematopoietic_and_lymphoid_tissue(5)	c.C1718T						PASS	.						45.0	34.0	38.0					19																	17948006		2201	4291	6492	SO:0001583	missense	3718	exon13			AAGCTCGCTGCTT	U31601	CCDS12366.1	19p13-p12	2014-09-17	2009-04-23		ENSG00000105639	ENSG00000105639	2.7.10.1		6193	protein-coding gene	gene with protein product	"""tyrosine-protein kinase JAK3"", ""leukocyte Janus kinase"""	600173				8921370, 9226382	Standard	NM_000215		Approved	L-JAK, JAKL, LJAK, JAK3_HUMAN, JAK-3	uc002nhn.4	P52333	OTTHUMG00000165648	ENST00000527670.1:c.1718C>T	19.37:g.17948006G>A	ENSP00000432511:p.Ala573Val	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	133	68	0.511278	NM_000215	Q13259|Q13260|Q13611|Q8N1E8|Q99699|Q9Y6S2	Missense_Mutation	SNP	ENST00000527670.1	37	CCDS12366.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.669605	0.88348	.	.	ENSG00000105639	ENST00000458235;ENST00000428406;ENST00000527670;ENST00000534444	T;T;T	0.60920	0.15;0.15;0.15	4.17	4.17	0.49024	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.064498	0.64402	D	0.000010	T	0.68467	0.3004	L	0.52206	1.635	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.65987	0.916;0.94	T	0.72312	-0.4331	10	0.87932	D	0	-22.3785	14.3465	0.66668	0.0:0.0:1.0:0.0	.	573;573	P52333-2;P52333	.;JAK3_HUMAN	V	573	ENSP00000391676:A573V;ENSP00000432511:A573V;ENSP00000436421:A573V	ENSP00000413248:A573V	A	-	2	0	JAK3	17809006	1.000000	0.71417	0.854000	0.33618	0.985000	0.73830	8.985000	0.93487	2.316000	0.78162	0.484000	0.47621	GCG	.	.	none		0.577	JAK3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385549.1	NM_000215	
CHST5	23563	hgsc.bcm.edu	37	16	75563962	75563962	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr16:75563962C>T	ENST00000336257.3	-	3	1715	c.321G>A	c.(319-321)gcG>gcA	p.A107A	RP11-77K12.7_ENST00000460606.1_3'UTR|CHST5_ENST00000541075.1_Silent_p.A113A	NM_024533.4	NP_078809.2	Q9GZS9	CHST5_HUMAN	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 5	107					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|N-acetylglucosamine metabolic process (GO:0006044)|protein sulfation (GO:0006477)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)	N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)|sulfotransferase activity (GO:0008146)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)	24						GCAGCGTTGCCGCGCTGCCCT	0.612																																					p.A107A		Atlas-SNP	.											CHST5,colon,carcinoma,-1,2	CHST5	47	2	0			c.G321A						scavenged	.						57.0	50.0	53.0					16																	75563962		2198	4300	6498	SO:0001819	synonymous_variant	23563	exon3			CGTTGCCGCGCTG	AF176839	CCDS10919.1	16q23.1	2008-02-05			ENSG00000135702	ENSG00000135702		"""Sulfotransferases, membrane-bound"""	1973	protein-coding gene	gene with protein product		604817				10491328, 11017086	Standard	NM_024533		Approved	I-GLCNAC-6-ST, FLJ22167	uc002fei.3	Q9GZS9	OTTHUMG00000137610	ENST00000336257.3:c.321G>A	16.37:g.75563962C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	90	2	0.0222222	NM_024533	B2RV23|Q7LCN3|Q9UBY3	Silent	SNP	ENST00000336257.3	37	CCDS10919.1																																																																																			.	.	none		0.612	CHST5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269025.2	NM_012126	
THADA	63892	hgsc.bcm.edu	37	2	43779431	43779431	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:43779431C>T	ENST00000405006.4	-	18	3073	c.2722G>A	c.(2722-2724)Gaa>Aaa	p.E908K	THADA_ENST00000415080.2_Missense_Mutation_p.E618K|THADA_ENST00000405975.2_Missense_Mutation_p.E908K|THADA_ENST00000402360.2_Missense_Mutation_p.E908K|THADA_ENST00000330266.7_Missense_Mutation_p.E618K	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	908								p.E908K(1)		breast(1)|endometrium(9)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	66		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				AGAGAATTTTCAGCCTGAGAT	0.368																																					p.E908K		Atlas-SNP	.											THADA,NS,carcinoma,0,1	THADA	131	1	1	Substitution - Missense(1)	endometrium(1)	c.G2722A						scavenged	.						54.0	53.0	53.0					2																	43779431		1871	4116	5987	SO:0001583	missense	63892	exon18			AATTTTCAGCCTG	AY149629	CCDS46268.1, CCDS62901.1, CCDS62902.1	2p21	2008-02-05			ENSG00000115970	ENSG00000115970			19217	protein-coding gene	gene with protein product		611800				12063398, 11214970	Standard	NM_022065		Approved	FLJ21877, KIAA1767, GITA	uc002rsx.4	Q6YHU6	OTTHUMG00000152398	ENST00000405006.4:c.2722G>A	2.37:g.43779431C>T	ENSP00000385995:p.Glu908Lys	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	191	2	0.0104712	NM_001083953	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	Missense_Mutation	SNP	ENST00000405006.4	37	CCDS46268.1	.	.	.	.	.	.	.	.	.	.	C	12.22	1.872053	0.33069	.	.	ENSG00000115970	ENST00000330266;ENST00000405975;ENST00000356975;ENST00000415080;ENST00000405006;ENST00000402360	T;T;T;T;T	0.32272	1.46;2.83;2.69;2.83;1.5	5.86	4.99	0.66335	Armadillo-type fold (1);	0.108059	0.64402	N	0.000009	T	0.25754	0.0627	L	0.49350	1.555	0.47547	D	0.999452	P;B;B;B;P	0.42556	0.783;0.058;0.374;0.431;0.635	B;B;B;B;B	0.39562	0.303;0.017;0.102;0.065;0.108	T	0.04203	-1.0969	10	0.10636	T	0.68	.	11.5298	0.50601	0.0:0.8464:0.0:0.1536	.	618;909;908;618;908	Q6YHU6-2;B6ZDQ0;Q6YHU6-5;C9JJB1;Q6YHU6	.;.;.;.;THADA_HUMAN	K	618;908;909;618;908;908	ENSP00000331105:E618K;ENSP00000386088:E908K;ENSP00000416048:E618K;ENSP00000385995:E908K;ENSP00000385441:E908K	ENSP00000331105:E618K	E	-	1	0	THADA	43632935	1.000000	0.71417	0.999000	0.59377	0.897000	0.52465	3.727000	0.54984	1.492000	0.48499	0.591000	0.81541	GAA	.	.	none		0.368	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326070.3	NM_022065	
DYSF	8291	hgsc.bcm.edu	37	2	71748030	71748030	+	Missense_Mutation	SNP	C	C	T	rs115279465	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:71748030C>T	ENST00000258104.3	+	11	1326	c.1049C>T	c.(1048-1050)gCg>gTg	p.A350V	DYSF_ENST00000409651.1_Missense_Mutation_p.A382V|DYSF_ENST00000429174.2_Missense_Mutation_p.A350V|DYSF_ENST00000410041.1_Missense_Mutation_p.A382V|DYSF_ENST00000413539.2_Missense_Mutation_p.A381V|DYSF_ENST00000409744.1_Missense_Mutation_p.A351V|DYSF_ENST00000409582.3_Missense_Mutation_p.A381V|DYSF_ENST00000410020.3_Missense_Mutation_p.A382V|DYSF_ENST00000409366.1_Missense_Mutation_p.A351V|DYSF_ENST00000409762.1_Missense_Mutation_p.A381V|DYSF_ENST00000394120.2_Missense_Mutation_p.A351V	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	350					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						GGGGACGAAGCGCCTGTGAGT	0.547													C|||	34	0.00678914	0.0242	0.0	5008	,	,		16178	0.002		0.0	False		,,,				2504	0.0				p.A382V		Atlas-SNP	.											DYSF_ENST00000410020,bladder,carcinoma,-1,2	DYSF	536	2	0			c.C1145T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	39,4367	43.1+/-76.7	0,39,2164	86.0	73.0	77.0		1052,1049,1049,1049,1142,1142,1142,1145,1052,1052,1145,1052,1145,1049	5.2	1.0	2	dbSNP_132	77	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	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	64,64,64,64,64,64,64,64,64,64,64,64,64,64	0,39,6464	TT,TC,CC		0.0,0.8852,0.2999	benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign	351/2082,350/2067,350/2088,350/2102,381/2112,381/2098,381/2119,382/2113,351/2103,351/2089,382/2099,351/2068,382/2120,350/2081	71748030	39,12967	2203	4300	6503	SO:0001583	missense	8291	exon12			ACGAAGCGCCTGT	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.1049C>T	2.37:g.71748030C>T	ENSP00000258104:p.Ala350Val	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	213	74	0.347418	NM_001130982	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Missense_Mutation	SNP	ENST00000258104.3	37	CCDS1918.1	16	0.007326007326007326	14	0.028455284552845527	0	0.0	1	0.0017482517482517483	1	0.0013192612137203166	C	18.71	3.681825	0.68042	0.008852	0.0	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	T;T;T;T;T;T;T;T;T;T;T	0.80566	-1.39;-1.39;-1.39;-1.39;-1.39;-1.39;-1.39;-1.39;-1.39;-1.39;-1.39	5.23	5.23	0.72850	C2 calcium/lipid-binding domain, CaLB (1);FerIin domain (1);	0.234979	0.43919	D	0.000501	T	0.51449	0.1675	N	0.25245	0.725	0.31618	N	0.65062	P;P;P;P;B;P;B;P;P;P;P;P;P;P	0.49559	0.775;0.775;0.775;0.648;0.423;0.622;0.423;0.925;0.775;0.633;0.797;0.648;0.775;0.812	B;B;B;B;B;B;B;P;B;B;P;B;B;P	0.49528	0.231;0.335;0.435;0.315;0.135;0.207;0.135;0.614;0.231;0.207;0.598;0.315;0.435;0.571	T	0.66015	-0.6028	10	0.20046	T	0.44	-3.0016	12.5642	0.56300	0.0:0.8325:0.1675:0.0	.	382;382;351;351;382;351;381;350;381;381;350;350;351;350	O75923-8;O75923-13;O75923-10;O75923-9;O75923-11;O75923-12;O75923-5;O75923-6;O75923-2;O75923-7;O75923-4;O75923-3;O75923-14;O75923	.;.;.;.;.;.;.;.;.;.;.;.;.;DYSF_HUMAN	V	381;381;381;350;350;382;351;351;351;382;382	ENSP00000407046:A381V;ENSP00000387137:A381V;ENSP00000386547:A381V;ENSP00000398305:A350V;ENSP00000258104:A350V;ENSP00000386683:A382V;ENSP00000377678:A351V;ENSP00000386285:A351V;ENSP00000386512:A351V;ENSP00000386881:A382V;ENSP00000386617:A382V	ENSP00000258104:A350V	A	+	2	0	DYSF	71601538	1.000000	0.71417	0.962000	0.40283	0.318000	0.28184	4.576000	0.60915	2.663000	0.90544	0.536000	0.68110	GCG	C|0.995;T|0.005	0.005	strong		0.547	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494	
OR8B3	390271	hgsc.bcm.edu	37	11	124266927	124266927	+	Silent	SNP	A	A	G	rs142812088		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:124266927A>G	ENST00000354597.3	-	1	337	c.321T>C	c.(319-321)ttT>ttC	p.F107F		NM_001005467.1	NP_001005467.1	Q8NGG8	OR8B3_HUMAN	olfactory receptor, family 8, subfamily B, member 3	107						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	14		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		CAGAGATGACAAAAAAGAGAA	0.388																																					p.F107F		Atlas-SNP	.											OR8B3,NS,carcinoma,0,1	OR8B3	36	1	0			c.T321C						scavenged	.						78.0	76.0	77.0					11																	124266927		2201	4299	6500	SO:0001819	synonymous_variant	390271	exon1			GATGACAAAAAAG	AB065827	CCDS31709.1	11q24.1	2012-08-09			ENSG00000196661	ENSG00000196661		"""GPCR / Class A : Olfactory receptors"""	8472	protein-coding gene	gene with protein product							Standard	NM_001005467		Approved		uc010saj.2	Q8NGG8	OTTHUMG00000165983	ENST00000354597.3:c.321T>C	11.37:g.124266927A>G		Somatic	309	16	0.0517799		WXS	Illumina HiSeq	Phase_I	386	16	0.0414508	NM_001005467	Q6IFQ8|Q8NGH1	Silent	SNP	ENST00000354597.3	37	CCDS31709.1																																																																																			A|1.000;G|0.000	0.000	weak		0.388	OR8B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387291.1	NM_001005467	
USP17L2	377630	hgsc.bcm.edu	37	8	11994795	11994795	+	Missense_Mutation	SNP	G	G	A	rs201012791	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr8:11994795G>A	ENST00000333796.3	-	1	1791	c.1475C>T	c.(1474-1476)aCg>aTg	p.T492M	FAM66D_ENST00000434078.2_RNA	NM_001256869.1|NM_001256871.1|NM_001256872.1|NM_001256873.1|NM_001256874.1|NM_201402.2	NP_001243798.1|NP_001243800.1|NP_001243801.1|NP_001243802.1|NP_001243803.1|NP_958804.2	Q6R6M4	U17L2_HUMAN	ubiquitin specific peptidase 17-like family member 2	492	Mediates interaction with SUDS3.				apoptotic process (GO:0006915)|CAAX-box protein processing (GO:0071586)|cell cycle checkpoint (GO:0000075)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of histone deacetylation (GO:0031064)|negative regulation of protein processing (GO:0010955)|negative regulation of protein targeting to membrane (GO:0090315)|negative regulation of Ras GTPase activity (GO:0034261)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of RIG-I signaling pathway (GO:1900246)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of apoptotic process (GO:0042981)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of defense response to virus by host (GO:0050691)|regulation of ruffle assembly (GO:1900027)|ubiquitin-dependent protein catabolic process (GO:0006511)	endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			central_nervous_system(1)|kidney(1)|large_intestine(11)|liver(1)|lung(8)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	29						TGTCCGGGTCGTCGAAGAGAG	0.512													G|||	2	0.000399361	0.0008	0.0	5008	,	,		21462	0.0		0.001	False		,,,				2504	0.0				p.T492M		Atlas-SNP	.											.	USP17L2	47	.	0			c.C1475T						PASS	.	A	MET/THR	3,2647		1,1,1323	62.0	67.0	65.0		1475	-0.7	0.0	8		65	2,5746		0,2,2872	no	missense	USP17L2	NM_201402.2	81	1,3,4195	AA,AG,GG		0.0348,0.1132,0.0595	benign	492/531	11994795	5,8393	1325	2874	4199	SO:0001583	missense	377630	exon1			CGGGTCGTCGAAG	BC156290	CCDS43713.1	8p23.1	2012-10-09	2012-10-09		ENSG00000223443	ENSG00000223443			34434	protein-coding gene	gene with protein product	"""deubiquitinating enzyme 3"""	610186	"""ubiquitin specific peptidase 17-like 2"""				Standard	NM_201402		Approved	DUB3	uc003wvc.1	Q6R6M4	OTTHUMG00000165295	ENST00000333796.3:c.1475C>T	8.37:g.11994795G>A	ENSP00000333329:p.Thr492Met	Somatic	293	0	0		WXS	Illumina HiSeq	Phase_I	362	96	0.265193	NM_201402		Missense_Mutation	SNP	ENST00000333796.3	37	CCDS43713.1	.	.	.	.	.	.	.	.	.	.	G	7.058	0.565875	0.13560	0.001132	3.48E-4	ENSG00000223443	ENST00000333796	T	0.11821	2.74	0.36	-0.721	0.11189	.	1.611680	0.04297	U	0.346582	T	0.12390	0.0301	.	.	.	0.09310	N	1	D	0.57571	0.98	B	0.44044	0.439	T	0.19063	-1.0317	8	0.51188	T	0.08	.	.	.	.	.	492	Q6R6M4	U17L2_HUMAN	M	492	ENSP00000333329:T492M	ENSP00000333329:T492M	T	-	2	0	USP17L2	12032204	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.296000	0.01142	-0.412000	0.07519	-0.410000	0.06199	ACG	.	.	weak		0.512	USP17L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383303.2	NM_201402	
RBMXL1	494115	hgsc.bcm.edu	37	1	89448812	89448812	+	Missense_Mutation	SNP	T	T	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:89448812T>G	ENST00000321792.5	-	2	1125	c.698A>C	c.(697-699)gAt>gCt	p.D233A	CCBL2_ENST00000446900.2_Intron|CCBL2_ENST00000370491.3_Intron|CCBL2_ENST00000370485.2_Intron|RBMXL1_ENST00000399794.2_Missense_Mutation_p.D233A|CCBL2_ENST00000260508.4_Intron|RBMXL1_ENST00000413769.1_5'Flank	NM_019610.5	NP_062556.2	Q96E39	RMXL1_HUMAN	RNA binding motif protein, X-linked-like 1	233					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.D233A(3)									TGGTGCATAATCTCTTGTATC	0.423																																					p.D233A		Atlas-SNP	.											CCBL2,NS,carcinoma,0,3	.	.	3	3	Substitution - Missense(3)	kidney(3)	c.A698C						scavenged	.						205.0	178.0	187.0					1																	89448812		2203	4300	6503	SO:0001583	missense	494115	exon3			GCATAATCTCTTG	BC012942	CCDS716.1	1p22.2	2013-02-12	2007-01-04	2007-01-04	ENSG00000213516	ENSG00000213516		"""RNA binding motif (RRM) containing"""	25073	protein-coding gene	gene with protein product	"""kynurenine aminotransferase III"""					10441733	Standard	NM_019610		Approved	KAT3	uc001dms.3	Q96E39	OTTHUMG00000010661	ENST00000321792.5:c.698A>C	1.37:g.89448812T>G	ENSP00000318415:p.Asp233Ala	Somatic	280	3	0.0107143		WXS	Illumina HiSeq	Phase_I	342	16	0.0467836	NM_001162536		Missense_Mutation	SNP	ENST00000321792.5	37	CCDS716.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.084835	0.76642	.	.	ENSG00000213516	ENST00000321792;ENST00000399794	D;D	0.83163	-1.69;-1.69	1.53	1.53	0.23141	.	0.000000	0.85682	D	0.000000	T	0.79100	0.4389	M	0.71036	2.16	0.46499	D	0.999078	D	0.59357	0.985	P	0.53102	0.718	T	0.78889	-0.2026	10	0.66056	D	0.02	.	6.8078	0.23786	0.0:0.0:0.0:1.0	.	233	Q96E39	RBMXL_HUMAN	A	233	ENSP00000318415:D233A;ENSP00000446099:D233A	ENSP00000318415:D233A	D	-	2	0	RBMXL1	89221400	1.000000	0.71417	0.996000	0.52242	0.787000	0.44495	5.062000	0.64326	0.706000	0.31912	0.254000	0.18369	GAT	.	.	none		0.423	RBMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029403.3	NM_019610	
ZNF502	91392	hgsc.bcm.edu	37	3	44762425	44762425	+	Missense_Mutation	SNP	G	G	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:44762425G>C	ENST00000296091.4	+	4	372	c.116G>C	c.(115-117)gGg>gCg	p.G39A	ZNF502_ENST00000436624.2_Missense_Mutation_p.G39A|ZNF502_ENST00000449836.1_Missense_Mutation_p.G39A	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	39					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|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)		GACTCATCAGGGATAGTAGTA	0.418																																					p.G39A		Atlas-SNP	.											.	ZNF502	58	.	0			c.G116C						PASS	.						73.0	75.0	74.0					3																	44762425		2203	4300	6503	SO:0001583	missense	91392	exon4			CATCAGGGATAGT	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.116G>C	3.37:g.44762425G>C	ENSP00000296091:p.Gly39Ala	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	96	21	0.21875	NM_001134440		Missense_Mutation	SNP	ENST00000296091.4	37	CCDS2719.1	.	.	.	.	.	.	.	.	.	.	G	10.61	1.398645	0.25205	.	.	ENSG00000196653	ENST00000449836;ENST00000296091;ENST00000436624;ENST00000427783;ENST00000411443	T;T;T;T	0.54675	3.42;3.42;3.42;0.56	4.92	0.917	0.19380	.	.	.	.	.	T	0.22513	0.0543	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.28073	-1.0055	9	0.05620	T	0.96	-3.7166	3.6154	0.08075	0.4034:0.1908:0.4058:0.0	.	39	Q8TBZ5	ZN502_HUMAN	A	39	ENSP00000397390:G39A;ENSP00000296091:G39A;ENSP00000406469:G39A;ENSP00000401717:G39A	ENSP00000296091:G39A	G	+	2	0	ZNF502	44737429	0.002000	0.14202	0.053000	0.19242	0.051000	0.14879	0.321000	0.19558	0.668000	0.31126	0.655000	0.94253	GGG	.	.	none		0.418	ZNF502-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256744.4	NM_033210	
NLRP2	55655	hgsc.bcm.edu	37	19	55494703	55494703	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:55494703G>A	ENST00000543010.1	+	6	1780	c.1637G>A	c.(1636-1638)aGg>aAg	p.R546K	NLRP2_ENST00000263437.6_Missense_Mutation_p.R543K|NLRP2_ENST00000391721.4_Missense_Mutation_p.R522K|NLRP2_ENST00000537859.1_Missense_Mutation_p.R524K|NLRP2_ENST00000538819.1_Missense_Mutation_p.R522K|NLRP2_ENST00000339757.7_Missense_Mutation_p.R524K|NLRP2_ENST00000448584.2_Missense_Mutation_p.R546K|NLRP2_ENST00000427260.2_Missense_Mutation_p.R523K	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	546					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)		GAAAGACTCAGGAACCCCGAC	0.567																																					p.R546K		Atlas-SNP	.											NLRP2_ENST00000543010,colon,carcinoma,0,1	NLRP2	161	1	0			c.G1637A						scavenged	.						87.0	81.0	83.0					19																	55494703		2203	4300	6503	SO:0001583	missense	55655	exon6			GACTCAGGAACCC	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.1637G>A	19.37:g.55494703G>A	ENSP00000445135:p.Arg546Lys	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	155	3	0.0193548	NM_017852	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Missense_Mutation	SNP	ENST00000543010.1	37	CCDS12913.1	.	.	.	.	.	.	.	.	.	.	G	0.008	-1.908855	0.00508	.	.	ENSG00000022556	ENST00000543010;ENST00000391721;ENST00000339757;ENST00000448584;ENST00000537859;ENST00000427260;ENST00000538819;ENST00000263437	T;T;T;T;T;T;T;T	0.72394	-0.65;-0.58;-0.58;-0.65;-0.58;-0.65;-0.58;-0.64	1.7	-1.81	0.07882	.	2.154850	0.02966	N	0.143790	T	0.36193	0.0958	N	0.01140	-0.99	0.09310	N	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.06405	0.002;0.001;0.0;0.001;0.0	T	0.48305	-0.9047	10	0.02654	T	1	.	5.9847	0.19428	0.4353:0.0:0.5647:0.0	.	523;524;543;522;546	B4DZL7;Q9NX02-2;A8K9G6;Q9NX02-4;Q9NX02	.;.;.;.;NALP2_HUMAN	K	546;522;524;546;524;523;522;543	ENSP00000445135:R546K;ENSP00000375601:R522K;ENSP00000344074:R524K;ENSP00000409370:R546K;ENSP00000440601:R524K;ENSP00000402474:R523K;ENSP00000441133:R522K;ENSP00000263437:R543K	ENSP00000263437:R543K	R	+	2	0	NLRP2	60186515	0.000000	0.05858	0.002000	0.10522	0.007000	0.05969	0.026000	0.13599	-0.643000	0.05473	-1.166000	0.01754	AGG	.	.	none		0.567	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852	
TBC1D12	23232	hgsc.bcm.edu	37	10	96259982	96259982	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr10:96259982A>G	ENST00000225235.4	+	6	1527	c.1417A>G	c.(1417-1419)Agt>Ggt	p.S473G		NM_015188.1	NP_056003.1	O60347	TBC12_HUMAN	TBC1 domain family, member 12	473							Rab GTPase activator activity (GO:0005097)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(2)	20		Colorectal(252;0.0429)				TTCTAGGCGTAGTACAAGAAG	0.403																																					p.S473G		Atlas-SNP	.											TBC1D12,NS,carcinoma,-1,1	TBC1D12	51	1	0			c.A1417G						scavenged	.						128.0	115.0	119.0					10																	96259982		1839	4096	5935	SO:0001583	missense	23232	exon6			AGGCGTAGTACAA	AB011180	CCDS41553.1	10q23.33	2013-09-20			ENSG00000108239	ENSG00000108239			29082	protein-coding gene	gene with protein product						9628581	Standard	NM_015188		Approved	KIAA0608	uc001kjr.2	O60347	OTTHUMG00000018794	ENST00000225235.4:c.1417A>G	10.37:g.96259982A>G	ENSP00000225235:p.Ser473Gly	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	75	3	0.04	NM_015188	Q5VYA6|Q8WX26|Q8WX59|Q9UG83	Missense_Mutation	SNP	ENST00000225235.4	37	CCDS41553.1	.	.	.	.	.	.	.	.	.	.	A	14.98	2.697073	0.48202	.	.	ENSG00000108239	ENST00000225235	T	0.57595	0.39	4.8	4.8	0.61643	Rab-GAP/TBC domain (1);	0.287488	0.39759	N	0.001273	T	0.31734	0.0806	N	0.10874	0.06	0.50039	D	0.999843	B	0.10296	0.003	B	0.06405	0.002	T	0.12400	-1.0549	10	0.19590	T	0.45	-15.3937	12.5865	0.56421	1.0:0.0:0.0:0.0	.	473	O60347	TBC12_HUMAN	G	473	ENSP00000225235:S473G	ENSP00000225235:S473G	S	+	1	0	TBC1D12	96249972	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.084000	0.57650	2.124000	0.65301	0.533000	0.62120	AGT	.	.	none		0.403	TBC1D12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049482.2		
DPYSL5	56896	hgsc.bcm.edu	37	2	27147877	27147877	+	Silent	SNP	C	C	T	rs147434661		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:27147877C>T	ENST00000288699.6	+	3	542	c.384C>T	c.(382-384)taC>taT	p.Y128Y	DPYSL5_ENST00000401478.1_Silent_p.Y128Y	NM_001253724.1|NM_020134.3	NP_001240653.1|NP_064519.2	Q9BPU6	DPYL5_HUMAN	dihydropyrimidinase-like 5	128					axon guidance (GO:0007411)|nervous system development (GO:0007399)|pyrimidine nucleobase catabolic process (GO:0006208)|signal transduction (GO:0007165)	cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			breast(1)|endometrium(5)|large_intestine(2)|lung(13)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	27	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCTGTGATTACGCCCTCCACG	0.602																																					p.Y128Y		Atlas-SNP	.											.	DPYSL5	69	.	0			c.C384T						PASS	.	C		0,4406		0,0,2203	100.0	87.0	91.0		384	-3.6	1.0	2	dbSNP_134	91	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	DPYSL5	NM_020134.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		128/565	27147877	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	56896	exon3			TGATTACGCCCTC	AF264015	CCDS1730.1	2p23.3	2008-02-05			ENSG00000157851	ENSG00000157851			20637	protein-coding gene	gene with protein product		608383				10851247, 11034345	Standard	NM_020134		Approved	CRMP5, Ulip6, CRMP-5, CRAM	uc002rhu.4	Q9BPU6	OTTHUMG00000097071	ENST00000288699.6:c.384C>T	2.37:g.27147877C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	105	34	0.32381	NM_001253724	Q8TCL6|Q9NQC4|Q9NRY9	Silent	SNP	ENST00000288699.6	37	CCDS1730.1																																																																																			C|1.000;T|0.000	0.000	weak		0.602	DPYSL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214187.2	NM_020134	
C4BPA	722	hgsc.bcm.edu	37	1	207300202	207300202	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:207300202A>G	ENST00000367070.3	+	7	1045	c.851A>G	c.(850-852)gAt>gGt	p.D284G		NM_000715.3	NP_000706.1	P04003	C4BPA_HUMAN	complement component 4 binding protein, alpha	284	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|negative regulation of complement activation, classical pathway (GO:0045959)|positive regulation of protein catabolic process (GO:0045732)|regulation of complement activation (GO:0030449)|regulation of opsonization (GO:1903027)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|other organism cell (GO:0044216)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(1)|urinary_tract(2)	28						TGTGATGCTGATAGCAAATGG	0.403																																					p.D284G		Atlas-SNP	.											C4BPA,NS,carcinoma,0,1	C4BPA	70	1	0			c.A851G						scavenged	.						178.0	150.0	160.0					1																	207300202		2203	4300	6503	SO:0001583	missense	722	exon7			ATGCTGATAGCAA	M31452	CCDS1477.1	1q32	2010-09-24	2001-11-28		ENSG00000123838	ENSG00000123838			1325	protein-coding gene	gene with protein product		120830	"""complement component 4-binding protein, alpha"""	C4BP			Standard	XM_005273251		Approved		uc001hfo.3	P04003	OTTHUMG00000036173	ENST00000367070.3:c.851A>G	1.37:g.207300202A>G	ENSP00000356037:p.Asp284Gly	Somatic	274	0	0		WXS	Illumina HiSeq	Phase_I	288	3	0.0104167	NM_000715	Q5VVQ8	Missense_Mutation	SNP	ENST00000367070.3	37	CCDS1477.1	.	.	.	.	.	.	.	.	.	.	A	12.82	2.052883	0.36181	.	.	ENSG00000123838	ENST00000367070	T	0.68181	-0.31	5.61	4.49	0.54785	Complement control module (2);Sushi/SCR/CCP (3);	0.333263	0.25680	N	0.029005	T	0.66268	0.2772	L	0.55213	1.73	0.09310	N	1	B	0.29481	0.245	B	0.41202	0.35	T	0.60782	-0.7195	10	0.48119	T	0.1	.	8.4965	0.33132	0.9117:0.0:0.0883:0.0	.	284	P04003	C4BPA_HUMAN	G	284	ENSP00000356037:D284G	ENSP00000356037:D284G	D	+	2	0	C4BPA	205366825	0.028000	0.19301	0.002000	0.10522	0.115000	0.19883	3.238000	0.51352	0.945000	0.37605	-0.386000	0.06593	GAT	.	.	none		0.403	C4BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088089.3		
MUC16	94025	hgsc.bcm.edu	37	19	9088930	9088930	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:9088930G>A	ENST00000397910.4	-	1	3088	c.2885C>T	c.(2884-2886)cCc>cTc	p.P962L		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	962	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						TGTGCTTTGGGGTGCAGCAGA	0.473																																					p.P962L		Atlas-SNP	.											MUC16,larynx,carcinoma,+1,1	MUC16	4315	1	0			c.C2885T						scavenged	.						217.0	214.0	215.0					19																	9088930		2025	4177	6202	SO:0001583	missense	94025	exon1			CTTTGGGGTGCAG	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.2885C>T	19.37:g.9088930G>A	ENSP00000381008:p.Pro962Leu	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	181	2	0.0110497	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	2.502	-0.315057	0.05422	.	.	ENSG00000181143	ENST00000397910	T	0.03212	4.01	1.27	-2.54	0.06307	.	.	.	.	.	T	0.01835	0.0058	N	0.08118	0	.	.	.	B	0.19817	0.039	B	0.11329	0.006	T	0.44128	-0.9348	8	0.87932	D	0	.	3.0087	0.06037	0.3893:0.2445:0.3662:0.0	.	962	B5ME49	.	L	962	ENSP00000381008:P962L	ENSP00000381008:P962L	P	-	2	0	MUC16	8949930	0.000000	0.05858	0.000000	0.03702	0.213000	0.24496	-0.343000	0.07791	-1.250000	0.02497	0.205000	0.17691	CCC	.	.	none		0.473	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
NAP1L3	4675	hgsc.bcm.edu	37	X	92928124	92928124	+	Missense_Mutation	SNP	G	G	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:92928124G>T	ENST00000373079.3	-	1	443	c.180C>A	c.(178-180)agC>agA	p.S60R	NAP1L3_ENST00000475430.2_Missense_Mutation_p.S53R|FAM133A_ENST00000322139.4_5'Flank|FAM133A_ENST00000332647.4_5'Flank|FAM133A_ENST00000355813.5_5'Flank|FAM133A_ENST00000538690.1_5'Flank	NM_004538.5	NP_004529.2	Q99457	NP1L3_HUMAN	nucleosome assembly protein 1-like 3	60	Ser-rich.				nucleosome assembly (GO:0006334)	nucleus (GO:0005634)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	34						tgctgctgctgctgccgctgc	0.617																																					p.S60R		Atlas-SNP	.											.	NAP1L3	81	.	0			c.C180A						PASS	.						8.0	9.0	9.0					X																	92928124		1938	3702	5640	SO:0001583	missense	4675	exon1			GCTGCTGCTGCCG		CCDS14465.1	Xq21.3-q22	2008-08-01			ENSG00000186310	ENSG00000186310			7639	protein-coding gene	gene with protein product		300117				8976385	Standard	NM_004538		Approved	MB20, NPL3, MGC26312	uc004efq.3	Q99457	OTTHUMG00000021974	ENST00000373079.3:c.180C>A	X.37:g.92928124G>T	ENSP00000362171:p.Ser60Arg	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	63	10	0.15873	NM_004538	B2RCM0|O60788	Missense_Mutation	SNP	ENST00000373079.3	37	CCDS14465.1	.	.	.	.	.	.	.	.	.	.	G	3.522	-0.097600	0.07010	.	.	ENSG00000186310	ENST00000373079;ENST00000543136	T	0.35048	1.33	1.57	1.57	0.23409	.	.	.	.	.	T	0.18045	0.0433	N	0.14661	0.345	0.09310	N	1	B	0.21225	0.053	B	0.13407	0.009	T	0.17137	-1.0379	9	0.28530	T	0.3	.	4.6764	0.12713	0.0:0.0:0.6303:0.3697	.	60	Q99457	NP1L3_HUMAN	R	60;53	ENSP00000362171:S60R	ENSP00000362171:S60R	S	-	3	2	NAP1L3	92814780	0.521000	0.26258	0.014000	0.15608	0.005000	0.04900	0.666000	0.25097	1.056000	0.40484	0.292000	0.19580	AGC	.	.	none		0.617	NAP1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057449.1	NM_004538	
CNOT2	4848	hgsc.bcm.edu	37	12	70724236	70724236	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:70724236T>C	ENST00000418359.3	+	7	1007	c.556T>C	c.(556-558)Ttt>Ctt	p.F186L	CNOT2_ENST00000548230.1_3'UTR|CNOT2_ENST00000229195.3_Missense_Mutation_p.F186L	NM_001199302.1	NP_001186231.1	Q9NZN8	CNOT2_HUMAN	CCR4-NOT transcription complex, subunit 2	186					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 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)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription from RNA polymerase II promoter (GO:0006366)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription corepressor binding (GO:0001226)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|pancreas(2)|urinary_tract(1)	20	Renal(347;0.236)		GBM - Glioblastoma multiforme(1;4.77e-09)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00243)|STAD - Stomach adenocarcinoma(21;0.0118)			TCGACAGCCTTTTACTGTGAA	0.413																																					p.F186L		Atlas-SNP	.											CNOT2,NS,carcinoma,-2,1	CNOT2	53	1	0			c.T556C						scavenged	.						133.0	124.0	127.0					12																	70724236		2203	4300	6503	SO:0001583	missense	4848	exon7			CAGCCTTTTACTG	AF180473	CCDS31857.1	12q15	2008-05-14				ENSG00000111596			7878	protein-coding gene	gene with protein product		604909		NOT2		10637334	Standard	NM_014515		Approved	CDC36, NOT2H	uc001svv.3	Q9NZN8		ENST00000418359.3:c.556T>C	12.37:g.70724236T>C	ENSP00000412091:p.Phe186Leu	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	210	3	0.0142857	NM_001199302	Q9H3E0|Q9NSX5|Q9NWR6|Q9P028	Missense_Mutation	SNP	ENST00000418359.3	37	CCDS31857.1	.	.	.	.	.	.	.	.	.	.	T	8.643	0.896369	0.17686	.	.	ENSG00000111596	ENST00000552231;ENST00000229195;ENST00000418359;ENST00000550641;ENST00000548159;ENST00000551043;ENST00000551873;ENST00000550194	T;T;T;T;T;T;T;T	0.73681	-0.77;-0.77;-0.77;-0.77;-0.77;-0.77;-0.77;-0.77	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.62563	0.2438	L	0.29908	0.895	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.57911	-0.7729	10	0.14252	T	0.57	-6.1986	15.6247	0.76845	0.0:0.0:0.0:1.0	.	186	Q9NZN8	CNOT2_HUMAN	L	186;186;186;166;177;186;101;186	ENSP00000450318:F186L;ENSP00000229195:F186L;ENSP00000412091:F186L;ENSP00000448024:F166L;ENSP00000449659:F177L;ENSP00000449260:F186L;ENSP00000450090:F101L;ENSP00000449446:F186L	ENSP00000229195:F186L	F	+	1	0	CNOT2	69010503	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.655000	0.83696	2.147000	0.66899	0.455000	0.32223	TTT	.	.	none		0.413	CNOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404260.1		
RSL1D1	26156	hgsc.bcm.edu	37	16	11944196	11944196	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr16:11944196T>C	ENST00000571133.1	-	2	257	c.185A>G	c.(184-186)gAa>gGa	p.E62G	RP11-166B2.8_ENST00000574364.1_RNA|RSL1D1_ENST00000542106.1_Intron	NM_015659.2	NP_056474.2	O76021	RL1D1_HUMAN	ribosomal L1 domain containing 1	62					osteoblast differentiation (GO:0001649)|regulation of apoptotic process (GO:0042981)|regulation of cellular senescence (GO:2000772)|regulation of protein localization (GO:0032880)	membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|stomach(2)|urinary_tract(2)	15						AAATAAACTTTCATTCTCATT	0.363																																					p.E62G		Atlas-SNP	.											.	RSL1D1	40	.	0			c.A185G						PASS	.						80.0	76.0	78.0					16																	11944196		2197	4300	6497	SO:0001583	missense	26156	exon2			AAACTTTCATTCT	AY154473	CCDS10551.1	16p13.13	2011-08-12			ENSG00000171490	ENSG00000171490			24534	protein-coding gene	gene with protein product		615874				15334068, 9859858	Standard	NM_015659		Approved	PBK1, L12, DKFZP564M182, CSIG, UTP30	uc002dbp.1	O76021	OTTHUMG00000129824	ENST00000571133.1:c.185A>G	16.37:g.11944196T>C	ENSP00000460871:p.Glu62Gly	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	101	5	0.049505	NM_015659	B4DJ58|D3DUG7|Q2M1T7|Q6PL22|Q8IWS7|Q8WUZ1|Q9HDA9|Q9Y3Z9	Missense_Mutation	SNP	ENST00000571133.1	37	CCDS10551.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.947427	0.73672	.	.	ENSG00000171490	ENST00000355674;ENST00000396503	T	0.52295	0.67	5.91	5.91	0.95273	Ribosomal protein L1, superfamily (1);	0.240132	0.42420	D	0.000719	T	0.69033	0.3066	M	0.80616	2.505	0.80722	D	1	P;D	0.63880	0.947;0.993	P;D	0.64687	0.849;0.928	T	0.73509	-0.3960	10	0.72032	D	0.01	-13.9832	15.1713	0.72875	0.0:0.0:0.0:1.0	.	62;62	Q32Q62;O76021	.;RL1D1_HUMAN	G	62	ENSP00000347897:E62G	ENSP00000347897:E62G	E	-	2	0	RSL1D1	11851697	0.997000	0.39634	0.850000	0.33497	0.298000	0.27526	5.671000	0.68095	2.266000	0.75297	0.454000	0.30748	GAA	.	.	none		0.363	RSL1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252059.2	NM_015659	
SLC45A1	50651	hgsc.bcm.edu	37	1	8390740	8390740	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:8390740C>T	ENST00000471889.1	+	5	1572	c.1187C>T	c.(1186-1188)cCc>cTc	p.P396L	SLC45A1_ENST00000289877.8_Missense_Mutation_p.P396L|SLC45A1_ENST00000481265.1_3'UTR|SLC45A1_ENST00000377479.2_Missense_Mutation_p.P430L|Y_RNA_ENST00000516445.1_RNA			Q9Y2W3	S45A1_HUMAN	solute carrier family 45, member 1	396					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)		GGCAGCGTCCCCAGGCCGCCC	0.672																																					p.P396L		Atlas-SNP	.											.	SLC45A1	85	.	0			c.C1187T						PASS	.						32.0	33.0	33.0					1																	8390740		2203	4300	6503	SO:0001583	missense	50651	exon4			GCGTCCCCAGGCC	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.1187C>T	1.37:g.8390740C>T	ENSP00000418096:p.Pro396Leu	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	59	17	0.288136	NM_001080397	Q5VY46|Q5VY49	Missense_Mutation	SNP	ENST00000471889.1	37	CCDS30577.1	.	.	.	.	.	.	.	.	.	.	C	8.089	0.774143	0.16051	.	.	ENSG00000162426	ENST00000471889;ENST00000377479;ENST00000289877	T;T;T	0.22134	2.01;1.97;2.01	4.66	4.66	0.58398	.	0.349376	0.30260	N	0.010030	T	0.22085	0.0532	M	0.64997	1.995	0.80722	D	1	P	0.40144	0.704	B	0.30495	0.116	T	0.10132	-1.0643	10	0.51188	T	0.08	-30.6706	16.5386	0.84378	0.0:1.0:0.0:0.0	.	396	Q9Y2W3	S45A1_HUMAN	L	396;430;396	ENSP00000418096:P396L;ENSP00000366699:P430L;ENSP00000289877:P396L	ENSP00000289877:P396L	P	+	2	0	SLC45A1	8313327	1.000000	0.71417	0.068000	0.19968	0.014000	0.08584	7.095000	0.76952	2.121000	0.65114	0.561000	0.74099	CCC	.	.	none		0.672	SLC45A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001245.5		
FAM46B	115572	hgsc.bcm.edu	37	1	27333242	27333242	+	Silent	SNP	G	G	A	rs142664149		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:27333242G>A	ENST00000289166.5	-	2	636	c.471C>T	c.(469-471)gcC>gcT	p.A157A		NM_052943.3	NP_443175.2	Q96A09	FA46B_HUMAN	family with sequence similarity 46, member B	157										breast(1)|central_nervous_system(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	10		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;7.71e-51)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-29)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|STAD - Stomach adenocarcinoma(196;0.00114)|READ - Rectum adenocarcinoma(331;0.0419)		GGCTCACACCGGCCGGCAGGA	0.612													G|||	1	0.000199681	0.0	0.0	5008	,	,		17271	0.0		0.001	False		,,,				2504	0.0				p.A157A		Atlas-SNP	.											FAM46B,NS,carcinoma,0,1	FAM46B	44	1	0			c.C471T						scavenged	.	G		0,4406		0,0,2203	104.0	101.0	102.0		471	-10.2	0.0	1	dbSNP_134	102	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	FAM46B	NM_052943.3		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		157/426	27333242	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	115572	exon2			CACACCGGCCGGC	AK122816	CCDS294.2	1p35.3	2008-02-05			ENSG00000158246	ENSG00000158246			28273	protein-coding gene	gene with protein product						12477932	Standard	NM_052943		Approved	MGC16491	uc010ofj.2	Q96A09	OTTHUMG00000004278	ENST00000289166.5:c.471C>T	1.37:g.27333242G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	123	3	0.0243902	NM_052943		Silent	SNP	ENST00000289166.5	37	CCDS294.2																																																																																			G|1.000;A|0.000	0.000	strong		0.612	FAM46B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012347.2	NM_052943	
MYO7A	4647	hgsc.bcm.edu	37	11	76871271	76871271	+	Silent	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:76871271G>A	ENST00000409709.3	+	11	1415	c.1143G>A	c.(1141-1143)acG>acA	p.T381T	MYO7A_ENST00000409893.1_Silent_p.T381T|MYO7A_ENST00000409619.2_Silent_p.T370T|MYO7A_ENST00000458637.2_Silent_p.T381T	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	381	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)	p.T381T(1)		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						GCGGGGAGACGGTGTCCACCC	0.667																																					p.T381T		Atlas-SNP	.											MYO7A,NS,carcinoma,0,1	MYO7A	164	1	1	Substitution - coding silent(1)	endometrium(1)	c.G1143A						scavenged	.						28.0	37.0	34.0					11																	76871271		2110	4186	6296	SO:0001819	synonymous_variant	4647	exon11			GGAGACGGTGTCC	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.1143G>A	11.37:g.76871271G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	57	2	0.0350877	NM_001127179	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Silent	SNP	ENST00000409709.3	37	CCDS53683.1																																																																																			.	.	none		0.667	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260	
ZFHX3	463	hgsc.bcm.edu	37	16	72830109	72830109	+	Nonsense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr16:72830109G>A	ENST00000268489.5	-	9	7144	c.6472C>T	c.(6472-6474)Cga>Tga	p.R2158*	ZFHX3_ENST00000397992.5_Nonsense_Mutation_p.R1244*	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	2158					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.R2158*(1)		NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				CGCAAGACTCGGAGCTGATCA	0.527																																					p.R2158X		Atlas-SNP	.											ZFHX3,NS,carcinoma,0,1	ZFHX3	404	1	1	Substitution - Nonsense(1)	breast(1)	c.C6472T						scavenged	.						71.0	68.0	69.0					16																	72830109		2198	4300	6498	SO:0001587	stop_gained	463	exon9			AGACTCGGAGCTG	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.6472C>T	16.37:g.72830109G>A	ENSP00000268489:p.Arg2158*	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	198	4	0.020202	NM_006885	D3DWS8|O15101|Q13719	Nonsense_Mutation	SNP	ENST00000268489.5	37	CCDS10908.1	.	.	.	.	.	.	.	.	.	.	G	49	16.052298	0.99853	.	.	ENSG00000140836	ENST00000268489;ENST00000397992	.	.	.	5.51	5.51	0.81932	.	0.000000	0.41396	D	0.000894	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08381	T	0.77	.	13.4414	0.61114	0.0:0.0:0.7375:0.2625	.	.	.	.	X	2158;1244	.	ENSP00000268489:R2158X	R	-	1	2	ZFHX3	71387610	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	1.772000	0.38552	2.570000	0.86706	0.561000	0.74099	CGA	.	.	none		0.527	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
SHROOM1	134549	hgsc.bcm.edu	37	5	132159799	132159799	+	Silent	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:132159799G>A	ENST00000378679.3	-	7	2358	c.1554C>T	c.(1552-1554)ccC>ccT	p.P518P	SHROOM1_ENST00000378676.1_Silent_p.P449P|SHROOM1_ENST00000488072.1_5'Flank|SHROOM1_ENST00000319854.3_Silent_p.P518P	NM_001172700.1	NP_001166171.1	Q2M3G4	SHRM1_HUMAN	shroom family member 1	518					actin filament bundle assembly (GO:0051017)|cell morphogenesis (GO:0000902)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|myosin II complex (GO:0016460)	actin filament binding (GO:0051015)			endometrium(1)|kidney(4)|large_intestine(2)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TATTGTGAGAGGGACCTGGAG	0.597																																					p.P518P		Atlas-SNP	.											.	SHROOM1	35	.	0			c.C1554T						PASS	.						71.0	70.0	70.0					5																	132159799		2203	4300	6503	SO:0001819	synonymous_variant	134549	exon4			GTGAGAGGGACCT	AF314142	CCDS4161.1, CCDS54902.1	5q31.1	2007-05-03			ENSG00000164403	ENSG00000164403			24084	protein-coding gene	gene with protein product		611179				11853319, 16615870	Standard	NM_133456		Approved	APXL2, KIAA1960	uc003kxy.2	Q2M3G4	OTTHUMG00000059835	ENST00000378679.3:c.1554C>T	5.37:g.132159799G>A		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	221	39	0.176471	NM_133456	B7WP40|B7ZL01|Q8TDP0|Q8TF41	Silent	SNP	ENST00000378679.3	37	CCDS54902.1																																																																																			.	.	none		0.597	SHROOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133033.1	NM_133456	
MFAP3L	9848	hgsc.bcm.edu	37	4	170913142	170913142	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr4:170913142T>C	ENST00000361618.3	-	3	924	c.617A>G	c.(616-618)aAg>aGg	p.K206R	RP11-6E9.4_ENST00000508955.1_RNA|MFAP3L_ENST00000393704.3_Missense_Mutation_p.K103R	NM_021647.6	NP_067679.6	O75121	MFA3L_HUMAN	microfibrillar-associated protein 3-like	206						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		Prostate(90;0.00601)|Renal(120;0.0183)|all_neural(102;0.122)|Melanoma(52;0.17)		GBM - Glioblastoma multiforme(119;0.0201)|LUSC - Lung squamous cell carcinoma(193;0.116)		GGGGATGCGCTTGGCGATCTC	0.512																																					p.K206R		Atlas-SNP	.											MFAP3L,caecum,carcinoma,0,1	MFAP3L	59	1	0			c.A617G						scavenged	.						136.0	141.0	139.0					4																	170913142		2203	4300	6503	SO:0001583	missense	9848	exon3			ATGCGCTTGGCGA	AB014526	CCDS34103.1, CCDS43281.1	4q33	2014-08-12			ENSG00000198948	ENSG00000198948		"""Immunoglobulin superfamily / I-set domain containing"""	29083	protein-coding gene	gene with protein product						9734811	Standard	XM_005263366		Approved	KIAA0626, NYD-sp9	uc003isp.4	O75121	OTTHUMG00000160942	ENST00000361618.3:c.617A>G	4.37:g.170913142T>C	ENSP00000354583:p.Lys206Arg	Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	250	4	0.016	NM_021647	A8K1X6|D3DP35|Q4W5N7|Q4W5N9|Q6TNA8|Q9BVE1|Q9BXK0	Missense_Mutation	SNP	ENST00000361618.3	37	CCDS34103.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.359264	0.82353	.	.	ENSG00000198948	ENST00000393704;ENST00000361618;ENST00000512698	D;D;D	0.98807	-5.15;-2.08;-4.93	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	D	0.98830	0.9605	M	0.61703	1.905	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99855	1.1076	10	0.54805	T	0.06	-15.6292	15.6799	0.77360	0.0:0.0:0.0:1.0	.	206	O75121	MFA3L_HUMAN	R	103;206;103	ENSP00000377307:K103R;ENSP00000354583:K206R;ENSP00000422791:K103R	ENSP00000354583:K206R	K	-	2	0	MFAP3L	171149717	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	8.040000	0.89188	2.104000	0.64026	0.454000	0.30748	AAG	.	.	none		0.512	MFAP3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363043.2	NM_021647	
LOXL2	4017	hgsc.bcm.edu	37	8	23167305	23167305	+	Nonsense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr8:23167305G>A	ENST00000389131.3	-	10	2125	c.1756C>T	c.(1756-1758)Cag>Tag	p.Q586*		NM_002318.2	NP_002309.1	Q9Y4K0	LOXL2_HUMAN	lysyl oxidase-like 2	586	Lysyl-oxidase like.				aging (GO:0007568)|cell adhesion (GO:0007155)|cellular protein modification process (GO:0006464)|collagen fibril organization (GO:0030199)|endothelial cell migration (GO:0043542)|endothelial cell proliferation (GO:0001935)|epithelial to mesenchymal transition (GO:0001837)|histone modification (GO:0016570)|negative regulation of transcription, DNA-templated (GO:0045892)|oxidation-reduction process (GO:0055114)|positive regulation of chondrocyte differentiation (GO:0032332)|protein deamination (GO:0018277)|response to copper ion (GO:0046688)|response to hypoxia (GO:0001666)|sprouting angiogenesis (GO:0002040)|transcription, DNA-templated (GO:0006351)	basement membrane (GO:0005604)|chromosome (GO:0005694)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|electron carrier activity (GO:0009055)|methylated histone binding (GO:0035064)|oligosaccharide binding (GO:0070492)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)|transcription corepressor activity (GO:0003714)			breast(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(5)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(55;0.0453)|Breast(100;0.143)		Colorectal(74;0.0288)|COAD - Colon adenocarcinoma(73;0.096)		GGGTCGGTCTGCGCGGCTGAG	0.657																																					p.Q586X		Atlas-SNP	.											LOXL2,NS,malignant_melanoma,+2,2	LOXL2	97	2	0			c.C1756T						scavenged	.						41.0	37.0	38.0					8																	23167305		2203	4300	6503	SO:0001587	stop_gained	4017	exon10			CGGTCTGCGCGGC	U89942	CCDS34864.1	8p21.3	2008-05-15				ENSG00000134013			6666	protein-coding gene	gene with protein product		606663				9722957	Standard	NM_002318		Approved	WS9-14	uc003xdh.1	Q9Y4K0		ENST00000389131.3:c.1756C>T	8.37:g.23167305G>A	ENSP00000373783:p.Gln586*	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	162	3	0.0185185	NM_002318	B2R5Q0|Q53HV3|Q9BW70|Q9Y5Y8	Nonsense_Mutation	SNP	ENST00000389131.3	37	CCDS34864.1	.	.	.	.	.	.	.	.	.	.	G	34	5.397083	0.96009	.	.	ENSG00000134013	ENST00000389131	.	.	.	5.67	-0.916	0.10489	.	0.854724	0.10971	N	0.613843	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05525	T	0.97	.	13.37	0.60707	0.0:0.098:0.2625:0.6395	.	.	.	.	X	586	.	ENSP00000373783:Q586X	Q	-	1	0	LOXL2	23223250	0.006000	0.16342	0.001000	0.08648	0.019000	0.09904	0.409000	0.21082	-0.521000	0.06426	-0.397000	0.06425	CAG	.	.	none		0.657	LOXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375603.1		
MGAT1	4245	hgsc.bcm.edu	37	5	180218805	180218805	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:180218805C>T	ENST00000446023.2	-	3	1917	c.1167G>A	c.(1165-1167)acG>acA	p.T389T	MGAT1_ENST00000333055.3_Silent_p.T389T|MGAT1_ENST00000393340.3_Silent_p.T389T|MGAT1_ENST00000427865.2_Silent_p.T389T|MGAT1_ENST00000307826.4_Silent_p.T389T	NM_001114617.1|NM_001114618.1	NP_001108089.1|NP_001108090.1	P26572	MGAT1_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,2-N-acetylglucosaminyltransferase	389					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine catabolic process (GO:0006049)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle (GO:0031982)	acetylglucosaminyltransferase activity (GO:0008375)|alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity (GO:0003827)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	13	all_cancers(89;1.11e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.0027)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00356)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TGTCCCTGCCCGTATACTGCA	0.607																																					p.T389T		Atlas-SNP	.											MGAT1,colon,carcinoma,-1,1	MGAT1	48	1	0			c.G1167A						scavenged	.						76.0	67.0	70.0					5																	180218805		2203	4300	6503	SO:0001819	synonymous_variant	4245	exon3			CCTGCCCGTATAC	M61829	CCDS4458.1	5q35.3	2013-02-25			ENSG00000131446	ENSG00000131446	2.4.1.101	"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	7044	protein-coding gene	gene with protein product		160995		MGAT, GLYT1		1827260	Standard	NM_002406		Approved	GNT-1, GLCNAC-TI	uc003mmg.4	P26572	OTTHUMG00000130937	ENST00000446023.2:c.1167G>A	5.37:g.180218805C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	119	2	0.0168067	NM_001114617	A8K404|B3KRU8|D3DWR1|Q6IBE3	Silent	SNP	ENST00000446023.2	37	CCDS4458.1																																																																																			.	.	none		0.607	MGAT1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368189.1	NM_001114618	
ACTB	60	hgsc.bcm.edu	37	7	5568917	5568917	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr7:5568917C>T	ENST00000331789.5	-	3	429	c.238G>A	c.(238-240)Gac>Aac	p.D80N	ACTB_ENST00000464611.1_5'Flank|AC006483.1_ENST00000579427.1_RNA	NM_001101.3	NP_001092.1	P63261	ACTG_HUMAN	actin, beta	80					adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|platelet aggregation (GO:0070527)|retina homeostasis (GO:0001895)|sarcomere organization (GO:0045214)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|membrane (GO:0016020)|myofibril (GO:0030016)|nucleus (GO:0005634)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(2)|prostate(2)	8		Ovarian(82;0.0606)		UCEC - Uterine corpus endometrioid carcinoma (126;0.175)|OV - Ovarian serous cystadenocarcinoma(56;4.24e-37)		TCCATGTCGTCCCAGTTGGTG	0.602																																					p.D80N		Atlas-SNP	.											.	ACTB	45	.	0			c.G238A						PASS	.						70.0	70.0	70.0					7																	5568917		2203	4300	6503	SO:0001583	missense	60	exon3			TGTCGTCCCAGTT	M28424	CCDS5341.1	7p22	2014-09-17			ENSG00000075624	ENSG00000075624			132	protein-coding gene	gene with protein product		102630				1505215	Standard	NM_001101		Approved		uc003sot.4	P60709	OTTHUMG00000023268	ENST00000331789.5:c.238G>A	7.37:g.5568917C>T	ENSP00000349960:p.Asp80Asn	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	108	24	0.222222	NM_001101	A8K7C2|P02571|P14104|P99022|Q5U032|Q96E67	Missense_Mutation	SNP	ENST00000331789.5	37	CCDS5341.1	.	.	.	.	.	.	.	.	.	.	C	19.24	3.788988	0.70337	.	.	ENSG00000075624	ENST00000331789;ENST00000445914;ENST00000400179;ENST00000432588;ENST00000443528;ENST00000417101;ENST00000414620	D;D;D;D;D	0.95853	-3.83;-3.83;-3.83;-3.83;-3.83	5.01	5.01	0.66863	.	0.000000	0.64402	D	0.000005	D	0.95306	0.8477	M	0.81112	2.525	0.52501	D	0.99995	B	0.02656	0.0	B	0.21917	0.037	D	0.93780	0.7083	10	0.87932	D	0	.	15.8267	0.78711	0.0:1.0:0.0:0.0	.	80	P60709	ACTB_HUMAN	N	80;80;52;80;80;83;80	ENSP00000349960:D80N;ENSP00000407473:D80N;ENSP00000393951:D80N;ENSP00000399487:D83N;ENSP00000401032:D80N	ENSP00000349960:D80N	D	-	1	0	ACTB	5535443	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.600000	0.82769	2.312000	0.78011	0.563000	0.77884	GAC	.	.	none		0.602	ACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059589.4	NM_001101	
DIS3L	115752	hgsc.bcm.edu	37	15	66621332	66621332	+	Silent	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr15:66621332T>C	ENST00000319212.4	+	13	2276	c.2226T>C	c.(2224-2226)tcT>tcC	p.S742S	DIS3L_ENST00000319194.5_Silent_p.S659S|RP11-352G18.2_ENST00000565993.1_RNA	NM_001143688.1	NP_001137160.1	Q8TF46	DI3L1_HUMAN	DIS3 like exosome 3'-5' exoribonuclease	742					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						TGGCTGATTCTCTGGATAATG	0.493																																					p.S742S		Atlas-SNP	.											.	DIS3L	175	.	0			c.T2226C						PASS	.						131.0	135.0	134.0					15																	66621332		2201	4299	6500	SO:0001819	synonymous_variant	115752	exon13			TGATTCTCTGGAT		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.2226T>C	15.37:g.66621332T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	94	4	0.0425532	NM_001143688	Q8N1N8|Q8WTU9|Q96CM7	Silent	SNP	ENST00000319212.4	37	CCDS45286.1																																																																																			.	.	none		0.493	DIS3L-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382792.2	NM_133375	
RIMS2	9699	hgsc.bcm.edu	37	8	104513283	104513283	+	Missense_Mutation	SNP	G	G	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr8:104513283G>C	ENST00000406091.3	+	1	169	c.169G>C	c.(169-171)Gtg>Ctg	p.V57L	RP11-1C8.4_ENST00000523422.1_RNA|RP11-1C8.4_ENST00000517376.1_RNA	NM_001100117.2	NP_001093587.1	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	75	RabBD. {ECO:0000255|PROSITE- ProRule:PRU00234}.				calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cAMP-mediated signaling (GO:0019933)|insulin secretion (GO:0030073)|intracellular protein transport (GO:0006886)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1)	144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			GGAGCAGTCCGTGCTCAAGTA	0.647										HNSCC(12;0.0054)																											p.V57L		Atlas-SNP	.											.	RIMS2	1357	.	0			c.G169C						PASS	.						34.0	39.0	38.0					8																	104513283		1986	4141	6127	SO:0001583	missense	9699	exon1			CAGTCCGTGCTCA	AB018294	CCDS43761.1, CCDS64948.1, CCDS64949.1	8q22.3	2008-08-08	2002-06-12	2002-06-14					17283	protein-coding gene	gene with protein product		606630	"""RAB3 interacting protein 3"""	RAB3IP3		9872452, 12578829	Standard	NM_014677		Approved	KIAA0751, RIM2, OBOE	uc003ylp.3	Q9UQ26		ENST00000406091.3:c.169G>C	8.37:g.104513283G>C	ENSP00000384892:p.Val57Leu	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	197	68	0.345178	NM_001100117	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Missense_Mutation	SNP	ENST00000406091.3	37	CCDS55269.1	.	.	.	.	.	.	.	.	.	.	G	14.58	2.577298	0.45902	.	.	ENSG00000176406	ENST00000504942;ENST00000406091	T;T	0.76060	-0.99;-0.99	3.76	3.76	0.43208	.	.	.	.	.	T	0.67192	0.2867	L	0.47716	1.5	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.63782	-0.6559	9	0.29301	T	0.29	.	14.5166	0.67824	0.0:0.0:1.0:0.0	.	57	F8WD47	.	L	57	ENSP00000427018:V57L;ENSP00000384892:V57L	ENSP00000384892:V57L	V	+	1	0	RIMS2	104582459	0.985000	0.35326	1.000000	0.80357	0.988000	0.76386	2.166000	0.42406	1.791000	0.52520	0.462000	0.41574	GTG	.	.	none		0.647	RIMS2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001100117	
GLOD4	51031	hgsc.bcm.edu	37	17	685705	685705	+	5'Flank	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr17:685705G>A	ENST00000301328.5	-	0	0				RNMTL1_ENST00000304478.4_Nonsense_Mutation_p.W29*|GLOD4_ENST00000536578.1_5'Flank|GLOD4_ENST00000301329.6_5'Flank			Q9HC38	GLOD4_HUMAN	glyoxalase domain containing 4							extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)				endometrium(1)|large_intestine(1)|prostate(1)	3				UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		CGAGGCGCTGGGTCCGGGCGC	0.667																																					p.W29X		Atlas-SNP	.											.	RNMTL1	25	.	0			c.G87A						PASS	.						31.0	35.0	34.0					17																	685705		2203	4299	6502	SO:0001631	upstream_gene_variant	55178	exon1			GCGCTGGGTCCGG	AF177342	CCDS32520.1	17p13.3	2008-02-05	2007-03-14	2007-03-14		ENSG00000167699			14111	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 25"""	C17orf25		11642406, 12528892	Standard	NM_016080		Approved	CGI-150, HC71	uc002fru.3	Q9HC38			17.37:g.685705G>A	Exception_encountered	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	35	21	0.6	NM_018146	D3DTG9|D3DTH1|Q96B89|Q9H3J8|Q9HC37|Q9NVN1	Nonsense_Mutation	SNP	ENST00000301328.5	37		.	.	.	.	.	.	.	.	.	.	G	36	5.630251	0.96671	.	.	ENSG00000171861	ENST00000304478	.	.	.	5.5	4.51	0.55191	.	0.465011	0.25355	N	0.031276	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.268	0.43466	0.0:0.1477:0.6992:0.1531	.	.	.	.	X	29	.	.	W	+	3	0	RNMTL1	632455	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	1.774000	0.38573	1.410000	0.46936	0.563000	0.77884	TGG	.	.	none		0.667	GLOD4-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000437190.1	NM_016080	
TMEM229A	730130	hgsc.bcm.edu	37	7	123672815	123672815	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr7:123672815C>T	ENST00000455783.1	-	1	708	c.243G>A	c.(241-243)ccG>ccA	p.P81P	RP5-921G16.1_ENST00000484322.1_RNA	NM_001136002.1	NP_001129474.1	B2RXF0	T229A_HUMAN	transmembrane protein 229A	81						host cell nucleus (GO:0042025)|integral component of membrane (GO:0016021)	sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(3)	6						TCCGCAGGTCCGGGCTGCGGG	0.687																																					p.P81P		Atlas-SNP	.											.	TMEM229A	31	.	0			c.G243A						PASS	.						37.0	44.0	42.0					7																	123672815		692	1591	2283	SO:0001819	synonymous_variant	730130	exon1			CAGGTCCGGGCTG	BC157828	CCDS47694.1	7q31.32	2009-09-22			ENSG00000234224	ENSG00000234224			37279	protein-coding gene	gene with protein product							Standard	NM_001136002		Approved		uc011kob.2	B2RXF0	OTTHUMG00000154762	ENST00000455783.1:c.243G>A	7.37:g.123672815C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	60	36	0.6	NM_001136002	A4D0X6	Silent	SNP	ENST00000455783.1	37	CCDS47694.1																																																																																			.	.	none		0.687	TMEM229A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336960.3	NM_001136002	
FRG1	2483	hgsc.bcm.edu	37	4	190873335	190873335	+	Missense_Mutation	SNP	C	C	T	rs191989708		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr4:190873335C>T	ENST00000226798.4	+	3	374	c.152C>T	c.(151-153)aCa>aTa	p.T51I	FRG1_ENST00000514482.1_3'UTR	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1	51					mRNA splicing, via spliceosome (GO:0000398)|muscle organ development (GO:0007517)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.T51I(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1)	32		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		TGGACAGTAACAAACTTTGGT	0.318																																					p.T51I		Atlas-SNP	.											FRG1,trunk,malignant_melanoma,0,1	FRG1	76	1	1	Substitution - Missense(1)	skin(1)	c.C152T						scavenged	.						75.0	88.0	84.0					4																	190873335		2201	4292	6493	SO:0001583	missense	2483	exon3			CAGTAACAAACTT	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.152C>T	4.37:g.190873335C>T	ENSP00000226798:p.Thr51Ile	Somatic	112	6	0.0535714		WXS	Illumina HiSeq	Phase_I	116	11	0.0948276	NM_004477	A8K775	Missense_Mutation	SNP	ENST00000226798.4	37	CCDS34121.1	.	.	.	.	.	.	.	.	.	.	.	10.16	1.274422	0.23307	.	.	ENSG00000109536	ENST00000226798	T	0.31510	1.49	3.47	3.47	0.39725	.	0.513050	0.23249	N	0.050263	T	0.16171	0.0389	N	0.19112	0.55	0.09310	N	1	P	0.34462	0.454	B	0.26969	0.075	T	0.13176	-1.0519	10	0.48119	T	0.1	-12.4703	8.4161	0.32672	0.2332:0.7668:0.0:0.0	.	51	Q14331	FRG1_HUMAN	I	51	ENSP00000226798:T51I	ENSP00000226798:T51I	T	+	2	0	FRG1	191110329	0.290000	0.24343	0.875000	0.34327	0.947000	0.59692	1.089000	0.30890	2.238000	0.73509	0.539000	0.68188	ACA	.	.	weak		0.318	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359622.4	NM_004477	
PPIB	5479	hgsc.bcm.edu	37	15	64455114	64455114	+	Silent	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr15:64455114G>A	ENST00000300026.3	-	1	290	c.72C>T	c.(70-72)ttC>ttT	p.F24F	PPIB_ENST00000558492.1_5'UTR	NM_000942.4	NP_000933.1	P23284	PPIB_HUMAN	peptidylprolyl isomerase B (cyclophilin B)	24					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)	GCAGCAGCAGGAAGAAGACGG	0.652																																					p.F24F	GBM(105;399 1481 32889 33051 36637)	Atlas-SNP	.											.	PPIB	20	.	0			c.C72T						PASS	.						24.0	28.0	27.0					15																	64455114		2203	4300	6503	SO:0001819	synonymous_variant	5479	exon1			CAGCAGGAAGAAG		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.72C>T	15.37:g.64455114G>A		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	162	27	0.166667	NM_000942	A8K534|Q6IBH5|Q9BVK5	Silent	SNP	ENST00000300026.3	37	CCDS10191.1																																																																																			.	.	none		0.652	PPIB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256604.1		
TYW1	55253	hgsc.bcm.edu	37	7	66548448	66548448	+	Missense_Mutation	SNP	C	C	T	rs116676724	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr7:66548448C>T	ENST00000359626.5	+	11	1470	c.1306C>T	c.(1306-1308)Cgg>Tgg	p.R436W		NM_018264.2	NP_060734.2	Q9NV66	TYW1_HUMAN	tRNA-yW synthesizing protein 1 homolog (S. cerevisiae)	436					tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|lyase activity (GO:0016829)|oxidoreductase activity (GO:0016491)			breast(1)|endometrium(8)|kidney(10)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(3)|stomach(2)|urinary_tract(2)	46		Lung NSC(55;0.0846)|all_lung(88;0.183)				CACTGAGTGGCGGTGGAAGAT	0.428													c|||	196	0.0391374	0.1422	0.0115	5008	,	,		19182	0.0		0.0	False		,,,				2504	0.0				p.R436W		Atlas-SNP	.											TYW1,NS,carcinoma,-2,1	TYW1	71	1	0			c.C1306T						scavenged	.	C	TRP/ARG	481,3925	226.5+/-242.0	33,415,1755	92.0	90.0	91.0		1306	3.7	1.0	7	dbSNP_132	91	5,8595	4.3+/-15.6	0,5,4295	yes	missense	TYW1	NM_018264.2	101	33,420,6050	TT,TC,CC		0.0581,10.9169,3.7367	benign	436/733	66548448	486,12520	2203	4300	6503	SO:0001583	missense	55253	exon11			GAGTGGCGGTGGA	AK001762	CCDS5538.1	7q11.21	2007-11-29	2007-11-29	2007-11-29	ENSG00000198874	ENSG00000198874			25598	protein-coding gene	gene with protein product	"""tRNA-yW synthesizing protein 1 homolog A (S. cerevisiae)"""	611243	"""radical S-adenosyl methionine and flavodoxin domains 1"""	RSAFD1		16162496, 17150819	Standard	NM_018264		Approved	FLJ10900, MGC23001, MGC60291, YPL207W, TYW1A	uc003tvn.4	Q9NV66	OTTHUMG00000129723	ENST00000359626.5:c.1306C>T	7.37:g.66548448C>T	ENSP00000352645:p.Arg436Trp	Somatic	149	1	0.00671141		WXS	Illumina HiSeq	Phase_I	146	3	0.0205479	NM_018264	Q6PJG8|Q75MG8|Q75MN3|Q86V12|Q8IVS7|Q9H9C4	Missense_Mutation	SNP	ENST00000359626.5	37	CCDS5538.1	86	0.039377289377289376	81	0.16463414634146342	3	0.008287292817679558	0	0.0	2	0.002638522427440633	C	16.76	3.213635	0.58452	0.109169	5.81E-4	ENSG00000198874	ENST00000359626	D	0.92099	-2.97	4.62	3.72	0.42706	Radical SAM (1);	0.000000	0.64402	U	0.000001	T	0.04227	0.0117	M	0.85197	2.74	0.09310	P	0.999999061496	B	0.27286	0.174	B	0.29598	0.104	T	0.62859	-0.6765	9	0.72032	D	0.01	.	10.1835	0.42984	0.3613:0.6387:0.0:0.0	.	436	Q9NV66	TYW1_HUMAN	W	436	ENSP00000352645:R436W	ENSP00000352645:R436W	R	+	1	2	TYW1	66185883	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	2.571000	0.45990	1.039000	0.40074	0.603000	0.83216	CGG	.	.	weak		0.428	TYW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251932.2	NM_018264	
ALKBH1	8846	hgsc.bcm.edu	37	14	78174250	78174250	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr14:78174250C>T	ENST00000216489.3	-	1	113	c.98G>A	c.(97-99)aGc>aAc	p.S33N	SLIRP_ENST00000238688.5_5'Flank|SLIRP_ENST00000557431.1_5'Flank|SLIRP_ENST00000557623.1_5'Flank|SLIRP_ENST00000557342.1_5'Flank	NM_006020.2	NP_006011.2	Q13686	ALKB1_HUMAN	alkB, alkylation repair homolog 1 (E. coli)	33					developmental growth (GO:0048589)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA demethylation (GO:0080111)|DNA repair (GO:0006281)|in utero embryonic development (GO:0001701)|negative regulation of neuron apoptotic process (GO:0043524)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|oxidative demethylation (GO:0070989)|placenta development (GO:0001890)|RNA repair (GO:0042245)	mitochondrion (GO:0005739)|nuclear euchromatin (GO:0005719)	chemoattractant activity (GO:0042056)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)			endometrium(2)|lung(4)|ovary(1)|prostate(1)|skin(1)	9			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0291)		CCCGGGCCGGCTCTGACGGTA	0.657																																					p.S33N		Atlas-SNP	.											.	ALKBH1	30	.	0			c.G98A						PASS	.						37.0	41.0	39.0					14																	78174250		2201	4298	6499	SO:0001583	missense	8846	exon1			GGCCGGCTCTGAC	X91992	CCDS32127.1	14q24	2014-07-23	2006-02-09	2006-02-09	ENSG00000100601	ENSG00000100601		"""Alkylation repair homologs"""	17911	protein-coding gene	gene with protein product		605345	"""alkB, alkylation repair homolog (E. coli)"""	ALKBH		8600462	Standard	XM_005268165		Approved	hABH, alkB, ABH	uc001xuc.1	Q13686	OTTHUMG00000171542	ENST00000216489.3:c.98G>A	14.37:g.78174250C>T	ENSP00000216489:p.Ser33Asn	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	93	4	0.0430108	NM_006020	Q8TAU1|Q9ULA7	Missense_Mutation	SNP	ENST00000216489.3	37	CCDS32127.1	.	.	.	.	.	.	.	.	.	.	C	17.16	3.318509	0.60524	.	.	ENSG00000100601	ENST00000216489	T	0.29655	1.56	5.96	5.05	0.67936	.	0.328069	0.36972	N	0.002319	T	0.26484	0.0647	L	0.44542	1.39	0.28458	N	0.916036	B	0.28128	0.201	B	0.23419	0.046	T	0.10405	-1.0631	10	0.24483	T	0.36	-11.9065	14.3693	0.66828	0.1594:0.8406:0.0:0.0	.	33	Q13686	ALKB1_HUMAN	N	33	ENSP00000216489:S33N	ENSP00000216489:S33N	S	-	2	0	ALKBH1	77244003	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	2.926000	0.48892	1.456000	0.47831	0.655000	0.94253	AGC	.	.	none		0.657	ALKBH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414037.1	NM_006020	
PCDHB4	56131	hgsc.bcm.edu	37	5	140503155	140503155	+	Silent	SNP	G	G	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:140503155G>T	ENST00000194152.1	+	1	1575	c.1575G>T	c.(1573-1575)gcG>gcT	p.A525A	AC005754.8_ENST00000606030.1_lincRNA	NM_018938.2	NP_061761.1	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4	525	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|lung(35)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	67			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCCTGCAGGCGTTCGAGTTCC	0.682																																					p.A525A		Atlas-SNP	.											PCDHB4,caecum,carcinoma,+1,1	PCDHB4	177	1	0			c.G1575T						scavenged	.						69.0	78.0	75.0					5																	140503155		2203	4298	6501	SO:0001819	synonymous_variant	56131	exon1			GCAGGCGTTCGAG	AF152497	CCDS4246.1	5q31	2010-01-26			ENSG00000081818	ENSG00000081818		"""Cadherins / Protocadherins : Clustered"""	8689	other	protocadherin		606330				10380929	Standard	NM_018938		Approved	PCDH-BETA4	uc003lip.1	Q9Y5E5	OTTHUMG00000129617	ENST00000194152.1:c.1575G>T	5.37:g.140503155G>T		Somatic	315	2	0.00634921		WXS	Illumina HiSeq	Phase_I	173	4	0.0231214	NM_018938	Q4V761	Silent	SNP	ENST00000194152.1	37	CCDS4246.1																																																																																			.	.	none		0.682	PCDHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251812.2	NM_018938	
SH3BP1	23616	hgsc.bcm.edu	37	22	38035817	38035817	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr22:38035817G>A	ENST00000357436.4	+	1	336	c.23G>A	c.(22-24)cGc>cAc	p.R8H	SH3BP1_ENST00000599616.1_5'Flank|Z83844.1_ENST00000456099.1_RNA|SH3BP1_ENST00000442465.2_Missense_Mutation_p.R8H|SH3BP1_ENST00000336738.5_Missense_Mutation_p.R8H	NM_018957.3	NP_061830.3	Q9Y3L3	3BP1_HUMAN	SH3-domain binding protein 1	8					signal transduction (GO:0007165)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	Melanoma(58;0.0574)					CAGCTGCACCGCATGCGGCAG	0.706																																					p.R8H		Atlas-SNP	.											.	SH3BP1	41	.	0			c.G23A						PASS	.						5.0	7.0	6.0					22																	38035817		1930	3890	5820	SO:0001583	missense	23616	exon1			TGCACCGCATGCG		CCDS13952.2	22q13.1	2011-07-04			ENSG00000100092	ENSG00000100092		"""Rho GTPase activating proteins"""	10824	protein-coding gene	gene with protein product						10591208, 12029088	Standard	NM_018957		Approved	ARHGAP43	uc003ati.3	Q9Y3L3	OTTHUMG00000030996	ENST00000357436.4:c.23G>A	22.37:g.38035817G>A	ENSP00000350018:p.Arg8His	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	61	7	0.114754	NM_018957	Q5R3N0|Q6IBZ2|Q6ZVL9|Q96HQ5|Q9NSQ9	Missense_Mutation	SNP	ENST00000357436.4	37	CCDS13952.2	.	.	.	.	.	.	.	.	.	.	G	29.5	5.015241	0.93404	.	.	ENSG00000100092	ENST00000357436;ENST00000336738;ENST00000442465	T;T;T	0.80653	-1.4;-1.4;-1.4	3.95	3.95	0.45737	BAR (1);	0.000000	0.47455	D	0.000234	D	0.86493	0.5946	L	0.54323	1.7	0.47621	D	0.999478	D;D	0.89917	1.0;0.999	D;D	0.76575	0.988;0.959	D	0.88038	0.2779	10	0.87932	D	0	.	14.2854	0.66243	0.0:0.0:1.0:0.0	.	8;8	F5GZA8;Q9Y3L3	.;3BP1_HUMAN	H	8	ENSP00000350018:R8H;ENSP00000337213:R8H;ENSP00000395126:R8H	ENSP00000337213:R8H	R	+	2	0	SH3BP1	36365763	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.636000	0.61339	2.187000	0.69744	0.609000	0.83330	CGC	.	.	none		0.706	SH3BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075884.4	NM_018957	
CCDC175	729665	hgsc.bcm.edu	37	14	60004844	60004844	+	Missense_Mutation	SNP	C	C	T	rs4261431	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr14:60004844C>T	ENST00000537690.2	-	13	1575	c.1520G>A	c.(1519-1521)gGa>gAa	p.G507E	CCDC175_ENST00000281581.4_Missense_Mutation_p.G507E	NM_001164399.1	NP_001157871.1	P0C221	CC175_HUMAN	coiled-coil domain containing 175	507			G -> E (in dbSNP:rs4261431).														TGCCACAAATCCACTGATCTC	0.323													T|||	2663	0.531749	0.2965	0.4827	5008	,	,		16872	0.8165		0.5646	False		,,,				2504	0.5573				p.G507E		Atlas-SNP	.											.	.	.	.	0			c.G1520A						PASS	.	T	GLU/GLY	473,911		76,321,295	162.0	123.0	135.0		1520	2.4	0.0	14	dbSNP_111	135	1843,1339		532,779,280	yes	missense	C14orf38	NM_001164399.1	98	608,1100,575	TT,TC,CC		42.0805,34.1763,49.2773		507/794	60004844	2316,2250	692	1591	2283	SO:0001583	missense	729665	exon13			ACAAATCCACTGA		CCDS53898.1	14q23.1	2012-09-24	2012-09-24	2012-09-24	ENSG00000151838	ENSG00000151838			19847	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 38"""	C14orf38			Standard	NM_001164399		Approved		uc021rtw.1	P0C221		ENST00000537690.2:c.1520G>A	14.37:g.60004844C>T	ENSP00000453940:p.Gly507Glu	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_001164399	G3V5J7	Missense_Mutation	SNP	ENST00000537690.2	37	CCDS53898.1	1266	0.5796703296703297	164	0.3333333333333333	184	0.5082872928176796	478	0.8356643356643356	440	0.5804749340369393	T	0.017	-1.508651	0.00984	0.341763	0.579195	ENSG00000151838	ENST00000555041	.	.	.	4.94	2.43	0.29744	.	0.896444	0.09365	N	0.812168	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	.	.	.	.	.	.	T	0.38457	-0.9660	6	0.02654	T	1	-1.6429	4.4497	0.11614	0.0:0.1786:0.167:0.6543	rs4261431;rs17834190;rs52829619;rs57511261;rs4261431	.	.	.	E	507	.	ENSP00000281581:G507E	G	-	2	0	C14orf38	59074597	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.265000	0.08644	0.081000	0.16988	-0.361000	0.07541	GGA	C|0.414;N|0.000	.	strong		0.323	CCDC175-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471273.1	NM_001164399	
SALL4	57167	hgsc.bcm.edu	37	20	50407072	50407072	+	Silent	SNP	G	G	A	rs149008635	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr20:50407072G>A	ENST00000217086.4	-	2	2061	c.1950C>T	c.(1948-1950)ggC>ggT	p.G650G	SALL4_ENST00000395997.3_Intron|SALL4_ENST00000483130.1_5'Flank|SALL4_ENST00000371539.3_Intron	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	650					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						GAATCTGACCGCCCATGTGCA	0.552																																					p.G650G		Atlas-SNP	.											SALL4,bladder,carcinoma,-1,1	SALL4	168	1	0			c.C1950T						scavenged	.	G		4,4402	8.1+/-20.4	0,4,2199	64.0	55.0	58.0		1950	-3.0	1.0	20	dbSNP_134	58	17,8583	12.6+/-44.7	0,17,4283	no	coding-synonymous	SALL4	NM_020436.3		0,21,6482	AA,AG,GG		0.1977,0.0908,0.1615		650/1054	50407072	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	57167	exon2			CTGACCGCCCATG	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.1950C>T	20.37:g.50407072G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	147	2	0.0136054	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Silent	SNP	ENST00000217086.4	37	CCDS13438.1																																																																																			G|0.999;A|0.001	0.001	strong		0.552	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3		
ZNF189	7743	hgsc.bcm.edu	37	9	104170651	104170651	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr9:104170651G>A	ENST00000339664.2	+	3	730	c.601G>A	c.(601-603)Gaa>Aaa	p.E201K	ZNF189_ENST00000259395.4_Missense_Mutation_p.E159K|ZNF189_ENST00000374861.3_Missense_Mutation_p.E187K	NM_001278240.1	NP_001265169.1	O75820	ZN189_HUMAN	zinc finger protein 189	201					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)				TCACACTGGGGAAAGGCCCTA	0.413																																					p.E201K		Atlas-SNP	.											.	ZNF189	79	.	0			c.G601A						PASS	.						77.0	81.0	80.0					9																	104170651		2203	4300	6503	SO:0001583	missense	7743	exon3			ACTGGGGAAAGGC	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.601G>A	9.37:g.104170651G>A	ENSP00000342019:p.Glu201Lys	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	132	55	0.416667	NM_003452	O75802|Q5T7D7|Q5T7D8|Q5T7D9|Q9UBL4|Q9UPE9|Q9UPF0|Q9UPF1	Missense_Mutation	SNP	ENST00000339664.2	37	CCDS6754.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.306653	0.81247	.	.	ENSG00000136870	ENST00000374861;ENST00000339664;ENST00000259395	T;T;T	0.24350	1.86;1.86;1.86	4.79	4.79	0.61399	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.50627	D	0.000113	T	0.48150	0.1484	M	0.64080	1.96	0.54753	D	0.999982	D;D;D	0.71674	0.985;0.995;0.998	P;D;D	0.74023	0.807;0.931;0.982	T	0.40156	-0.9578	10	0.62326	D	0.03	.	16.1533	0.81636	0.0:0.0:1.0:0.0	.	186;187;201	B7ZLK9;Q5T7D8;O75820	.;.;ZN189_HUMAN	K	187;201;159	ENSP00000363995:E187K;ENSP00000342019:E201K;ENSP00000259395:E159K	ENSP00000259395:E159K	E	+	1	0	ZNF189	103210472	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.478000	0.73596	2.941000	0.99782	0.655000	0.94253	GAA	.	.	none		0.413	ZNF189-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053447.1	NM_003452	
HOXC8	3224	hgsc.bcm.edu	37	12	54403503	54403503	+	Splice_Site	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:54403503C>T	ENST00000040584.4	+	1	672	c.435C>T	c.(433-435)caC>caT	p.H145H	RP11-834C11.12_ENST00000513209.1_Intron	NM_022658.3	NP_073149.1	P31273	HXC8_HUMAN	homeobox C8	145					anterior/posterior pattern specification (GO:0009952)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.H145Q(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|skin(3)	8						TGAGACCCCACGGTGAGAAGC	0.552																																					p.H145H	GBM(197;701 2226 7002 18822 41696)	Atlas-SNP	.											HOXC8,NS,carcinoma,0,1	HOXC8	15	1	1	Substitution - Missense(1)	lung(1)	c.C435T						scavenged	.						100.0	98.0	99.0					12																	54403503		2203	4300	6503	SO:0001630	splice_region_variant	3224	exon1			ACCCCACGGTGAG	X99680	CCDS8870.1	12q13.13	2011-06-20	2005-12-22			ENSG00000037965		"""Homeoboxes / ANTP class : HOXL subclass"""	5129	protein-coding gene	gene with protein product		142970	"""homeo box C8"""	HOX3, HOX3A		1973146, 1358459	Standard	NM_022658		Approved		uc001ser.3	P31273		ENST00000040584.4:c.436+1C>T	12.37:g.54403503C>T		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	174	3	0.0172414	NM_022658	A8K4J4|O15221|O15362	Silent	SNP	ENST00000040584.4	37	CCDS8870.1																																																																																			.	.	none		0.552	HOXC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358957.2		Silent
FAM107B	83641	hgsc.bcm.edu	37	10	14816655	14816655	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr10:14816655G>A	ENST00000181796.2	-	1	241	c.8C>T	c.(7-9)aCg>aTg	p.T3M		NM_031453.2	NP_113641.2	Q9H098	F107B_HUMAN	family with sequence similarity 107, member B	0					sensory perception of sound (GO:0007605)					breast(7)|kidney(1)|large_intestine(4)|lung(7)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TGCTTTCCACGTGGACATGAC	0.483																																					p.T3M		Atlas-SNP	.											.	FAM107B	43	.	0			c.C8T						PASS	.						82.0	65.0	71.0					10																	14816655		2203	4300	6503	SO:0001583	missense	83641	exon1			TTCCACGTGGACA	AK127413	CCDS7102.1, CCDS60486.1	10p14	2006-01-17	2006-01-17	2005-11-20	ENSG00000065809	ENSG00000065809			23726	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 45"""	C10orf45		11230166	Standard	XM_005252616		Approved	FLJ45505, MGC11034	uc001ina.1	Q9H098	OTTHUMG00000017709	ENST00000181796.2:c.8C>T	10.37:g.14816655G>A	ENSP00000181796:p.Thr3Met	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	152	44	0.289474	NM_031453	A8K1P4|D3DRT2|Q5T9K7|Q5T9K8|Q6ZSI4	Missense_Mutation	SNP	ENST00000181796.2	37	CCDS7102.1	.	.	.	.	.	.	.	.	.	.	G	11.55	1.672163	0.29693	.	.	ENSG00000065809	ENST00000181796	T	0.39229	1.09	5.84	1.91	0.25777	.	0.778029	0.11243	N	0.584448	T	0.20577	0.0495	N	0.14661	0.345	0.80722	D	1	B	0.31054	0.306	B	0.22152	0.038	T	0.12656	-1.0539	10	0.87932	D	0	-0.0064	2.2074	0.03939	0.2697:0.1203:0.4863:0.1237	.	3	Q9H098-2	.	M	3	ENSP00000181796:T3M	ENSP00000181796:T3M	T	-	2	0	FAM107B	14856661	0.013000	0.17824	1.000000	0.80357	0.694000	0.40290	0.028000	0.13644	0.389000	0.25086	0.650000	0.86243	ACG	.	.	none		0.483	FAM107B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000356966.1	NM_031453	
CCDC168	643677	hgsc.bcm.edu	37	13	103383853	103383853	+	Silent	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr13:103383853T>C	ENST00000322527.2	-	1	5306	c.5307A>G	c.(5305-5307)aaA>aaG	p.K1769K		NM_001146197.1	NP_001139669.1	Q8NDH2	CC168_HUMAN	coiled-coil domain containing 168	1769																	TGTGCTGCGTTTTGGGATATA	0.368																																					p.K6398K		Atlas-SNP	.											C13orf40,NS,carcinoma,-2,1	.	.	1	0			c.A19194G						scavenged	.						85.0	71.0	75.0					13																	103383853		692	1591	2283	SO:0001819	synonymous_variant	643677	exon4			CTGCGTTTTGGGA		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.5307A>G	13.37:g.103383853T>C		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	158	2	0.0126582	NM_001146197	Q8N800	Silent	SNP	ENST00000322527.2	37																																																																																				.	.	none		0.368	CCDC168-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146197	
KMT2C	58508	hgsc.bcm.edu	37	7	151896386	151896386	+	Silent	SNP	A	A	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr7:151896386A>G	ENST00000262189.6	-	27	4469	c.4251T>C	c.(4249-4251)gcT>gcC	p.A1417A	KMT2C_ENST00000355193.2_Silent_p.A1417A	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	1417					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)										ATTTTGTTGGAGCCGAGGATG	0.333																																					p.A1417A		Atlas-SNP	.											MLL3_ENST00000355193,NS,carcinoma,-2,2	MLL3	1564	2	0			c.T4251C						scavenged	.						71.0	70.0	70.0					7																	151896386		2203	4300	6503	SO:0001819	synonymous_variant	58508	exon27			TGTTGGAGCCGAG	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.4251T>C	7.37:g.151896386A>G		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	181	3	0.0165746	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Silent	SNP	ENST00000262189.6	37	CCDS5931.1																																																																																			.	.	none		0.333	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
MFSD3	113655	hgsc.bcm.edu	37	8	145738768	145738768	+	IGR	SNP	G	G	C	rs11342077|rs398010167|rs199605511		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr8:145738768G>C	ENST00000301327.4	+	0	1548				RECQL4_ENST00000532237.1_5'UTR|RECQL4_ENST00000428558.2_Splice_Site_p.R766G|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)			ACCACCACCCGGCAACTGGCC	0.677																																					.		Atlas-SNP	.											.	RECQL4	75	.	0			c.2296+1C>G						PASS	.																																			SO:0001628	intergenic_variant	9401	exon15			CCACCCGGCAACT		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.145738768G>C		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	34	7	0.205882	NM_004260		Splice_Site	SNP	ENST00000301327.4	37	CCDS6431.1																																																																																			.	.	weak		0.677	MFSD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382478.2	NM_138431	
VPS13D	55187	hgsc.bcm.edu	37	1	12333079	12333079	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:12333079C>T	ENST00000358136.3	+	18	2253	c.2123C>T	c.(2122-2124)aCc>aTc	p.T708I	VPS13D_ENST00000356315.4_Missense_Mutation_p.T708I	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)		AAACGATGGACCGTGCGGCTG	0.428																																					p.T708I		Atlas-SNP	.											VPS13D,right_upper_lobe,carcinoma,0,1	VPS13D	316	1	0			c.C2123T						scavenged	.						144.0	134.0	137.0					1																	12333079		2203	4300	6503	SO:0001583	missense	55187	exon18			GATGGACCGTGCG	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.2123C>T	1.37:g.12333079C>T	ENSP00000350854:p.Thr708Ile	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	153	3	0.0196078	NM_015378		Missense_Mutation	SNP	ENST00000358136.3	37	CCDS30588.1	.	.	.	.	.	.	.	.	.	.	C	14.77	2.635458	0.47049	.	.	ENSG00000048707	ENST00000356315;ENST00000358136	T;T	0.45276	0.9;0.9	5.16	0.627	0.17675	.	0.176098	0.48286	D	0.000185	T	0.39145	0.1067	L	0.55481	1.735	0.80722	D	1	P;P	0.50617	0.937;0.624	P;B	0.44394	0.448;0.261	T	0.30238	-0.9985	10	0.66056	D	0.02	.	11.3336	0.49490	0.0:0.4778:0.4528:0.0694	.	708;708	Q5THJ4-2;Q5THJ4	.;VP13D_HUMAN	I	708	ENSP00000348666:T708I;ENSP00000350854:T708I	ENSP00000348666:T708I	T	+	2	0	VPS13D	12255666	0.995000	0.38212	0.789000	0.31954	0.398000	0.30690	3.158000	0.50723	-0.161000	0.10983	0.585000	0.79938	ACC	.	.	none		0.428	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378	
CRCT1	54544	hgsc.bcm.edu	37	1	152488146	152488146	+	Missense_Mutation	SNP	G	G	A	rs16834168	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:152488146G>A	ENST00000368790.3	+	2	360	c.287G>A	c.(286-288)tGc>tAc	p.C96Y		NM_019060.2	NP_061933.1	Q9UGL9	CRCT1_HUMAN	cysteine-rich C-terminal 1	96	Cys-rich.		C -> Y (in dbSNP:rs16834168).							lung(1)|ovary(1)	2	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCAGGATGCTGCTCCGGCTGC	0.726													G|||	463	0.0924521	0.0734	0.1816	5008	,	,		10222	0.1032		0.0288	False		,,,				2504	0.1094				p.C96Y		Atlas-SNP	.											.	CRCT1	6	.	0			c.G287A						PASS	.	G	TYR/CYS	146,3402		0,146,1628	3.0	4.0	4.0		287	3.7	1.0	1	dbSNP_123	4	118,7426		0,118,3654	yes	missense	CRCT1	NM_019060.2	194	0,264,5282	AA,AG,GG		1.5642,4.115,2.3801	probably-damaging	96/100	152488146	264,10828	1774	3772	5546	SO:0001583	missense	54544	exon2			GATGCTGCTCCGG	AJ243662	CCDS1012.1	1q21	2008-02-05	2006-12-18	2006-12-18	ENSG00000169509	ENSG00000169509			29875	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 42"""	C1orf42		11230159	Standard	NM_019060		Approved	NICE-1	uc001ezz.3	Q9UGL9	OTTHUMG00000012391	ENST00000368790.3:c.287G>A	1.37:g.152488146G>A	ENSP00000357779:p.Cys96Tyr	Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	8	5	0.625	NM_019060	A4QN00|Q6IAD7	Missense_Mutation	SNP	ENST00000368790.3	37	CCDS1012.1	165	0.07554945054945054	32	0.06504065040650407	48	0.13259668508287292	63	0.11013986013986014	22	0.029023746701846966	G	7.153	0.584146	0.13749	0.04115	0.015642	ENSG00000169509	ENST00000368790	T	0.47177	0.85	4.73	3.74	0.42951	.	0.000000	0.46442	D	0.000292	T	0.57475	0.2056	.	.	.	0.30777	P	0.74237	D	0.89917	1.0	D	0.85130	0.997	T	0.63418	-0.6642	8	0.87932	D	0	-38.9083	10.3495	0.43927	0.0:0.1997:0.8003:0.0	rs16834168;rs16834168	96	Q9UGL9	CRCT1_HUMAN	Y	96	ENSP00000357779:C96Y	ENSP00000357779:C96Y	C	+	2	0	CRCT1	150754770	0.985000	0.35326	0.987000	0.45799	0.238000	0.25445	1.916000	0.39986	2.300000	0.77407	0.650000	0.86243	TGC	G|0.916;A|0.084	0.084	strong		0.726	CRCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034511.1	NM_019060	
TUBB8	347688	hgsc.bcm.edu	37	10	94004	94004	+	Missense_Mutation	SNP	C	C	T	rs145405488	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr10:94004C>T	ENST00000309812.4	-	4	390	c.328G>A	c.(328-330)Gcg>Acg	p.A110T	TUBB8_ENST00000447903.2_Missense_Mutation_p.A38T|TUBB8_ENST00000332708.5_Silent_p.A73A|TUBB8_ENST00000413237.3_5'UTR	NM_177987.2	NP_817124.1	Q3ZCM7	TBB8_HUMAN	tubulin, beta 8 class VIII	110					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.A110T(1)		NS(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(12)|ovary(2)|prostate(3)|skin(3)|stomach(1)	32		all_cancers(4;0.00131)|all_lung(4;0.000777)|Lung NSC(4;0.0043)|all_epithelial(10;0.0154)|Colorectal(49;0.235)		Epithelial(11;0.00341)|all cancers(11;0.00922)|OV - Ovarian serous cystadenocarcinoma(14;0.0508)|Lung(33;0.132)		ATCAGCTCCGCGCCTTCGGTG	0.607																																					p.A110T	Pancreas(192;2041 3010 9013 18103)	Atlas-SNP	.											TUBB8,colon,carcinoma,+2,2	TUBB8	62	2	1	Substitution - Missense(1)	skin(1)	c.G328A						scavenged	.	C	THR/ALA	55,4351	38.4+/-70.7	0,55,2148	71.0	61.0	64.0		328		0.3	10	dbSNP_134	64	2,8598	1.2+/-3.3	0,2,4298	no	missense	TUBB8	NM_177987.2	58	0,57,6446	TT,TC,CC		0.0233,1.2483,0.4383	probably-damaging	110/445	94004	57,12949	2203	4300	6503	SO:0001583	missense	347688	exon4			GCTCCGCGCCTTC	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.328G>A	10.37:g.94004C>T	ENSP00000311042:p.Ala110Thr	Somatic	300	0	0		WXS	Illumina HiSeq	Phase_I	298	3	0.0100671	NM_177987	Q5SQX9|Q8WZ78	Missense_Mutation	SNP	ENST00000309812.4	37	CCDS7051.1	.	.	.	.	.	.	.	.	.	.	C	10.26	1.300454	0.23650	0.012483	2.33E-4	ENSG00000173876	ENST00000447903;ENST00000272035;ENST00000440680;ENST00000328974	T	0.69306	-0.39	.	.	.	Tubulin/FtsZ, GTPase domain (4);	0.000000	0.64402	U	0.000011	T	0.67468	0.2896	M	0.83223	2.63	0.36308	D	0.857475	D;P	0.57571	0.98;0.67	P;B	0.56434	0.798;0.13	T	0.73799	-0.3869	9	0.87932	D	0	.	5.9051	0.18992	0.0:0.9992:0.0:8.0E-4	.	73;110	C9JAA5;Q3ZCM7	.;TBB8_HUMAN	T	38;76;73;110	ENSP00000403895:A38T	ENSP00000272035:A76T	A	-	1	0	RP11-631M21.2	84004	0.998000	0.40836	0.290000	0.24890	0.293000	0.27360	5.268000	0.65536	0.119000	0.18210	0.121000	0.15741	GCG	C|0.991;T|0.009	0.009	strong		0.607	TUBB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467795.1	NM_177987	
NEFH	4744	hgsc.bcm.edu	37	22	29885564	29885564	+	Silent	SNP	A	A	G	rs202065964|rs371230849		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr22:29885564A>G	ENST00000310624.6	+	4	1968	c.1935A>G	c.(1933-1935)gaA>gaG	p.E645E		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	645	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						CGAAGGAGGAAGCAAAGTCCC	0.562																																					p.E645E		Atlas-SNP	.											NEFH,rectum,carcinoma,0,1	NEFH	178	1	0			c.A1935G						PASS	.						83.0	89.0	87.0					22																	29885564		2203	4300	6503	SO:0001819	synonymous_variant	4744	exon4			GGAGGAAGCAAAG		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1935A>G	22.37:g.29885564A>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	66	11	0.166667	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Silent	SNP	ENST00000310624.6	37	CCDS13858.1																																																																																			.	.	weak		0.562	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
TRIOBP	11078	hgsc.bcm.edu	37	22	38119859	38119859	+	Silent	SNP	C	C	T	rs66505048	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr22:38119859C>T	ENST00000406386.3	+	7	1551	c.1296C>T	c.(1294-1296)tgC>tgT	p.C432C		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	432					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.C432C(6)		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)					GAACATCCTGCGCCCAGCGGG	0.582																																					p.C432C		Atlas-SNP	.											TRIOBP_ENST00000344404,NS,carcinoma,0,8	TRIOBP	262	8	6	Substitution - coding silent(6)	kidney(3)|cervix(1)|lung(1)|endometrium(1)	c.C1296T						scavenged	.																																			SO:0001819	synonymous_variant	11078	exon7			ATCCTGCGCCCAG	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.1296C>T	22.37:g.38119859C>T		Somatic	215	2	0.00930233		WXS	Illumina HiSeq	Phase_I	233	3	0.0128755	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Silent	SNP	ENST00000406386.3	37	CCDS43015.1																																																																																			C|0.500;T|0.500	0.500	strong		0.582	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
DND1	373863	hgsc.bcm.edu	37	5	140052331	140052331	+	Silent	SNP	G	G	T	rs200268202	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:140052331G>T	ENST00000542735.1	-	3	346	c.303C>A	c.(301-303)gcC>gcA	p.A101A		NM_194249.2	NP_919225.1	Q8IYX4	DND1_HUMAN	DND microRNA-mediated repression inhibitor 1	101	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of gene silencing by miRNA (GO:0060965)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)	p.A101A(1)		central_nervous_system(1)|prostate(4)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCGGGCATAGGCGAAGCCGC	0.687																																					p.A101A		Atlas-SNP	.											DND1,NS,carcinoma,0,1	DND1	15	1	1	Substitution - coding silent(1)	prostate(1)	c.C303A						scavenged	.						10.0	13.0	12.0					5																	140052331		2186	4289	6475	SO:0001819	synonymous_variant	373863	exon3			GGCATAGGCGAAG	AY321065	CCDS4236.1	5q31.3	2013-07-31	2013-07-31		ENSG00000256453	ENSG00000256453		"""RNA binding motif (RRM) containing"""	23799	protein-coding gene	gene with protein product		609385	"""dead end homolog 1 (zebrafish)"""			12932328	Standard	NM_194249		Approved	MGC34750, RBMS4	uc003lgt.3	Q8IYX4	OTTHUMG00000129499	ENST00000542735.1:c.303C>A	5.37:g.140052331G>T		Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	8	5	0.625	NM_194249		Silent	SNP	ENST00000542735.1	37	CCDS4236.1																																																																																			G|0.952;T|0.047	0.047	strong		0.687	DND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251669.2	NM_194249	
KDM4E	390245	hgsc.bcm.edu	37	11	94759726	94759726	+	Silent	SNP	C	C	T	rs76354273	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:94759726C>T	ENST00000450979.2	+	1	1305	c.1005C>T	c.(1003-1005)caC>caT	p.H335H		NM_001161630.1	NP_001155102.1	B2RXH2	KDM4E_HUMAN	lysine (K)-specific demethylase 4E	335					histone H3-K9 demethylation (GO:0033169)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			breast(1)|endometrium(7)|kidney(1)|lung(3)	12						TCTGGAAACACAGGCAAGACT	0.512													C|||	220	0.0439297	0.0174	0.0014	5008	,	,		21472	0.1637		0.001	False		,,,				2504	0.0307				p.H335H		Atlas-SNP	.											.	KDM4E	60	.	0			c.C1005T						PASS	.	C		34,1350		0,34,658	64.0	59.0	61.0		1005	1.4	0.2	11	dbSNP_132	61	6,3176		0,6,1585	no	coding-synonymous	KDM4DL	NM_001161630.1		0,40,2243	TT,TC,CC		0.1886,2.4566,0.876		335/507	94759726	40,4526	692	1591	2283	SO:0001819	synonymous_variant	390245	exon1			GAAACACAGGCAA	BC157851	CCDS44713.1	11q21	2012-03-30	2012-03-28	2012-03-28		ENSG00000235268		"""Chromatin-modifying enzymes / K-demethylases"""	37098	protein-coding gene	gene with protein product			"""lysine (K)-specific demethylase 4D-like"""	KDM4DL		21076780	Standard	NM_001161630		Approved	JMJD2E	uc010ruf.1	B2RXH2		ENST00000450979.2:c.1005C>T	11.37:g.94759726C>T		Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	12	6	0.5	NM_001161630		Silent	SNP	ENST00000450979.2	37	CCDS44713.1																																																																																			C|0.947;T|0.053	0.053	strong		0.512	KDM4E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396649.1	NM_001161630	
FBXL6	26233	hgsc.bcm.edu	37	8	145579964	145579964	+	Silent	SNP	A	A	G	rs75159950	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr8:145579964A>G	ENST00000331890.5	-	7	1285	c.1221T>C	c.(1219-1221)tgT>tgC	p.C407C	FBXL6_ENST00000455319.2_Silent_p.C401C|FBXL6_ENST00000526524.1_5'UTR|SLC52A2_ENST00000527078.1_5'Flank|TMEM249_ENST00000531225.1_5'Flank|SLC52A2_ENST00000530047.1_5'Flank|SLC52A2_ENST00000402965.1_5'Flank|SLC52A2_ENST00000329994.2_5'Flank|SLC52A2_ENST00000540505.1_5'Flank|TMEM249_ENST00000398633.3_5'Flank|SLC52A2_ENST00000526752.1_5'Flank|SLC52A2_ENST00000532887.1_5'Flank	NM_012162.2	NP_036294.2	Q8N531	FBXL6_HUMAN	F-box and leucine-rich repeat protein 6	407					protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)		ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|lung(3)|ovary(1)	5	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;4.43e-40)|Epithelial(56;1.48e-39)|all cancers(56;1.49e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0441)|Colorectal(110;0.055)			GCTGACCCCGACATGGCAGAT	0.642																																					p.C407C		Atlas-SNP	.											FBXL6,colon,carcinoma,0,1	FBXL6	26	1	0			c.T1221C						scavenged	.																																			SO:0001819	synonymous_variant	26233	exon7			ACCCCGACATGGC	AF174592	CCDS6422.1, CCDS47942.1	8q24.3	2011-06-09			ENSG00000182325	ENSG00000182325		"""F-boxes / Leucine-rich repeats"""	13603	protein-coding gene	gene with protein product		609076				10531035, 10531037	Standard	NM_012162		Approved	FBL6	uc003zcb.3	Q8N531	OTTHUMG00000165169	ENST00000331890.5:c.1221T>C	8.37:g.145579964A>G		Somatic	61	2	0.0327869		WXS	Illumina HiSeq	Phase_I	78	8	0.102564	NM_012162	Q53G43|Q9H5W9|Q9UKC7	Silent	SNP	ENST00000331890.5	37	CCDS6422.1																																																																																			A|0.928;G|0.072	0.072	strong		0.642	FBXL6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382413.1	NM_024555	
RIMBP3	85376	hgsc.bcm.edu	37	22	20457383	20457383	+	Missense_Mutation	SNP	G	G	T	rs199673858	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr22:20457383G>T	ENST00000426804.1	-	1	4403	c.3919C>A	c.(3919-3921)Cct>Act	p.P1307T	RN7SKP131_ENST00000363006.1_RNA|SCARNA17_ENST00000516762.1_RNA|SCARNA18_ENST00000516215.1_RNA	NM_015672.1	NP_056487.1	Q9UFD9	RIM3A_HUMAN	RIMS binding protein 3	1307				P -> T (in Ref. 4; AAH35246). {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)			TTCTCCCCAGGCTGGTCACTG	0.582													g|||	482	0.096246	0.0635	0.1455	5008	,	,		12204	0.128		0.0805	False		,,,				2504	0.089				p.P1307T		Atlas-SNP	.											RIMBP3,NS,carcinoma,0,1	RIMBP3	42	1	0			c.C3919A						scavenged	.	G	THR/PRO	79,2731		10,59,1336	26.0	28.0	28.0		3919	-6.4	0.0	22	dbSNP_134	28	171,6761		16,139,3311	no	missense	RIMBP3	NM_015672.1	38	26,198,4647	TT,TG,GG		2.4668,2.8114,2.5662	benign	1307/1640	20457383	250,9492	1405	3466	4871	SO:0001583	missense	85376	exon1			CCCCAGGCTGGTC	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.3919C>A	22.37:g.20457383G>T	ENSP00000391564:p.Pro1307Thr	Somatic	51	51	1		WXS	Illumina HiSeq	Phase_I	62	62	1	NM_015672	Q8IYP7|Q9BY94|Q9UFQ5	Missense_Mutation	SNP	ENST00000426804.1	37	CCDS46665.1	103	0.04716117216117216	10	0.02032520325203252	20	0.055248618784530384	41	0.07167832167832168	32	0.04221635883905013	G	9.207	1.029914	0.19512	0.028114	0.024668	ENSG00000196622	ENST00000355186;ENST00000426804	T	0.16597	2.33	3.38	-6.4	0.01944	.	1.053850	0.07468	N	0.901812	T	0.00496	0.0016	N	0.24115	0.695	0.09310	N	1	B	0.22003	0.063	B	0.19666	0.026	T	0.39563	-0.9608	10	0.11182	T	0.66	0.5061	1.52	0.02514	0.263:0.1812:0.4054:0.1503	.	1213	Q9UFD9	RIM3A_HUMAN	T	1213;1307	ENSP00000391564:P1307T	ENSP00000347318:P1213T	P	-	1	0	RIMBP3	18837383	0.000000	0.05858	0.003000	0.11579	0.023000	0.10783	-1.468000	0.02350	-1.021000	0.03350	0.423000	0.28283	CCT	G|0.500;T|0.500	0.500	weak		0.582	RIMBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318945.2	NM_015672	
SP8	221833	hgsc.bcm.edu	37	7	20824614	20824614	+	Silent	SNP	C	C	T	rs34908430	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr7:20824614C>T	ENST00000361443.4	-	3	1005	c.768G>A	c.(766-768)tcG>tcA	p.S256S	SP8_ENST00000418710.2_Silent_p.S274S	NM_198956.2	NP_945194.1	Q8IXZ3	SP8_HUMAN	Sp8 transcription factor	256					dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|proximal/distal pattern formation (GO:0009954)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	8						GACTCAGGCCCGAGTAATCCG	0.706													c|||	1351	0.269768	0.0635	0.379	5008	,	,		12232	0.3958		0.2893	False		,,,				2504	0.3211				p.S274S		Atlas-SNP	.											.	SP8	43	.	0			c.G822A						PASS	.	C	,	317,3303		22,273,1515	5.0	6.0	5.0		822,768	-5.1	1.0	7	dbSNP_126	5	1820,5582		247,1326,2128	no	coding-synonymous,coding-synonymous	SP8	NM_182700.4,NM_198956.2	,	269,1599,3643	TT,TC,CC		24.5879,8.7569,19.3885	,	274/509,256/491	20824614	2137,8885	1810	3701	5511	SO:0001819	synonymous_variant	221833	exon2			CAGGCCCGAGTAA		CCDS5372.1, CCDS43555.1	7p21.2	2013-01-08			ENSG00000164651	ENSG00000164651		"""Specificity protein transcription factors"", ""Zinc fingers, C2H2-type"""	19196	protein-coding gene	gene with protein product		608306					Standard	NM_182700		Approved		uc003suz.3	Q8IXZ3	OTTHUMG00000094788	ENST00000361443.4:c.768G>A	7.37:g.20824614C>T		Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	9	5	0.555556	NM_182700	Q7Z615|Q7Z616|Q96MJ1	Silent	SNP	ENST00000361443.4	37	CCDS5372.1																																																																																			C|0.738;T|0.262	0.262	strong		0.706	SP8-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326904.2		
PGR	5241	hgsc.bcm.edu	37	11	100922186	100922186	+	Missense_Mutation	SNP	G	G	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:100922186G>T	ENST00000325455.5	-	5	3779	c.2326C>A	c.(2326-2328)Ctg>Atg	p.L776M	PGR_ENST00000534013.1_Missense_Mutation_p.L182M|PGR_ENST00000263463.5_Missense_Mutation_p.L674M	NM_000926.4|NM_001202474.1|NM_001271162.1	NP_000917.3|NP_001189403.1|NP_001258091.1	P06401	PRGR_HUMAN	progesterone receptor	776	Steroid-binding.				cell-cell signaling (GO:0007267)|epithelial cell maturation (GO:0002070)|gene expression (GO:0010467)|negative regulation of gene expression (GO:0010629)|ovulation from ovarian follicle (GO:0001542)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|progesterone receptor signaling pathway (GO:0050847)|regulation of epithelial cell proliferation (GO:0050678)|signal transduction (GO:0007165)|tertiary branching involved in mammary gland duct morphogenesis (GO:0060748)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mitochondrial outer membrane (GO:0005741)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|liver(1)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	36		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)		LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164)	Allylestrenol(DB01431)|Danazol(DB01406)|Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluticasone Propionate(DB00588)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Megestrol acetate(DB00351)|Mifepristone(DB00834)|Norelgestromin(DB06713)|Norethindrone(DB00717)|Norgestimate(DB00957)|Progesterone(DB00396)|Spironolactone(DB00421)	GCAAAATACAGCATCTGCCCA	0.333																																					p.L776M	Pancreas(124;2271 2354 21954 22882)	Atlas-SNP	.											.	PGR	115	.	0			c.C2326A						PASS	.						125.0	120.0	122.0					11																	100922186		2203	4300	6503	SO:0001583	missense	5241	exon5			AATACAGCATCTG	M15716	CCDS8310.1, CCDS59229.1	11q22-q23	2013-01-16			ENSG00000082175	ENSG00000082175		"""Nuclear hormone receptors"""	8910	protein-coding gene	gene with protein product		607311					Standard	NM_000926		Approved	PR, NR3C3	uc001pgh.2	P06401	OTTHUMG00000167531	ENST00000325455.5:c.2326C>A	11.37:g.100922186G>T	ENSP00000325120:p.Leu776Met	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	199	71	0.356784	NM_000926	A7LQ08|A7X8B0|B4E3T0|Q8TDS3|Q9UPF7	Missense_Mutation	SNP	ENST00000325455.5	37	CCDS8310.1	.	.	.	.	.	.	.	.	.	.	G	15.63	2.891764	0.52014	.	.	ENSG00000082175	ENST00000325455;ENST00000534013;ENST00000263463;ENST00000537623	D;D;D	0.97620	-4.46;-4.46;-4.46	5.24	2.36	0.29203	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.000000	0.64402	D	0.000002	D	0.98526	0.9508	M	0.93808	3.46	0.33891	D	0.637314	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.99898	1.1153	10	0.87932	D	0	.	9.8858	0.41260	0.2843:0.0:0.7157:0.0	.	674;776;157	Q8TDS3;P06401;A7LQ08	.;PRGR_HUMAN;.	M	776;182;674;674	ENSP00000325120:L776M;ENSP00000436561:L182M;ENSP00000263463:L674M	ENSP00000263463:L674M	L	-	1	2	PGR	100427396	1.000000	0.71417	0.972000	0.41901	0.980000	0.70556	0.819000	0.27308	0.220000	0.20860	-0.157000	0.13467	CTG	.	.	none		0.333	PGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394934.1		
FAT2	2196	hgsc.bcm.edu	37	5	150922656	150922656	+	Nonsense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:150922656G>A	ENST00000261800.5	-	9	8044	c.8032C>T	c.(8032-8034)Cga>Tga	p.R2678*		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	2678	Cadherin 23. {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)			ACCTGAAGTCGTACTGGCACC	0.473																																					p.R2678X		Atlas-SNP	.											FAT2,NS,carcinoma,+1,1	FAT2	465	1	0			c.C8032T						scavenged	.						74.0	72.0	72.0					5																	150922656		2203	4300	6503	SO:0001587	stop_gained	2196	exon9			GAAGTCGTACTGG	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.8032C>T	5.37:g.150922656G>A	ENSP00000261800:p.Arg2678*	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	149	3	0.0201342	NM_001447	O75091|Q9NSR7	Nonsense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	G	47	12.995082	0.99711	.	.	ENSG00000086570	ENST00000261800	.	.	.	5.55	1.01	0.19927	.	0.345671	0.24014	N	0.042342	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10111	T	0.7	.	9.7117	0.40249	0.0741:0.0:0.3658:0.5601	.	.	.	.	X	2678	.	ENSP00000261800:R2678X	R	-	1	2	FAT2	150902849	0.729000	0.28090	0.494000	0.27515	0.688000	0.40055	2.397000	0.44477	0.248000	0.21435	-0.521000	0.04368	CGA	.	.	none		0.473	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
DHRS7B	25979	hgsc.bcm.edu	37	17	21092024	21092024	+	Splice_Site	SNP	A	A	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr17:21092024A>G	ENST00000395511.3	+	6	940	c.620A>G	c.(619-621)tAt>tGt	p.Y207C	DHRS7B_ENST00000579303.1_Splice_Site_p.Y192C|DHRS7B_ENST00000581463.1_Splice_Site_p.Y27C	NM_015510.4	NP_056325.2	Q6IAN0	DRS7B_HUMAN	dehydrogenase/reductase (SDR family) member 7B	207						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	oxidoreductase activity (GO:0016491)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|lung(2)|pancreas(2)	7						ACATGTGTAGATGCAGCCTCC	0.547																																					p.Y207C		Atlas-SNP	.											.	DHRS7B	27	.	0			c.A620G						PASS	.						225.0	183.0	197.0					17																	21092024		2203	4300	6503	SO:0001630	splice_region_variant	25979	exon6			GTGTAGATGCAGC	BC004126	CCDS11215.1	17p12	2011-09-20				ENSG00000109016		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	24547	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 32C, member 1"""					10810093, 11230166, 19027726	Standard	NM_015510		Approved	DKFZp566O084, MGC8916, CGI-93, SDR32C1	uc002gyo.3	Q6IAN0		ENST00000395511.3:c.620-1A>G	17.37:g.21092024A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	94	41	0.43617	NM_015510	B5MEF4|Q6UX59|Q9BTF9|Q9UFM6|Q9Y3A1	Missense_Mutation	SNP	ENST00000395511.3	37	CCDS11215.1	.	.	.	.	.	.	.	.	.	.	A	9.784	1.176052	0.21704	.	.	ENSG00000109016	ENST00000395511;ENST00000346603	D	0.97352	-4.35	5.28	5.28	0.74379	Short-chain dehydrogenase/reductase, conserved site (1);NAD(P)-binding domain (1);	0.055538	0.85682	N	0.000000	D	0.98940	0.9640	H	0.97186	3.955	0.80722	D	1	D	0.76494	0.999	D	0.68943	0.961	D	0.99482	1.0948	9	.	.	.	.	15.2134	0.73244	1.0:0.0:0.0:0.0	.	207	Q6IAN0	DRS7B_HUMAN	C	207	ENSP00000378887:Y207C	.	Y	+	2	0	DHRS7B	21032616	1.000000	0.71417	0.897000	0.35233	0.109000	0.19521	9.179000	0.94861	2.001000	0.58596	0.383000	0.25322	TAT	.	.	none		0.547	DHRS7B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000444066.3	NM_015510	Missense_Mutation
SLFN11	91607	hgsc.bcm.edu	37	17	33689860	33689860	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr17:33689860C>T	ENST00000394566.1	-	4	1239	c.967G>A	c.(967-969)Gca>Aca	p.A323T	SLFN11_ENST00000308377.4_Missense_Mutation_p.A323T	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	323					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)		GAGAACACTGCACAGCAGAAG	0.473																																					p.A323T		Atlas-SNP	.											SLFN11,right_upper_lobe,carcinoma,0,1	SLFN11	112	1	0			c.G967A						scavenged	.						134.0	123.0	127.0					17																	33689860		2203	4300	6503	SO:0001583	missense	91607	exon2			ACACTGCACAGCA	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.967G>A	17.37:g.33689860C>T	ENSP00000378067:p.Ala323Thr	Somatic	321	0	0		WXS	Illumina HiSeq	Phase_I	398	4	0.0100503	NM_152270	E1P643|Q8N3S8|Q8N762|Q8TEE0	Missense_Mutation	SNP	ENST00000394566.1	37	CCDS11294.1	.	.	.	.	.	.	.	.	.	.	C	16.36	3.102264	0.56183	.	.	ENSG00000172716	ENST00000308377;ENST00000394566	T;T	0.59364	0.27;0.27	4.32	1.13	0.20643	.	0.196095	0.25230	N	0.032176	T	0.60881	0.2303	M	0.71036	2.16	0.09310	N	1	D	0.53462	0.96	P	0.54100	0.742	T	0.52177	-0.8610	10	0.56958	D	0.05	.	4.5775	0.12241	0.0:0.6095:0.183:0.2075	.	323	Q7Z7L1	SLN11_HUMAN	T	323	ENSP00000312402:A323T;ENSP00000378067:A323T	ENSP00000312402:A323T	A	-	1	0	SLFN11	30713973	0.256000	0.24012	0.146000	0.22360	0.005000	0.04900	0.493000	0.22451	0.463000	0.27118	0.650000	0.86243	GCA	.	.	none		0.473	SLFN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256480.1	NM_152270	
KIF16B	55614	hgsc.bcm.edu	37	20	16360313	16360313	+	Silent	SNP	G	G	A	rs374151470		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr20:16360313G>A	ENST00000354981.2	-	19	2491	c.2334C>T	c.(2332-2334)ctC>ctT	p.L778L	KIF16B_ENST00000355755.3_Silent_p.L778L|KIF16B_ENST00000408042.1_Silent_p.L778L|KIF16B_ENST00000378003.2_Silent_p.L4L	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B	778	Glu-rich.				ATP catabolic process (GO:0006200)|early endosome to late endosome transport (GO:0045022)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|formation of primary germ layer (GO:0001704)|Golgi to endosome transport (GO:0006895)|microtubule-based movement (GO:0007018)|receptor catabolic process (GO:0032801)|regulation of receptor recycling (GO:0001919)	early endosome (GO:0005769)|endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(24)|ovary(1)|prostate(15)|skin(3)|upper_aerodigestive_tract(2)	74						CACGCCGCAGGAGCTGGATCA	0.597																																					p.L778L		Atlas-SNP	.											.	KIF16B	305	.	0			c.C2334T						PASS	.						97.0	95.0	96.0					20																	16360313		2203	4300	6503	SO:0001819	synonymous_variant	55614	exon19			CCGCAGGAGCTGG	AK000142	CCDS13122.1, CCDS56178.1	20p11.23	2008-03-03	2008-03-03	2008-03-03	ENSG00000089177	ENSG00000089177		"""Kinesins"""	15869	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 23"""	C20orf23		16084724, 16782399	Standard	NM_024704		Approved	FLJ20135, dJ971B4.1, SNX23	uc010gci.2	Q96L93	OTTHUMG00000031927	ENST00000354981.2:c.2334C>T	20.37:g.16360313G>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	202	73	0.361386	NM_001199865	A6NKJ9|A7E2A8|B1AKG3|B1AKT7|C9JDN5|C9JI52|C9JSM8|C9JWJ7|Q2TBF5|Q5HYC0|Q5HYK1|Q5JWW3|Q5TFK5|Q86VL9|Q86YS5|Q8IYU0|Q9BQJ8|Q9BQM0|Q9BQM1|Q9BQM5|Q9H5U0|Q9HCI2|Q9NXN9	Silent	SNP	ENST00000354981.2	37	CCDS13122.1																																																																																			.	.	alt		0.597	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683	
CD200	4345	hgsc.bcm.edu	37	3	112059764	112059764	+	Missense_Mutation	SNP	T	T	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:112059764T>G	ENST00000315711.8	+	2	85	c.28T>G	c.(28-30)Ttc>Gtc	p.F10V	CD200_ENST00000473539.1_Missense_Mutation_p.F35V|CD200_ENST00000383681.3_Intron	NM_005944.5	NP_005935.4	P41217	OX2G_HUMAN	CD200 molecule	10					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)				CAGGATGCCCTTCTCTCATCT	0.483																																					p.F35V		Atlas-SNP	.											.	CD200	33	.	0			c.T103G						PASS	.						153.0	126.0	135.0					3																	112059764		2203	4300	6503	SO:0001583	missense	4345	exon3			ATGCCCTTCTCTC		CCDS2965.1, CCDS33818.1	3q13.2	2013-09-20	2006-03-28	2004-09-01	ENSG00000091972	ENSG00000091972		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7203	protein-coding gene	gene with protein product		155970	"""antigen identified by monoclonal antibody MRC OX-2"", ""CD200 antigen"""	MOX1, MOX2			Standard	XM_005247482		Approved	MRC, OX-2	uc003dyw.3	P41217	OTTHUMG00000159248	ENST00000315711.8:c.28T>G	3.37:g.112059764T>G	ENSP00000312766:p.Phe10Val	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	94	24	0.255319	NM_001004196	B3KQI1|B4DLW9|D3DN65|Q6J2Q6|Q6PIQ4|Q8TB85|Q9H3J3	Missense_Mutation	SNP	ENST00000315711.8	37	CCDS2965.1	.	.	.	.	.	.	.	.	.	.	T	11.59	1.685253	0.29872	.	.	ENSG00000091972	ENST00000315711;ENST00000473539	T;T	0.72505	1.05;-0.66	5.18	4.01	0.46588	.	0.230049	0.31102	N	0.008250	T	0.54351	0.1853	N	0.24115	0.695	0.47183	D	0.999341	B;B	0.23249	0.082;0.01	B;B	0.19946	0.027;0.011	T	0.51076	-0.8751	10	0.49607	T	0.09	-6.9091	9.0178	0.36182	0.0:0.0:0.1864:0.8136	.	10;35	P41217-2;P41217-3	.;.	V	10;35	ENSP00000312766:F10V;ENSP00000420298:F35V	ENSP00000312766:F10V	F	+	1	0	CD200	113542454	0.584000	0.26766	0.303000	0.25071	0.960000	0.62799	0.805000	0.27112	0.971000	0.38288	0.533000	0.62120	TTC	.	.	none		0.483	CD200-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354078.1		
NRXN3	9369	hgsc.bcm.edu	37	14	79933659	79933659	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr14:79933659G>A	ENST00000557594.1	+	2	1296	c.343G>A	c.(343-345)Gtg>Atg	p.V115M	NRXN3_ENST00000281127.7_Missense_Mutation_p.V115M|NRXN3_ENST00000428277.2_Missense_Mutation_p.V115M|NRXN3_ENST00000556003.1_3'UTR|NRXN3_ENST00000554719.1_Missense_Mutation_p.V747M|NRXN3_ENST00000335750.5_Missense_Mutation_p.V747M	NM_001272020.1	NP_001258949.1	Q9HDB5	NRX3B_HUMAN	neurexin 3	115	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)		CCGCCTTGCCGTGGGCTTCAG	0.582																																					p.V747M		Atlas-SNP	.											NRXN3_ENST00000428277,NS,carcinoma,0,2	NRXN3	342	2	0			c.G2239A						scavenged	.						121.0	103.0	109.0					14																	79933659		2203	4300	6503	SO:0001583	missense	9369	exon13			CTTGCCGTGGGCT	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		ENST00000557594.1:c.343G>A	14.37:g.79933659G>A	ENSP00000451672:p.Val115Met	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	127	2	0.015748	NM_004796	A5PKW8|A8MPU5|B3KPM7|Q6NUR0|Q8IUD8	Missense_Mutation	SNP	ENST00000557594.1	37		.	.	.	.	.	.	.	.	.	.	G	28.0	4.878615	0.91740	.	.	ENSG00000021645	ENST00000330071;ENST00000332068;ENST00000554719;ENST00000335750;ENST00000557594;ENST00000281127;ENST00000428277	T;T;T;T;T	0.78924	-1.22;-1.22;0.96;0.96;0.96	5.93	5.93	0.95920	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);	0.000000	0.85682	D	0.000000	D	0.89150	0.6633	M	0.79805	2.47	0.58432	D	0.99999	D;D;D;P	0.89917	1.0;1.0;1.0;0.636	D;D;D;B	0.75484	0.97;0.986;0.967;0.212	D	0.88096	0.2816	9	.	.	.	.	20.3311	0.98718	0.0:0.0:1.0:0.0	.	115;115;115;747	Q9HDB5-4;Q9HDB5-2;Q9HDB5;Q9Y4C0-3	.;.;NRX3B_HUMAN;.	M	1120;1109;747;747;115;115;115	ENSP00000451648:V747M;ENSP00000338349:V747M;ENSP00000451672:V115M;ENSP00000281127:V115M;ENSP00000394426:V115M	.	V	+	1	0	NRXN3	79003412	1.000000	0.71417	0.990000	0.47175	0.986000	0.74619	7.995000	0.88328	2.797000	0.96272	0.655000	0.94253	GTG	.	.	none		0.582	NRXN3-004	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000413790.1	NM_001105250	
PLIN4	729359	hgsc.bcm.edu	37	19	4512945	4512945	+	Missense_Mutation	SNP	C	C	T	rs75031432	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	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	376	3	0.00797872		WXS	Illumina HiSeq	Phase_I	348	6	0.0172414	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	
RBM20	282996	hgsc.bcm.edu	37	10	112572301	112572301	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr10:112572301C>T	ENST00000369519.3	+	9	2204	c.2146C>T	c.(2146-2148)Cgg>Tgg	p.R716W		NM_001134363.1	NP_001127835.1	Q5T481	RBM20_HUMAN	RNA binding motif protein 20	716			R -> Q (in CMD1DD). {ECO:0000269|PubMed:20590677}.		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						ACACCACCCCCGGCAACTGGA	0.632																																					p.R716W		Atlas-SNP	.											.	RBM20	50	.	0			c.C2146T						PASS	.						53.0	69.0	64.0					10																	112572301		692	1591	2283	SO:0001583	missense	282996	exon9			CACCCCCGGCAAC	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.2146C>T	10.37:g.112572301C>T	ENSP00000358532:p.Arg716Trp	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	54	16	0.296296	NM_001134363	A6NIP5|B5A868|Q5JVI1	Missense_Mutation	SNP	ENST00000369519.3	37	CCDS44477.1	.	.	.	.	.	.	.	.	.	.	C	11.95	1.790539	0.31685	.	.	ENSG00000203867	ENST00000369519;ENST00000539821	T	0.75704	-0.96	5.75	0.337	0.15966	.	0.417679	0.21776	N	0.069282	T	0.55545	0.1927	L	0.34521	1.04	0.31765	N	0.632879	B	0.06786	0.001	B	0.01281	0.0	T	0.42932	-0.9422	10	0.31617	T	0.26	-5.8678	4.0402	0.09748	0.2624:0.4539:0.0:0.2837	.	716	Q5T481	RBM20_HUMAN	W	716	ENSP00000358532:R716W	ENSP00000358532:R716W	R	+	1	2	RBM20	112562291	0.232000	0.23762	0.973000	0.42090	0.957000	0.61999	0.480000	0.22244	-0.209000	0.10156	-0.244000	0.11960	CGG	.	.	none		0.632	RBM20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050339.2	NM_001134363	
ACSS3	79611	hgsc.bcm.edu	37	12	81472143	81472143	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:81472143G>A	ENST00000548058.1	+	1	1154	c.244G>A	c.(244-246)Gag>Aag	p.E82K	ACSS3_ENST00000261206.3_Missense_Mutation_p.E82K			Q9H6R3	ACSS3_HUMAN	acyl-CoA synthetase short-chain family member 3	82						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						CAAAGCTGCCGAGCAGATCAG	0.617																																					p.E82K		Atlas-SNP	.											.	ACSS3	118	.	0			c.G244A						PASS	.						46.0	43.0	44.0					12																	81472143		1984	4018	6002	SO:0001583	missense	79611	exon1			GCTGCCGAGCAGA		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.244G>A	12.37:g.81472143G>A	ENSP00000449535:p.Glu82Lys	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	56	20	0.357143	NM_024560	Q8NC66	Missense_Mutation	SNP	ENST00000548058.1	37	CCDS9022.1	.	.	.	.	.	.	.	.	.	.	G	8.471	0.857542	0.17106	.	.	ENSG00000111058	ENST00000548058;ENST00000261206	T;T	0.10960	2.82;2.82	5.03	4.11	0.48088	Acyl-CoA synthase, domain of unknown function DUF3448 (1);	0.506389	0.20979	N	0.082246	T	0.04407	0.0121	N	0.04636	-0.2	0.80722	D	1	P	0.39520	0.676	B	0.35413	0.202	T	0.49093	-0.8975	10	0.11182	T	0.66	-23.7543	11.5895	0.50938	0.0:0.3487:0.6513:0.0	.	82	Q9H6R3	ACSS3_HUMAN	K	82	ENSP00000449535:E82K;ENSP00000261206:E82K	ENSP00000261206:E82K	E	+	1	0	ACSS3	79996274	0.962000	0.33011	0.863000	0.33907	0.385000	0.30292	1.612000	0.36889	1.292000	0.44672	0.655000	0.94253	GAG	.	.	none		0.617	ACSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407794.1	NM_024560	
NLRP2	55655	hgsc.bcm.edu	37	19	55494691	55494691	+	Missense_Mutation	SNP	T	T	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:55494691T>A	ENST00000543010.1	+	6	1768	c.1625T>A	c.(1624-1626)gTa>gAa	p.V542E	NLRP2_ENST00000263437.6_Missense_Mutation_p.V539E|NLRP2_ENST00000391721.4_Missense_Mutation_p.V518E|NLRP2_ENST00000537859.1_Missense_Mutation_p.V520E|NLRP2_ENST00000538819.1_Missense_Mutation_p.V518E|NLRP2_ENST00000339757.7_Missense_Mutation_p.V520E|NLRP2_ENST00000448584.2_Missense_Mutation_p.V542E|NLRP2_ENST00000427260.2_Missense_Mutation_p.V519E	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	542					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)		CTTTCCGGAGTAGAAAGACTC	0.557																																					p.V542E		Atlas-SNP	.											NLRP2_ENST00000543010,colon,carcinoma,0,1	NLRP2	161	1	0			c.T1625A						scavenged	.						88.0	82.0	84.0					19																	55494691		2203	4300	6503	SO:0001583	missense	55655	exon6			CCGGAGTAGAAAG	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.1625T>A	19.37:g.55494691T>A	ENSP00000445135:p.Val542Glu	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	153	5	0.0326797	NM_017852	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Missense_Mutation	SNP	ENST00000543010.1	37	CCDS12913.1	.	.	.	.	.	.	.	.	.	.	c	0.003	-2.421230	0.00188	.	.	ENSG00000022556	ENST00000543010;ENST00000391721;ENST00000339757;ENST00000448584;ENST00000537859;ENST00000427260;ENST00000538819;ENST00000263437	T;T;T;T;T;T;T;T	0.74209	-0.81;-0.73;-0.73;-0.81;-0.73;-0.82;-0.73;-0.81	1.7	-0.443	0.12249	.	0.241233	0.21362	N	0.075796	T	0.30759	0.0775	N	0.00661	-1.28	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	0.35301	-0.9794	10	0.07482	T	0.82	.	2.6624	0.05030	0.4647:0.2699:0.0:0.2654	.	519;520;539;518;542	B4DZL7;Q9NX02-2;A8K9G6;Q9NX02-4;Q9NX02	.;.;.;.;NALP2_HUMAN	E	542;518;520;542;520;519;518;539	ENSP00000445135:V542E;ENSP00000375601:V518E;ENSP00000344074:V520E;ENSP00000409370:V542E;ENSP00000440601:V520E;ENSP00000402474:V519E;ENSP00000441133:V518E;ENSP00000263437:V539E	ENSP00000263437:V539E	V	+	2	0	NLRP2	60186503	0.000000	0.05858	0.003000	0.11579	0.000000	0.00434	-0.407000	0.07178	-0.214000	0.10078	-1.701000	0.00721	GTA	.	.	none		0.557	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852	
PLCB4	5332	hgsc.bcm.edu	37	20	9374297	9374297	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr20:9374297C>T	ENST00000378493.1	+	15	1401	c.1386C>T	c.(1384-1386)aaC>aaT	p.N462N	PLCB4_ENST00000378473.3_Silent_p.N462N|PLCB4_ENST00000334005.3_Silent_p.N462N|PLCB4_ENST00000378501.2_Silent_p.N462N|PLCB4_ENST00000492632.1_3'UTR|PLCB4_ENST00000278655.4_Silent_p.N462N|PLCB4_ENST00000414679.2_Silent_p.N462N			Q15147	PLCB4_HUMAN	phospholipase C, beta 4	462	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|smooth endoplasmic reticulum (GO:0005790)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(2)|breast(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(11)|liver(4)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(19)|upper_aerodigestive_tract(1)	87						TCATAAAAAACAAGCGGCTGA	0.393											OREG0025771	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.N462N		Atlas-SNP	.											.	PLCB4	204	.	0			c.C1386T						PASS	.						60.0	62.0	61.0					20																	9374297		2203	4300	6503	SO:0001819	synonymous_variant	5332	exon16			AAAAAACAAGCGG		CCDS13104.1, CCDS13105.1, CCDS54447.1	20p12	2008-03-18			ENSG00000101333	ENSG00000101333	3.1.4.11		9059	protein-coding gene	gene with protein product		600810				8530101	Standard	NM_000933		Approved		uc021wam.1	Q15147	OTTHUMG00000031853	ENST00000378493.1:c.1386C>T	20.37:g.9374297C>T		Somatic	32	0	0	656	WXS	Illumina HiSeq	Phase_I	58	10	0.172414	NM_182797	B7ZLK6|E2QRH8|Q17R56|Q5JYS8|Q5JYS9|Q5JYT0|Q5JYT3|Q5JYT4|Q9BQW5|Q9BQW6|Q9BQW8|Q9UJQ2	Silent	SNP	ENST00000378493.1	37	CCDS13105.1																																																																																			.	.	none		0.393	PLCB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077948.2		
NPAT	4863	hgsc.bcm.edu	37	11	108044441	108044441	+	Nonsense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:108044441G>A	ENST00000278612.8	-	13	1375	c.1270C>T	c.(1270-1272)Cag>Tag	p.Q424*	NPAT_ENST00000610253.1_5'UTR	NM_002519.2	NP_002510.2	Q14207	NPAT_HUMAN	nuclear protein, ataxia-telangiectasia locus	424					positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression (GO:0010468)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|Gemini of coiled bodies (GO:0097504)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(21)|ovary(2)|prostate(2)|skin(5)	46		all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116)		GCCTTTTTCTGTATGCTGGTA	0.383																																					p.Q424X		Atlas-SNP	.											.	NPAT	124	.	0			c.C1270T						PASS	.						147.0	138.0	141.0					11																	108044441		1860	4091	5951	SO:0001587	stop_gained	4863	exon13			TTTTCTGTATGCT	X97186	CCDS41710.1	11q22-q23	2008-02-01			ENSG00000149308	ENSG00000149308			7896	protein-coding gene	gene with protein product		601448				9205109	Standard	NM_002519		Approved	E14	uc001pjz.4	Q14207	OTTHUMG00000166385	ENST00000278612.8:c.1270C>T	11.37:g.108044441G>A	ENSP00000278612:p.Gln424*	Somatic	331	0	0		WXS	Illumina HiSeq	Phase_I	381	54	0.141732	NM_002519	A8K1V5|A8K6M2|Q13632|Q14967|Q16580|Q86W55|Q8IWE9	Nonsense_Mutation	SNP	ENST00000278612.8	37	CCDS41710.1	.	.	.	.	.	.	.	.	.	.	G	14.02	2.409649	0.42715	.	.	ENSG00000149308	ENST00000278612	.	.	.	5.54	5.54	0.83059	.	0.297500	0.30989	N	0.008468	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12430	T	0.62	-1.0278	12.4896	0.55893	0.0:0.0:0.8223:0.1777	.	.	.	.	X	424	.	ENSP00000278612:Q424X	Q	-	1	0	NPAT	107549651	1.000000	0.71417	0.998000	0.56505	0.034000	0.12701	3.320000	0.51991	2.765000	0.95021	0.557000	0.71058	CAG	.	.	none		0.383	NPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389506.2	NM_002519	
ATG3	64422	hgsc.bcm.edu	37	3	112255439	112255439	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:112255439G>A	ENST00000283290.5	-	10	1111	c.677C>T	c.(676-678)cCt>cTt	p.P226L	ATG3_ENST00000495756.1_5'UTR|ATG3_ENST00000402314.2_Missense_Mutation_p.P226L	NM_022488.3	NP_071933.2	Q9NT62	ATG3_HUMAN	autophagy related 3	226					autophagic vacuole assembly (GO:0000045)|cellular protein modification process (GO:0006464)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)|protein targeting to membrane (GO:0006612)|protein ubiquitination (GO:0016567)|regulation of cilium assembly (GO:1902017)	cytoplasmic ubiquitin ligase complex (GO:0000153)|cytosol (GO:0005829)	Atg12 ligase activity (GO:0019777)|Atg8 ligase activity (GO:0019776)|enzyme binding (GO:0019899)|small conjugating protein ligase activity (GO:0019787)			breast(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(3)	9						AACTGTTAAAGGCTGCCGTTG	0.463																																					p.P226L		Atlas-SNP	.											ATG3,NS,carcinoma,+1,1	ATG3	23	1	0			c.C677T						scavenged	.						185.0	158.0	167.0					3																	112255439		2203	4300	6503	SO:0001583	missense	64422	exon10			GTTAAAGGCTGCC		CCDS2966.1, CCDS63721.1	3q13.2	2014-02-12	2012-06-06	2005-09-11	ENSG00000144848	ENSG00000144848			20962	protein-coding gene	gene with protein product		609606	"""APG3 autophagy 3-like (S. cerevisiae)"", ""ATG3 autophagy related 3 homolog (S. cerevisiae)"""	APG3L		11825910	Standard	NM_022488		Approved	PC3-96, FLJ22125, MGC15201, DKFZp564M1178	uc003dzd.3	Q9NT62	OTTHUMG00000159260	ENST00000283290.5:c.677C>T	3.37:g.112255439G>A	ENSP00000283290:p.Pro226Leu	Somatic	133	1	0.0075188		WXS	Illumina HiSeq	Phase_I	170	2	0.0117647	NM_022488	Q6PKC5|Q9H6L9	Missense_Mutation	SNP	ENST00000283290.5	37	CCDS2966.1	.	.	.	.	.	.	.	.	.	.	.	25.5	4.648701	0.87958	.	.	ENSG00000144848	ENST00000283290;ENST00000402314	.	.	.	5.57	5.57	0.84162	Autophagy-related protein 3 (1);	0.102146	0.64402	D	0.000002	T	0.68796	0.3040	L	0.51422	1.61	0.80722	D	1	B;P	0.46064	0.245;0.872	B;P	0.50934	0.439;0.654	T	0.66701	-0.5857	9	0.40728	T	0.16	-4.6845	19.5516	0.95323	0.0:0.0:1.0:0.0	.	226;226	Q9NT62;Q9NT62-2	ATG3_HUMAN;.	L	226	.	ENSP00000283290:P226L	P	-	2	0	ATG3	113738129	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.309000	0.96252	2.623000	0.88846	0.563000	0.77884	CCT	.	.	none		0.463	ATG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354147.1	NM_022488	
HIST1H2BB	3018	hgsc.bcm.edu	37	6	26043725	26043725	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr6:26043725C>T	ENST00000357905.2	-	1	160	c.161G>A	c.(160-162)gGc>gAc	p.G54D	HIST1H3C_ENST00000540144.1_5'Flank	NM_021062.2	NP_066406.1	P33778	H2B1B_HUMAN	histone cluster 1, H2bb	54					chromatin organization (GO:0006325)|nucleosome assembly (GO:0006334)	nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)	7						GGATGAGATGCCGGTGTCGGG	0.547																																					p.G54D		Atlas-SNP	.											HIST1H2BB,NS,carcinoma,0,1	HIST1H2BB	20	1	0			c.G161A						scavenged	.						194.0	188.0	190.0					6																	26043725		2203	4300	6503	SO:0001583	missense	3018	exon1			GAGATGCCGGTGT	AF531285	CCDS4575.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000196226			"""Histones / Replication-dependent"""	4751	protein-coding gene	gene with protein product		602803	"""H2B histone family, member F"", ""histone 1, H2bb"""	H2BFF		8227173, 12408966	Standard	NM_021062		Approved	H2B/f	uc003nfu.3	P33778	OTTHUMG00000014421	ENST00000357905.2:c.161G>A	6.37:g.26043725C>T	ENSP00000350580:p.Gly54Asp	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	218	3	0.0137615	NM_021062	Q4KN36	Missense_Mutation	SNP	ENST00000357905.2	37	CCDS4575.1	.	.	.	.	.	.	.	.	.	.	c	11.23	1.578593	0.28180	.	.	ENSG00000196226	ENST00000357905	T	0.69435	-0.4	5.08	5.08	0.68730	Histone-fold (2);Histone core (1);	0.000000	0.64402	U	0.000016	D	0.82770	0.5109	M	0.93150	3.385	0.58432	D	0.99999	P	0.42161	0.772	P	0.56700	0.804	D	0.86555	0.1837	10	0.87932	D	0	.	17.8155	0.88632	0.0:1.0:0.0:0.0	.	54	P33778	H2B1B_HUMAN	D	54	ENSP00000350580:G54D	ENSP00000350580:G54D	G	-	2	0	HIST1H2BB	26151704	1.000000	0.71417	0.578000	0.28575	0.003000	0.03518	7.779000	0.85648	2.498000	0.84270	0.467000	0.42956	GGC	.	.	none		0.547	HIST1H2BB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040083.1	NM_021062	
C19orf45	374877	hgsc.bcm.edu	37	19	7573099	7573099	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:7573099A>G	ENST00000361664.2	+	9	1442	c.1301A>G	c.(1300-1302)tAc>tGc	p.Y434C	CTD-2207O23.12_ENST00000599312.1_Intron	NM_198534.2	NP_940936.2	Q8NA69	CS045_HUMAN	chromosome 19 open reading frame 45	434			Y -> N (in dbSNP:rs475923). {ECO:0000269|PubMed:14702039}.							endometrium(1)|kidney(1)|liver(1)|lung(2)|ovary(2)|stomach(1)	8						CAGTGCAAGTACAGCCACATG	0.607																																					p.Y434C		Atlas-SNP	.											C19orf45,NS,carcinoma,+1,1	C19orf45	36	1	0			c.A1301G						scavenged	.						41.0	41.0	41.0					19																	7573099		2203	4299	6502	SO:0001583	missense	374877	exon9			GCAAGTACAGCCA	BC029824	CCDS12179.2	19p13.2	2008-02-05			ENSG00000198723	ENSG00000198723			24745	protein-coding gene	gene with protein product						12477932	Standard	NM_198534		Approved	FLJ35784	uc002mgm.2	Q8NA69	OTTHUMG00000157183	ENST00000361664.2:c.1301A>G	19.37:g.7573099A>G	ENSP00000355241:p.Tyr434Cys	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	139	2	0.0143885	NM_198534	Q8N115	Missense_Mutation	SNP	ENST00000361664.2	37	CCDS12179.2	.	.	.	.	.	.	.	.	.	.	A	14.08	2.427402	0.43122	.	.	ENSG00000198723	ENST00000361664	T	0.36878	1.23	4.05	4.05	0.47172	.	0.306075	0.27349	N	0.019762	T	0.53270	0.1786	M	0.61703	1.905	0.31768	N	0.632505	D	0.89917	1.0	D	0.91635	0.999	T	0.61023	-0.7146	10	0.59425	D	0.04	-30.0092	9.5768	0.39463	1.0:0.0:0.0:0.0	.	434	Q8NA69	CS045_HUMAN	C	434	ENSP00000355241:Y434C	ENSP00000355241:Y434C	Y	+	2	0	C19orf45	7479099	0.905000	0.30787	0.998000	0.56505	0.562000	0.35680	4.379000	0.59575	1.839000	0.53478	0.379000	0.24179	TAC	.	.	none		0.607	C19orf45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347808.1	NM_198534	
PLEC	5339	hgsc.bcm.edu	37	8	144993567	144993567	+	Silent	SNP	G	G	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr8:144993567G>T	ENST00000322810.4	-	32	11002	c.10833C>A	c.(10831-10833)atC>atA	p.I3611I	PLEC_ENST00000357649.2_Silent_p.I3478I|PLEC_ENST00000345136.3_Silent_p.I3474I|PLEC_ENST00000356346.3_Silent_p.I3460I|PLEC_ENST00000527096.1_Silent_p.I3497I|PLEC_ENST00000398774.2_Silent_p.I3442I|PLEC_ENST00000354589.3_Silent_p.I3474I|PLEC_ENST00000354958.2_Silent_p.I3452I|PLEC_ENST00000436759.2_Silent_p.I3501I	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	3611	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						CGGGGTCGATGATGCCGCCCG	0.687																																					p.I3611I		Atlas-SNP	.											PLEC_ENST00000436759,bladder,carcinoma,-2,6	PLEC	1144	6	0			c.C10833A						scavenged	.						47.0	52.0	50.0					8																	144993567		2042	4183	6225	SO:0001819	synonymous_variant	5339	exon32			GTCGATGATGCCG	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.10833C>A	8.37:g.144993567G>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	37	2	0.0540541	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			.	.	none		0.687	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
C14orf37	145407	hgsc.bcm.edu	37	14	58605920	58605920	+	Missense_Mutation	SNP	C	C	T	rs373177726		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr14:58605920C>T	ENST00000267485.7	-	2	351	c.157G>A	c.(157-159)Gat>Aat	p.D53N	C14orf37_ENST00000334342.5_5'UTR	NM_001001872.2	NP_001001872.2	Q86TY3	CN037_HUMAN	chromosome 14 open reading frame 37	53						integral component of membrane (GO:0016021)		p.D53N(1)		breast(7)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|skin(1)	33						TCTAGGTCATCGGTGTTCATC	0.478																																					p.D53N		Atlas-SNP	.											C14orf37,NS,carcinoma,0,1	C14orf37	87	1	1	Substitution - Missense(1)	breast(1)	c.G157A						scavenged	.	C	ASN/ASP	0,4406		0,0,2203	271.0	267.0	268.0		157	5.4	0.8	14		268	1,8599	1.2+/-3.3	0,1,4299	no	missense	C14orf37	NM_001001872.2	23	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	53/775	58605920	1,13005	2203	4300	6503	SO:0001583	missense	145407	exon2			GGTCATCGGTGTT		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.157G>A	14.37:g.58605920C>T	ENSP00000267485:p.Asp53Asn	Somatic	338	1	0.00295858		WXS	Illumina HiSeq	Phase_I	322	5	0.015528	NM_001001872	A8K8Z8|Q6P5Q1|Q86TY1	Missense_Mutation	SNP	ENST00000267485.7	37	CCDS32089.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.838020	0.91117	0.0	1.16E-4	ENSG00000139971	ENST00000267485;ENST00000438670	T	0.34072	1.38	5.42	5.42	0.78866	.	0.361004	0.27100	N	0.020939	T	0.54175	0.1842	M	0.64997	1.995	0.33496	D	0.589324	D;D;D;D	0.76494	0.996;0.999;0.996;0.996	P;P;P;P	0.61070	0.811;0.883;0.811;0.811	T	0.65455	-0.6164	10	0.51188	T	0.08	-9.9146	15.9513	0.79840	0.0:1.0:0.0:0.0	.	91;53;53;53	B4DMS4;Q86TY3-2;A8K990;Q86TY3	.;.;.;CN037_HUMAN	N	53;91	ENSP00000267485:D53N	ENSP00000267485:D53N	D	-	1	0	C14orf37	57675673	0.002000	0.14202	0.833000	0.33012	0.076000	0.17211	1.405000	0.34635	2.559000	0.86315	0.655000	0.94253	GAT	.	.	weak		0.478	C14orf37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412059.1	NM_001001872	
TLK1	9874	hgsc.bcm.edu	37	2	171902832	171902832	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:171902832T>C	ENST00000431350.2	-	11	1425	c.1021A>G	c.(1021-1023)Agg>Ggg	p.R341G	TLK1_ENST00000442919.2_Missense_Mutation_p.R293G|TLK1_ENST00000521943.1_Missense_Mutation_p.R293G|TLK1_ENST00000434911.2_Missense_Mutation_p.R245G|TLK1_ENST00000360843.3_Missense_Mutation_p.R362G			Q9UKI8	TLK1_HUMAN	tousled-like kinase 1	341					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|intracellular protein transport (GO:0006886)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of chromatin assembly or disassembly (GO:0001672)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(8)|liver(3)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	33						TTCCTTTGCCTTTCAATATCT	0.373																																					p.R341G		Atlas-SNP	.											TLK1_ENST00000431350,NS,carcinoma,+1,2	TLK1	134	2	0			c.A1021G						scavenged	.						201.0	181.0	188.0					2																	171902832		2203	4300	6503	SO:0001583	missense	9874	exon11			TTTGCCTTTCAAT	AB004885	CCDS2241.1, CCDS46447.1, CCDS46448.1	2q31.1	2010-04-19			ENSG00000198586	ENSG00000198586			11841	protein-coding gene	gene with protein product		608438				9427565, 12660173	Standard	NM_012290		Approved	KIAA0137, PKU-BETA	uc002ugp.2	Q9UKI8	OTTHUMG00000132243	ENST00000431350.2:c.1021A>G	2.37:g.171902832T>C	ENSP00000411099:p.Arg341Gly	Somatic	273	1	0.003663		WXS	Illumina HiSeq	Phase_I	276	5	0.0181159	NM_012290	B3KR15|B4DX87|Q14150|Q8N591|Q9NYH2|Q9Y4F6	Missense_Mutation	SNP	ENST00000431350.2	37	CCDS2241.1	.	.	.	.	.	.	.	.	.	.	T	20.5	3.999462	0.74818	.	.	ENSG00000198586	ENST00000442919;ENST00000431350;ENST00000360843;ENST00000521943;ENST00000434911	T;T;T;T;T	0.66280	-0.17;-0.2;-0.16;-0.17;-0.13	5.33	1.4	0.22301	.	0.000000	0.85682	D	0.000000	T	0.79094	0.4388	M	0.84585	2.705	0.58432	D	0.999995	P;P;D	0.89917	0.892;0.934;1.0	P;P;D	0.85130	0.647;0.852;0.997	T	0.80596	-0.1312	10	0.87932	D	0	-5.903	13.0736	0.59075	0.0:0.0:0.3931:0.6069	.	245;362;341	B4DX87;Q9UKI8-2;Q9UKI8	.;.;TLK1_HUMAN	G	293;341;362;293;245	ENSP00000402165:R293G;ENSP00000411099:R341G;ENSP00000354089:R362G;ENSP00000428113:R293G;ENSP00000409222:R245G	ENSP00000354089:R362G	R	-	1	2	TLK1	171611078	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.172000	0.58243	0.055000	0.16094	0.482000	0.46254	AGG	.	.	none		0.373	TLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255314.1	NM_012290	
NBEA	26960	hgsc.bcm.edu	37	13	35691562	35691562	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr13:35691562C>T	ENST00000400445.3	+	14	2548	c.2014C>T	c.(2014-2016)Cca>Tca	p.P672S	NBEA_ENST00000540320.1_Missense_Mutation_p.P672S|NBEA_ENST00000379939.2_Missense_Mutation_p.P672S|NBEA_ENST00000310336.4_Missense_Mutation_p.P672S	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	672					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		TGGTCCCCGGCCATCACAAAA	0.269																																					p.P672S		Atlas-SNP	.											.	NBEA	340	.	0			c.C2014T						PASS	.						4.0	4.0	4.0					13																	35691562		1566	3452	5018	SO:0001583	missense	26960	exon14			CCCCGGCCATCAC	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"""A-kinase anchor proteins"", ""WD repeat domain containing"""	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.2014C>T	13.37:g.35691562C>T	ENSP00000383295:p.Pro672Ser	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	120	22	0.183333	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	37	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.106573	0.77096	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336	T;T;T;T	0.39229	1.09;1.09;1.09;1.09	4.29	4.29	0.51040	.	0.000000	0.85682	D	0.000000	T	0.66548	0.2800	M	0.82056	2.57	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.73062	-0.4101	10	0.62326	D	0.03	.	16.7133	0.85391	0.0:1.0:0.0:0.0	.	672	Q5T321	.	S	672	ENSP00000440951:P672S;ENSP00000383295:P672S;ENSP00000369271:P672S;ENSP00000308534:P672S	ENSP00000308534:P672S	P	+	1	0	NBEA	34589562	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.265000	0.78442	1.929000	0.55896	0.460000	0.39030	CCA	.	.	none		0.269	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678	
SPTA1	6708	hgsc.bcm.edu	37	1	158617450	158617450	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:158617450C>T	ENST00000368147.4	-	27	3955	c.3775G>A	c.(3775-3777)Gac>Aac	p.D1259N		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1259					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)					CTCTGCAGGTCCTCAGTGGCA	0.532																																					p.D1259N		Atlas-SNP	.											SPTA1,NS,carcinoma,+2,1	SPTA1	720	1	0			c.G3775A						scavenged	.						85.0	85.0	85.0					1																	158617450		1967	4170	6137	SO:0001583	missense	6708	exon27			GCAGGTCCTCAGT	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.3775G>A	1.37:g.158617450C>T	ENSP00000357129:p.Asp1259Asn	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	138	3	0.0217391	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	C	16.23	3.065721	0.55539	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.50813	0.73;0.73	4.71	3.78	0.43462	.	0.245751	0.21100	N	0.080173	T	0.38480	0.1042	L	0.50333	1.59	0.41450	D	0.987975	P	0.37015	0.578	P	0.46208	0.507	T	0.31166	-0.9953	10	0.39692	T	0.17	.	13.9263	0.63964	0.0:0.8462:0.1538:0.0	.	1259	P02549	SPTA1_HUMAN	N	1259	ENSP00000357130:D1259N;ENSP00000357129:D1259N	ENSP00000357129:D1259N	D	-	1	0	SPTA1	156884074	1.000000	0.71417	0.835000	0.33067	0.452000	0.32318	5.370000	0.66144	1.299000	0.44798	0.563000	0.77884	GAC	.	.	none		0.532	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
GJD2	57369	hgsc.bcm.edu	37	15	35045017	35045017	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr15:35045017C>T	ENST00000290374.4	-	2	1104	c.628G>A	c.(628-630)Gaa>Aaa	p.E210K	RP11-814P5.1_ENST00000503496.1_RNA|RP11-814P5.1_ENST00000558707.1_RNA	NM_020660.2	NP_065711.1	Q9UKL4	CXD2_HUMAN	gap junction protein, delta 2, 36kDa	210					action potential (GO:0001508)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gap junction channel activity (GO:0005243)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|urinary_tract(1)	19		all_lung(180;9.67e-07)		all cancers(64;2.75e-18)|GBM - Glioblastoma multiforme(113;1.9e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0156)		AACCCAATTTCCAGGGCATTT	0.488																																					p.E210K		Atlas-SNP	.											GJD2,NS,malignant_melanoma,0,2	GJD2	49	2	0			c.G628A						scavenged	.						86.0	84.0	84.0					15																	35045017		2201	4298	6499	SO:0001583	missense	57369	exon2			CAATTTCCAGGGC	AB037509	CCDS10040.1	15q13.1	2008-02-04	2007-11-06	2007-11-06	ENSG00000159248	ENSG00000159248		"""Ion channels / Gap junction proteins (connexins)"""	19154	protein-coding gene	gene with protein product	"""connexin 36"""	607058	"""gap junction protein, alpha 9, 36kDa"""	GJA9		10462698	Standard	NM_020660		Approved	CX36	uc001zis.2	Q9UKL4	OTTHUMG00000129674	ENST00000290374.4:c.628G>A	15.37:g.35045017C>T	ENSP00000290374:p.Glu210Lys	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	145	2	0.0137931	NM_020660	Q2M241|Q9P2R0	Missense_Mutation	SNP	ENST00000290374.4	37	CCDS10040.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.752832	0.89753	.	.	ENSG00000159248	ENST00000290374	D	0.97831	-4.56	5.86	5.86	0.93980	Gap junction protein, cysteine-rich domain (1);	0.000000	0.64402	D	0.000002	D	0.99266	0.9744	H	0.96861	3.895	0.80722	D	1	D	0.76494	0.999	D	0.72982	0.979	D	0.98824	1.0748	10	0.87932	D	0	.	20.1864	0.98220	0.0:1.0:0.0:0.0	.	210	Q9UKL4	CXD2_HUMAN	K	210	ENSP00000290374:E210K	ENSP00000290374:E210K	E	-	1	0	GJD2	32832309	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.818000	0.86416	2.781000	0.95711	0.650000	0.86243	GAA	.	.	none		0.488	GJD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251875.2		
RIMKLB	57494	hgsc.bcm.edu	37	12	8926159	8926159	+	Missense_Mutation	SNP	C	C	T	rs201378504		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:8926159C>T	ENST00000538135.1	+	6	1765	c.940C>T	c.(940-942)Cgg>Tgg	p.R314W	RIMKLB_ENST00000299673.5_Intron|A2ML1-AS1_ENST00000537288.1_RNA|RIMKLB_ENST00000535829.1_Missense_Mutation_p.R314W|RIMKLB_ENST00000357529.3_Missense_Mutation_p.R314W			Q9ULI2	RIMKB_HUMAN	ribosomal modification protein rimK-like family member B	314					cellular protein modification process (GO:0006464)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|citrate-L-glutamate ligase activity (GO:0072591)|metal ion binding (GO:0046872)|N-acetyl-L-aspartate-L-glutamate ligase activity (GO:0072590)	p.R314W(1)		central_nervous_system(2)|kidney(3)|large_intestine(5)|lung(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						CCGGCTCACCCGGCGTATGTC	0.552																																					p.R314W		Atlas-SNP	.											RIMKLB,colon,carcinoma,0,1	RIMKLB	47	1	1	Substitution - Missense(1)	large_intestine(1)	c.C940T						scavenged	.	C	TRP/ARG	0,3872		0,0,1936	61.0	64.0	63.0		940	4.8	1.0	12		63	2,8272		0,2,4135	yes	missense	RIMKLB	NM_020734.2	101	0,2,6071	TT,TC,CC		0.0242,0.0,0.0165	probably-damaging	314/387	8926159	2,12144	1936	4137	6073	SO:0001583	missense	57494	exon7			CTCACCCGGCGTA	AB033064	CCDS41748.1	12p13.31	2011-09-21	2008-10-13	2008-10-13	ENSG00000166532	ENSG00000166532	6.3.2.N6		29228	protein-coding gene	gene with protein product	"""N-acetylaspartyl-glutamate synthetase"""	614054	"""family with sequence similarity 80, member B"""	FAM80B		10574462, 20643647	Standard	XM_006719116		Approved	KIAA1238, NAAGS, NAAGS-I	uc001qux.2	Q9ULI2		ENST00000538135.1:c.940C>T	12.37:g.8926159C>T	ENSP00000440943:p.Arg314Trp	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	182	2	0.010989	NM_020734	B7Z834|D3DUV2|Q8N4P4|Q8WTW6	Missense_Mutation	SNP	ENST00000538135.1	37	CCDS41748.1	.	.	.	.	.	.	.	.	.	.	C	15.51	2.854515	0.51376	0.0	2.42E-4	ENSG00000166532	ENST00000535829;ENST00000357529;ENST00000538135	.	.	.	5.72	4.82	0.62117	.	0.069207	0.56097	U	0.000025	T	0.39682	0.1087	L	0.29908	0.895	0.58432	D	0.999994	D	0.58620	0.983	B	0.39738	0.308	T	0.21449	-1.0245	8	.	.	.	.	14.7578	0.69579	0.1458:0.8542:0.0:0.0	.	314	Q9ULI2	RIMKB_HUMAN	W	314	.	.	R	+	1	2	RIMKLB	8817426	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.397000	0.59690	1.387000	0.46486	0.591000	0.81541	CGG	C|0.999;T|0.001	0.001	weak		0.552	RIMKLB-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398874.1	NM_020734	
LGI1	9211	hgsc.bcm.edu	37	10	95552602	95552602	+	Silent	SNP	C	C	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr10:95552602C>A	ENST00000371418.4	+	6	866	c.606C>A	c.(604-606)ggC>ggA	p.G202G	LGI1_ENST00000371413.3_Silent_p.G202G|LGI1_ENST00000542308.1_Silent_p.G154G	NM_005097.2	NP_005088.1	O95970	LGI1_HUMAN	leucine-rich, glioma inactivated 1	202	LRRCT.				axon guidance (GO:0007411)|cell proliferation (GO:0008283)|nervous system development (GO:0007399)|neuron projection development (GO:0031175)|positive regulation of cell growth (GO:0030307)|positive regulation of synaptic transmission (GO:0050806)|protein homooligomerization (GO:0051260)	cell junction (GO:0030054)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|synapse (GO:0045202)	receptor binding (GO:0005102)	p.E205fs*9(1)		central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(18)|ovary(2)|skin(1)	29		Colorectal(252;0.124)				ACTGCGAAGGCCCCCCAGAAT	0.418																																					p.G202G		Atlas-SNP	.											.	LGI1	69	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.C606A						PASS	.						133.0	135.0	134.0					10																	95552602		2203	4300	6503	SO:0001819	synonymous_variant	9211	exon6			CGAAGGCCCCCCA	AF055636	CCDS7431.1	10q24	2008-08-01	2002-06-05		ENSG00000108231	ENSG00000108231			6572	protein-coding gene	gene with protein product		604619	"""epilepsy, partial"""	EPT		9879993, 11978770, 15079011	Standard	NM_005097		Approved	IB1099, ETL1, EPITEMPIN	uc001kjc.4	O95970	OTTHUMG00000018777	ENST00000371418.4:c.606C>A	10.37:g.95552602C>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	134	61	0.455224	NM_005097	A8K0Z1|B4E1S0|Q5W001|Q5W002|Q8NI23|Q96LF5	Silent	SNP	ENST00000371418.4	37	CCDS7431.1																																																																																			.	.	none		0.418	LGI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049445.1	NM_005097	
OXSR1	9943	hgsc.bcm.edu	37	3	38291481	38291481	+	Silent	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:38291481T>C	ENST00000446845.1	+	15	1719	c.1347T>C	c.(1345-1347)gaT>gaC	p.D449D	OXSR1_ENST00000311806.3_Silent_p.D449D					oxidative stress responsive 1											skin(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		AACTAAATGATATTCGATTTG	0.303																																					p.D449D		Atlas-SNP	.											OXSR1_ENST00000311806,colon,carcinoma,+2,1	OXSR1	74	1	0			c.T1347C						scavenged	.						54.0	57.0	56.0					3																	38291481		2203	4298	6501	SO:0001819	synonymous_variant	9943	exon15			AAATGATATTCGA	AB017642	CCDS2675.1	3p22.2	2013-05-17	2013-05-17	2004-11-26	ENSG00000172939	ENSG00000172939			8508	protein-coding gene	gene with protein product		604046	"""oxidative-stress responsive 1"""	OSR1		10083736	Standard	XM_005265638		Approved	KIAA1101	uc003chy.3	O95747	OTTHUMG00000131084	ENST00000446845.1:c.1347T>C	3.37:g.38291481T>C		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	166	2	0.0120482	NM_005109		Silent	SNP	ENST00000446845.1	37																																																																																				.	.	none		0.303	OXSR1-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000342708.1	NM_005109	
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12907708	12907708	+	Silent	SNP	A	A	G	rs4026149	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	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	330	17	0.0515152		WXS	Illumina HiSeq	Phase_I	298	17	0.057047	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	
IGSF3	3321	hgsc.bcm.edu	37	1	117158745	117158745	+	Missense_Mutation	SNP	A	A	C	rs373093989		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:117158745A>C	ENST00000369486.3	-	3	1143	c.378T>G	c.(376-378)gaT>gaG	p.D126E	IGSF3_ENST00000318837.6_Missense_Mutation_p.D126E|IGSF3_ENST00000369483.1_Missense_Mutation_p.D126E	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	126	Ig-like C2-type 1.				lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)		p.D126E(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)		AGTATTGCTTATCAGTGCTGG	0.498																																					p.D126E		Atlas-SNP	.											IGSF3,extremity,malignant_melanoma,0,1	IGSF3	294	1	1	Substitution - Missense(1)	skin(1)	c.T378G						scavenged	.						61.0	55.0	57.0					1																	117158745		2203	4300	6503	SO:0001583	missense	3321	exon3			TTGCTTATCAGTG	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.378T>G	1.37:g.117158745A>C	ENSP00000358498:p.Asp126Glu	Somatic	461	20	0.0433839		WXS	Illumina HiSeq	Phase_I	397	24	0.0604534	NM_001542	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	37	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	A	8.319	0.823848	0.16678	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.65364	-0.15;-0.15;-0.15	4.63	-8.69	0.00855	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.109427	0.64402	N	0.000011	T	0.34250	0.0891	M	0.69523	2.12	0.30895	N	0.729963	B;B	0.10296	0.003;0.002	B;B	0.20384	0.015;0.029	T	0.06481	-1.0824	10	0.66056	D	0.02	-9.8434	10.4193	0.44341	0.1981:0.2275:0.5744:0.0	.	126;126	O75054;A6NJZ6	IGSF3_HUMAN;.	E	126	ENSP00000358498:D126E;ENSP00000358495:D126E;ENSP00000321184:D126E	ENSP00000321184:D126E	D	-	3	2	IGSF3	116960268	0.000000	0.05858	0.000000	0.03702	0.048000	0.14542	-2.110000	0.01334	-1.801000	0.01245	0.454000	0.30748	GAT	.	.	none		0.498	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542	
OR52E2	119678	hgsc.bcm.edu	37	11	5080687	5080687	+	Silent	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:5080687T>C	ENST00000321522.2	-	1	170	c.171A>G	c.(169-171)ctA>ctG	p.L57L		NM_001005164.2	NP_001005164.2	Q8NGJ4	O52E2_HUMAN	olfactory receptor, family 52, subfamily E, member 2	57						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			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)		TGGGCTGGTGTAGGCTGCTGT	0.493																																					p.L57L		Atlas-SNP	.											OR52E2,NS,carcinoma,-1,1	OR52E2	63	1	0			c.A171G						scavenged	.						111.0	97.0	102.0					11																	5080687		2201	4298	6499	SO:0001819	synonymous_variant	119678	exon1			CTGGTGTAGGCTG	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.171A>G	11.37:g.5080687T>C		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	216	4	0.0185185	NM_001005164		Silent	SNP	ENST00000321522.2	37	CCDS31371.1																																																																																			.	.	none		0.493	OR52E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142815.1	NM_001005164	
SCML4	256380	hgsc.bcm.edu	37	6	108070921	108070921	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr6:108070921C>T	ENST00000369020.3	-	3	498	c.253G>A	c.(253-255)Gtc>Atc	p.V85I	SCML4_ENST00000369021.3_Missense_Mutation_p.V56I|SCML4_ENST00000369022.2_Missense_Mutation_p.V27I	NM_198081.3	NP_932347.2	Q8N228	SCML4_HUMAN	sex comb on midleg-like 4 (Drosophila)	85					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(1)	25		all_cancers(87;3.26e-06)|Acute lymphoblastic leukemia(125;3.08e-08)|all_hematologic(75;1.15e-06)|all_epithelial(87;0.00142)|Colorectal(196;0.0316)		BRCA - Breast invasive adenocarcinoma(108;0.01)|Epithelial(106;0.0509)|all cancers(137;0.0586)|OV - Ovarian serous cystadenocarcinoma(136;0.0758)		AAGCTGGGGACCGTGGCTGCG	0.592																																					p.V85I		Atlas-SNP	.											.	SCML4	65	.	0			c.G253A						PASS	.						73.0	77.0	76.0					6																	108070921		2203	4300	6503	SO:0001583	missense	256380	exon3			TGGGGACCGTGGC		CCDS5060.2, CCDS69163.1, CCDS75500.1	6q21	2013-01-10			ENSG00000146285	ENSG00000146285		"""Sterile alpha motif (SAM) domain containing"""	21397	protein-coding gene	gene with protein product							Standard	NM_001286409		Approved	dJ47M23.1	uc010kdf.3	Q8N228	OTTHUMG00000015313	ENST00000369020.3:c.253G>A	6.37:g.108070921C>T	ENSP00000358016:p.Val85Ile	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	106	42	0.396226	NM_198081	B0QZ10|B0QZ11|B7ZBX3|Q5JXD0|Q5T0T6|Q8IYY6	Missense_Mutation	SNP	ENST00000369020.3	37	CCDS5060.2	.	.	.	.	.	.	.	.	.	.	C	1.726	-0.495425	0.04291	.	.	ENSG00000146285	ENST00000369022;ENST00000369020;ENST00000369021;ENST00000440927	T;T;T;T	0.42513	0.98;0.99;0.98;0.97	5.15	-4.99	0.03010	.	0.692695	0.12891	N	0.430560	T	0.07954	0.0199	N	0.17872	0.535	0.09310	N	1	B;B;B	0.12630	0.001;0.0;0.006	B;B;B	0.11329	0.002;0.001;0.006	T	0.48896	-0.8994	10	0.02654	T	1	.	17.2554	0.87055	0.0:0.7296:0.0:0.2704	.	85;85;56	B4E0X3;Q8N228;Q8N228-3	.;SCML4_HUMAN;.	I	27;85;56;56	ENSP00000358018:V27I;ENSP00000358016:V85I;ENSP00000358017:V56I;ENSP00000404688:V56I	ENSP00000358016:V85I	V	-	1	0	SCML4	108177614	0.000000	0.05858	0.000000	0.03702	0.684000	0.39900	-1.014000	0.03641	-0.689000	0.05149	0.655000	0.94253	GTC	.	.	none		0.592	SCML4-005	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000041700.3	XM_171128	
RAX	30062	hgsc.bcm.edu	37	18	56940307	56940307	+	Missense_Mutation	SNP	G	G	T	rs2271733	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr18:56940307G>T	ENST00000334889.3	-	1	318	c.132C>A	c.(130-132)gaC>gaA	p.D44E	RAX_ENST00000256852.7_Missense_Mutation_p.D44E	NM_013435.2	NP_038463.2	Q9Y2V3	RX_HUMAN	retina and anterior neural fold homeobox	44			D -> E (in dbSNP:rs2271733). {ECO:0000269|PubMed:14662654}.		camera-type eye development (GO:0043010)|hypothalamus development (GO:0021854)|limb development (GO:0060173)|pattern specification process (GO:0007389)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|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)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|prostate(1)	6		Lung NSC(161;0.0804)|Colorectal(73;0.0946)		STAD - Stomach adenocarcinoma(84;0.18)		GGATCCCGTCGTCCTTGGTAA	0.746													G|||	980	0.195687	0.1452	0.1571	5008	,	,		10556	0.128		0.3002	False		,,,				2504	0.2536				p.D44E	GBM(150;770 1898 17679 24325 37807)	Atlas-SNP	.											RAX,NS,carcinoma,0,1	RAX	19	1	0			c.C132A						scavenged	.	G	GLU/ASP	490,2640		39,412,1114	11.0	9.0	10.0		132	0.1	1.0	18	dbSNP_100	10	1484,4096		212,1060,1518	yes	missense	RAX	NM_013435.2	45	251,1472,2632	TT,TG,GG		26.595,15.655,22.6636	benign	44/347	56940307	1974,6736	1565	2790	4355	SO:0001583	missense	30062	exon1			CCCGTCGTCCTTG	AF115392	CCDS11972.1	18q21.31	2011-06-20			ENSG00000134438	ENSG00000134438		"""Homeoboxes / PRD class"""	18662	protein-coding gene	gene with protein product		601881				10625658, 10766016, 14662654	Standard	NM_013435		Approved	RX	uc002lhx.3	Q9Y2V3	OTTHUMG00000132757	ENST00000334889.3:c.132C>A	18.37:g.56940307G>T	ENSP00000334813:p.Asp44Glu	Somatic	1	1	1		WXS	Illumina HiSeq	Phase_I	5	3	0.6	NM_013435	Q86V11	Missense_Mutation	SNP	ENST00000334889.3	37	CCDS11972.1	453	0.20741758241758243	75	0.1524390243902439	69	0.19060773480662985	76	0.13286713286713286	233	0.3073878627968338	G	12.43	1.936984	0.34189	0.15655	0.26595	ENSG00000134438	ENST00000256852;ENST00000334889;ENST00000555288	T;D;T	0.87966	0.09;-2.32;0.09	5.56	0.117	0.14652	.	0.213892	0.50627	N	0.000107	T	0.00012	0.0000	N	0.12182	0.205	0.42455	P	0.0072349999999999914	B;B	0.22800	0.075;0.004	B;B	0.23574	0.047;0.009	T	0.06481	-1.0824	9	0.06365	T	0.9	.	0.4639	0.00520	0.2353:0.2064:0.3162:0.2421	rs2271733;rs58469971;rs2271733	44;44	Q86V11;Q9Y2V3	.;RX_HUMAN	E	44	ENSP00000256852:D44E;ENSP00000334813:D44E;ENSP00000450583:D44E	ENSP00000256852:D44E	D	-	3	2	RAX	55091287	0.002000	0.14202	0.999000	0.59377	0.992000	0.81027	-0.819000	0.04462	0.271000	0.22005	0.561000	0.74099	GAC	G|0.801;T|0.199	0.199	strong		0.746	RAX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256128.2		
ACACA	31	hgsc.bcm.edu	37	17	35598929	35598929	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr17:35598929C>T	ENST00000394406.2	-	23	3051	c.2861G>A	c.(2860-2862)cGg>cAg	p.R954Q	ACACA_ENST00000353139.5_Missense_Mutation_p.R991Q|ACACA_ENST00000335166.5_Missense_Mutation_p.R876Q|ACACA_ENST00000360679.3_Missense_Mutation_p.R896Q	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	954					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	TTCAGATTTCCGGTTCAATGT	0.423																																					p.R991Q	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)	Atlas-SNP	.											ACACA_ENST00000353139,NS,carcinoma,+1,2	ACACA	395	2	0			c.G2972A						scavenged	.						141.0	126.0	131.0					17																	35598929		2203	4300	6503	SO:0001583	missense	31	exon23			GATTTCCGGTTCA	U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"""acetyl-CoA carboxylase 1"""	200350	"""acetyl-Coenzyme A carboxylase alpha"""	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.2861G>A	17.37:g.35598929C>T	ENSP00000377928:p.Arg954Gln	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	188	3	0.0159574	NM_198834	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Missense_Mutation	SNP	ENST00000394406.2	37	CCDS11317.1	.	.	.	.	.	.	.	.	.	.	C	17.46	3.395087	0.62066	.	.	ENSG00000132142	ENST00000353139;ENST00000360679;ENST00000394406;ENST00000452074;ENST00000335166	T;T;T;T	0.64803	-0.12;-0.12;-0.12;-0.12	4.89	4.89	0.63831	Acetyl-CoA carboxylase, central domain (1);	0.053651	0.64402	D	0.000001	T	0.71762	0.3378	M	0.75447	2.3	0.80722	D	1	P;B;B	0.51537	0.946;0.021;0.018	P;B;B	0.53313	0.723;0.029;0.01	T	0.69045	-0.5249	10	0.21014	T	0.42	-13.0961	17.2142	0.86938	0.0:1.0:0.0:0.0	.	991;954;896	Q13085-4;Q13085;Q13085-2	.;ACACA_HUMAN;.	Q	991;896;954;978;876	ENSP00000344789:R991Q;ENSP00000353898:R896Q;ENSP00000377928:R954Q;ENSP00000335323:R876Q	ENSP00000335323:R876Q	R	-	2	0	ACACA	32673042	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.746000	0.62133	2.535000	0.85469	0.591000	0.81541	CGG	.	.	none		0.423	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836	
IFT122	55764	hgsc.bcm.edu	37	3	129185836	129185836	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:129185836T>C	ENST00000348417.2	+	8	744	c.667T>C	c.(667-669)Tac>Cac	p.Y223H	IFT122_ENST00000440957.2_Intron|IFT122_ENST00000504021.1_Intron|IFT122_ENST00000347300.2_Intron|IFT122_ENST00000296266.3_Missense_Mutation_p.Y274H|IFT122_ENST00000431818.2_Missense_Mutation_p.Y73H|IFT122_ENST00000349441.2_Intron|IFT122_ENST00000507564.1_Intron	NM_052989.1	NP_443715.1	Q9HBG6	IF122_HUMAN	intraflagellar transport 122	223					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						GTCAGCAGTGTACAGTAGTCA	0.502																																					p.Y274H		Atlas-SNP	.											IFT122,caecum,carcinoma,-2,1	IFT122	117	1	0			c.T820C						scavenged	.						152.0	153.0	152.0					3																	129185836		2203	4300	6503	SO:0001583	missense	55764	exon9			GCAGTGTACAGTA	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.667T>C	3.37:g.129185836T>C	ENSP00000324005:p.Tyr223His	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	83	2	0.0240964	NM_052985	B3KW53|B4DEY9|B4DPW7|E7EQF4|E9PDG2|E9PDX2|G3XAB1|H7C3C0|Q53G36|Q8TC06|Q9BTB9|Q9BTY4|Q9HAT9|Q9HBG5|Q9NV68|Q9UF80	Missense_Mutation	SNP	ENST00000348417.2	37	CCDS3061.1	.	.	.	.	.	.	.	.	.	.	T	15.06	2.720777	0.48728	.	.	ENSG00000163913	ENST00000296266;ENST00000431818;ENST00000348417	T;T;T	0.60797	0.16;0.35;0.76	4.74	4.74	0.60224	WD40 repeat-like-containing domain (1);	0.514389	0.17407	N	0.175313	T	0.50922	0.1644	N	0.14661	0.345	0.80722	D	1	P;P	0.47191	0.826;0.891	B;P	0.51355	0.347;0.667	T	0.54846	-0.8232	10	0.56958	D	0.05	-10.7144	11.8651	0.52488	0.0:0.0:0.0:1.0	.	223;274	Q9HBG6;G3XAB1	IF122_HUMAN;.	H	274;73;223	ENSP00000296266:Y274H;ENSP00000410946:Y73H;ENSP00000324005:Y223H	ENSP00000296266:Y274H	Y	+	1	0	IFT122	130668526	1.000000	0.71417	1.000000	0.80357	0.786000	0.44442	2.667000	0.46808	1.999000	0.58509	0.379000	0.24179	TAC	.	.	none		0.502	IFT122-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355852.1	NM_018262	
AFG3L2	10939	hgsc.bcm.edu	37	18	12356754	12356754	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr18:12356754G>A	ENST00000269143.3	-	9	1334	c.1103C>T	c.(1102-1104)cCc>cTc	p.P368L		NM_006796.2	NP_006787.2	Q9Y4W6	AFG32_HUMAN	AFG3-like AAA ATPase 2	368					axonogenesis (GO:0007409)|cell death (GO:0008219)|cristae formation (GO:0042407)|mitochondrial fusion (GO:0008053)|mitochondrial protein processing (GO:0034982)|muscle fiber development (GO:0048747)|myelination (GO:0042552)|nerve development (GO:0021675)|neuromuscular junction development (GO:0007528)|regulation of multicellular organism growth (GO:0040014)|righting reflex (GO:0060013)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metalloendopeptidase activity (GO:0004222)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(12)|prostate(3)|skin(1)|stomach(3)|urinary_tract(1)	27					Adenosine triphosphate(DB00171)	GGTGATGAAGGGGACATTGGC	0.502																																					p.P368L		Atlas-SNP	.											.	AFG3L2	60	.	0			c.C1103T						PASS	.						166.0	124.0	138.0					18																	12356754		2203	4300	6503	SO:0001583	missense	10939	exon9			ATGAAGGGGACAT	Y18314	CCDS11859.1	18p11.21	2014-09-17	2013-10-17		ENSG00000141385	ENSG00000141385		"""ATPases / AAA-type"""	315	protein-coding gene	gene with protein product		604581	"""AFG3 (ATPase family gene 3, yeast)-like 2"", ""spinocerebellar ataxia 28"", ""AFG3 ATPase family gene 3-like 2 (yeast)"", ""AFG3 ATPase family gene 3-like 2 (S. cerevisiae)"", ""AFG3 ATPase family member 3-like 2 (S. cerevisiae)"""	SCA28		10395799, 18769991	Standard	NM_006796		Approved	SPAX5	uc002kqz.2	Q9Y4W6	OTTHUMG00000131695	ENST00000269143.3:c.1103C>T	18.37:g.12356754G>A	ENSP00000269143:p.Pro368Leu	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	97	4	0.0412371	NM_006796	Q6P1L0	Missense_Mutation	SNP	ENST00000269143.3	37	CCDS11859.1	.	.	.	.	.	.	.	.	.	.	G	33	5.231900	0.95207	.	.	ENSG00000141385	ENST00000269143;ENST00000537174	T	0.80824	-1.42	5.28	5.28	0.74379	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);Peptidase M41, FtsH (2);	0.000000	0.85682	D	0.000000	D	0.90191	0.6934	M	0.78344	2.41	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91042	0.4872	10	0.87932	D	0	-24.2564	19.282	0.94055	0.0:0.0:1.0:0.0	.	368	Q9Y4W6	AFG32_HUMAN	L	368;383	ENSP00000269143:P368L	ENSP00000269143:P368L	P	-	2	0	AFG3L2	12346754	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.813000	0.99286	2.631000	0.89168	0.563000	0.77884	CCC	.	.	none		0.502	AFG3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254603.2	NM_006796	
ZNF205	7755	hgsc.bcm.edu	37	16	3168942	3168942	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr16:3168942C>T	ENST00000382192.3	+	6	726	c.521C>T	c.(520-522)gCg>gTg	p.A174V	ZNF205_ENST00000219091.4_Missense_Mutation_p.A174V|RP11-473M20.14_ENST00000576490.1_RNA|RP11-473M20.14_ENST00000575139.1_RNA	NM_001278158.1|NM_003456.2	NP_001265087.1|NP_003447.2	O95201	ZN205_HUMAN	zinc finger protein 205	174	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of hydrogen peroxide biosynthetic process (GO:0010729)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	20						GCCCCTCAAGCGCACGGCAAG	0.657																																					p.A174V		Atlas-SNP	.											ZNF205,NS,carcinoma,-1,1	ZNF205	42	1	0			c.C521T						scavenged	.						61.0	72.0	68.0					16																	3168942		2197	4300	6497	SO:0001583	missense	7755	exon6			CTCAAGCGCACGG	AF060865	CCDS10494.2	16p13.3	2013-01-08			ENSG00000122386	ENSG00000122386		"""Zinc fingers, C2H2-type"", ""-"""	12996	protein-coding gene	gene with protein product		603436		ZNF210		9787081	Standard	NM_003456		Approved	Zfp13	uc002cub.3	O95201	OTTHUMG00000148676	ENST00000382192.3:c.521C>T	16.37:g.3168942C>T	ENSP00000371627:p.Ala174Val	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	173	2	0.0115607	NM_003456	A8MZK0|D3DUB4|Q9BU95	Missense_Mutation	SNP	ENST00000382192.3	37	CCDS10494.2	.	.	.	.	.	.	.	.	.	.	C	2.193	-0.384821	0.04966	.	.	ENSG00000122386	ENST00000382192;ENST00000219091;ENST00000414351	T;T;T	0.06608	3.28;3.28;3.38	4.89	-0.476	0.12100	Krueppel-associated box (3);	0.710645	0.11569	N	0.550997	T	0.02047	0.0064	N	0.02169	-0.655	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.46938	-0.9155	10	0.23891	T	0.37	-4.9086	4.5307	0.12004	0.0:0.1883:0.3534:0.4582	.	174	O95201	ZN205_HUMAN	V	174	ENSP00000371627:A174V;ENSP00000219091:A174V;ENSP00000403306:A174V	ENSP00000219091:A174V	A	+	2	0	ZNF205	3108943	0.000000	0.05858	0.002000	0.10522	0.020000	0.10135	0.078000	0.14761	-0.213000	0.10094	-0.459000	0.05422	GCG	.	.	none		0.657	ZNF205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309057.1	NM_003456	
PIGW	284098	hgsc.bcm.edu	37	17	34894125	34894125	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr17:34894125A>G	ENST00000592983.1	+	2	1755	c.1175A>G	c.(1174-1176)gAt>gGt	p.D392G	PIGW_ENST00000328396.2_Missense_Mutation_p.D392G|MYO19_ENST00000590081.1_Intron			Q7Z7B1	PIGW_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class W	392					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)	transferase activity, transferring acyl groups (GO:0016746)			breast(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		TTACTGGGTGATATAATTTTG	0.338																																					p.D392G		Atlas-SNP	.											.	PIGW	50	.	0			c.A1175G						PASS	.						61.0	65.0	64.0					17																	34894125		2192	4296	6488	SO:0001583	missense	284098	exon2			TGGGTGATATAAT	AB097818	CCDS11313.1	17q21.1	2014-05-06	2006-06-28		ENSG00000184886	ENSG00000277161		"""Phosphatidylinositol glycan anchor biosynthesis"""	23213	protein-coding gene	gene with protein product		610275	"""phosphatidylinositol glycan, class W"""			14517336, 12714589	Standard	XM_005257238		Approved	Gwt1, FLJ37433	uc002hmz.1	Q7Z7B1	OTTHUMG00000188438	ENST00000592983.1:c.1175A>G	17.37:g.34894125A>G	ENSP00000468778:p.Asp392Gly	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	57	25	0.438596	NM_178517	Q8N9G3	Missense_Mutation	SNP	ENST00000592983.1	37	CCDS11313.1	.	.	.	.	.	.	.	.	.	.	A	13.25	2.181962	0.38511	.	.	ENSG00000184886	ENST00000328396	.	.	.	5.79	4.72	0.59763	.	0.105198	0.64402	N	0.000006	T	0.41581	0.1165	N	0.16833	0.445	0.52501	D	0.999957	B	0.29162	0.235	B	0.34824	0.19	T	0.19877	-1.0292	8	.	.	.	-4.2695	10.3149	0.43732	0.922:0.0:0.078:0.0	.	392	Q7Z7B1	PIGW_HUMAN	G	392	.	.	D	+	2	0	PIGW	31968238	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.836000	0.75349	1.039000	0.40074	0.459000	0.35465	GAT	.	.	none		0.338	PIGW-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451318.1	NM_178517	
OR8K5	219453	hgsc.bcm.edu	37	11	55927379	55927379	+	Nonsense_Mutation	SNP	G	G	A	rs199580379		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:55927379G>A	ENST00000313447.1	-	1	414	c.415C>T	c.(415-417)Cga>Tga	p.R139*		NM_001004058.2	NP_001004058.2	Q8NH50	OR8K5_HUMAN	olfactory receptor, family 8, subfamily K, member 5	139						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(3)|lung(24)|ovary(2)|pancreas(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	34	Esophageal squamous(21;0.00693)	Lung NSC(402;0.197)|all_epithelial(135;0.236)				TGACACAGTCGCTGAGACATA	0.403																																					p.R139X		Atlas-SNP	.											.	OR8K5	82	.	0			c.C415T						PASS	.	G	stop/ARG	0,4402		0,0,2201	84.0	86.0	85.0		415	-0.1	0.0	11		85	5,8585	4.3+/-15.6	0,5,4290	yes	stop-gained	OR8K5	NM_001004058.2		0,5,6491	AA,AG,GG		0.0582,0.0,0.0385		139/308	55927379	5,12987	2201	4295	6496	SO:0001587	stop_gained	219453	exon1			ACAGTCGCTGAGA	BK004347	CCDS31521.1	11q11	2012-08-09			ENSG00000181752	ENSG00000181752		"""GPCR / Class A : Olfactory receptors"""	15315	protein-coding gene	gene with protein product							Standard	NM_001004058		Approved		uc010rja.2	Q8NH50	OTTHUMG00000166820	ENST00000313447.1:c.415C>T	11.37:g.55927379G>A	ENSP00000323853:p.Arg139*	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	80	4	0.05	NM_001004058	Q6IFB5	Nonsense_Mutation	SNP	ENST00000313447.1	37	CCDS31521.1	.	.	.	.	.	.	.	.	.	.	G	4.734	0.136431	0.09032	0.0	5.82E-4	ENSG00000181752	ENST00000313447	.	.	.	4.18	-0.0501	0.13832	.	0.217057	0.32952	N	0.005447	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.1815	0.48631	0.0:0.0:0.4694:0.5306	.	.	.	.	X	139	.	ENSP00000323853:R139X	R	-	1	2	OR8K5	55683955	0.000000	0.05858	0.004000	0.12327	0.008000	0.06430	-1.402000	0.02499	0.222000	0.20900	-0.612000	0.04053	CGA	.	.	weak		0.403	OR8K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391543.1	NM_001004058	
ZBBX	79740	hgsc.bcm.edu	37	3	167039925	167039925	+	Silent	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:167039925T>C	ENST00000392766.2	-	12	1303	c.963A>G	c.(961-963)ttA>ttG	p.L321L	ZBBX_ENST00000469220.1_Intron|ZBBX_ENST00000392764.1_Silent_p.L292L|ZBBX_ENST00000455345.2_Silent_p.L321L|ZBBX_ENST00000307529.5_Silent_p.L321L|ZBBX_ENST00000392767.2_Silent_p.L321L	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	321						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(9)|liver(1)|lung(38)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	70						TTTTAAGCCATAATTTTTCCA	0.294																																					p.L321L		Atlas-SNP	.											ZBBX_ENST00000455345,caecum,carcinoma,-2,2	ZBBX	299	2	0			c.A963G						scavenged	.						60.0	57.0	58.0					3																	167039925		1784	4035	5819	SO:0001819	synonymous_variant	79740	exon12			AAGCCATAATTTT	AK026702	CCDS3199.2, CCDS56295.1, CCDS56296.1	3q26.1	2010-03-23			ENSG00000169064	ENSG00000169064			26245	protein-coding gene	gene with protein product						12477932	Standard	NM_024687		Approved	FLJ23049	uc011bpc.2	A8MT70	OTTHUMG00000133560	ENST00000392766.2:c.963A>G	3.37:g.167039925T>C		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	172	4	0.0232558	NM_024687	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Silent	SNP	ENST00000392766.2	37	CCDS3199.2																																																																																			.	.	none		0.294	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687	
CSGALNACT2	55454	hgsc.bcm.edu	37	10	43659372	43659372	+	Nonsense_Mutation	SNP	C	C	T	rs76607193	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr10:43659372C>T	ENST00000374466.3	+	5	1374	c.1039C>T	c.(1039-1041)Cga>Tga	p.R347*		NM_018590.3	NP_061060.3	Q8N6G5	CGAT2_HUMAN	chondroitin sulfate N-acetylgalactosaminyltransferase 2	347					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050653)|dermatan sulfate proteoglycan biosynthetic process (GO:0050651)|dermatan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050652)|glycosaminoglycan metabolic process (GO:0030203)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	acetylgalactosaminyltransferase activity (GO:0008376)|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047237)|metal ion binding (GO:0046872)	p.R347*(1)		endometrium(12)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						TAATCGTGGACGAGGACTAAA	0.408																																					p.R347X		Atlas-SNP	.											CSGALNACT2,trunk,malignant_melanoma,0,1	CSGALNACT2	67	1	1	Substitution - Nonsense(1)	skin(1)	c.C1039T						scavenged	.						191.0	181.0	184.0					10																	43659372		2203	4300	6503	SO:0001587	stop_gained	55454	exon5			CGTGGACGAGGAC	AF116646	CCDS7201.1	10q11.21	2013-02-19			ENSG00000169826	ENSG00000169826		"""Beta 4-glycosyltransferases"""	24292	protein-coding gene	gene with protein product	"""chondroitin beta1,4 N-acetylgalactosaminyltransferase 2"""					12446672	Standard	NM_018590		Approved	GALNACT2, MGC40204, PRO0082, GALNACT-2	uc001jan.4	Q8N6G5	OTTHUMG00000018023	ENST00000374466.3:c.1039C>T	10.37:g.43659372C>T	ENSP00000363590:p.Arg347*	Somatic	181	1	0.00552486		WXS	Illumina HiSeq	Phase_I	201	5	0.0248756	NM_018590	B3KWL7|Q6MZJ5|Q6MZP6|Q8TCH4|Q9P1I6	Nonsense_Mutation	SNP	ENST00000374466.3	37	CCDS7201.1	.	.	.	.	.	.	.	.	.	.	C	41	8.712957	0.98925	.	.	ENSG00000169826	ENST00000374466	.	.	.	6.08	4.19	0.49359	.	0.110120	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.08599	T	0.76	-3.2438	15.5126	0.75795	0.253:0.747:0.0:0.0	.	.	.	.	X	347	.	ENSP00000363590:R347X	R	+	1	2	CSGALNACT2	42979378	0.998000	0.40836	1.000000	0.80357	0.999000	0.98932	1.226000	0.32563	0.852000	0.35287	0.591000	0.81541	CGA	C|0.997;T|0.003	0.003	strong		0.408	CSGALNACT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047693.1	NM_018590	
MUM1L1	139221	hgsc.bcm.edu	37	X	105449437	105449437	+	Silent	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:105449437G>A	ENST00000357175.2	+	4	661	c.12G>A	c.(10-12)gaG>gaA	p.E4E	MUM1L1_ENST00000337685.2_Silent_p.E4E|MUM1L1_ENST00000372552.1_Silent_p.E4E	NM_001171020.1	NP_001164491.1	Q5H9M0	MUML1_HUMAN	melanoma associated antigen (mutated) 1-like 1	4						extracellular vesicular exosome (GO:0070062)				autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31						TGGAGTCTGAGTATGTCCTAT	0.398																																					p.E4E		Atlas-SNP	.											.	MUM1L1	166	.	0			c.G12A						PASS	.						20.0	20.0	20.0					X																	105449437		1900	4117	6017	SO:0001819	synonymous_variant	139221	exon5			GTCTGAGTATGTC	AK090835	CCDS55469.1	Xq22.3	2008-02-05			ENSG00000157502	ENSG00000157502			26583	protein-coding gene	gene with protein product							Standard	NM_152423		Approved	FLJ33516	uc004emf.2	Q5H9M0	OTTHUMG00000022146	ENST00000357175.2:c.12G>A	X.37:g.105449437G>A		Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	261	136	0.521073	NM_152423	D3DUX2|Q49AS5|Q8N2C0|Q96MT6	Silent	SNP	ENST00000357175.2	37	CCDS55469.1																																																																																			.	.	none		0.398	MUM1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057795.1	NM_152423	
ATG101	60673	hgsc.bcm.edu	37	12	52467630	52467630	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:52467630C>T	ENST00000336854.4	+	3	674	c.196C>T	c.(196-198)Cgt>Tgt	p.R66C	RP11-1100L3.7_ENST00000550301.1_RNA	NM_001098673.1|NM_021934.4	NP_001092143.1|NP_068753.2	Q9BSB4	ATGA1_HUMAN		66					autophagic vacuole assembly (GO:0000045)	pre-autophagosomal structure (GO:0000407)	identical protein binding (GO:0042802)|protein complex binding (GO:0032403)			endometrium(1)|lung(2)|ovary(1)	4				BRCA - Breast invasive adenocarcinoma(357;0.0978)		CACTTATGTGCGTGTCTCTTC	0.542																																					p.R66C		Atlas-SNP	.											C12orf44,caecum,carcinoma,0,1	C12orf44	14	1	0			c.C196T						scavenged	.						218.0	153.0	175.0					12																	52467630		2203	4300	6503	SO:0001583	missense	60673	exon3			TATGTGCGTGTCT																												ENST00000336854.4:c.196C>T	12.37:g.52467630C>T	ENSP00000338990:p.Arg66Cys	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	151	2	0.013245	NM_001098673	Q9HAE2|Q9HBN1	Missense_Mutation	SNP	ENST00000336854.4	37	CCDS8820.1	.	.	.	.	.	.	.	.	.	.	C	11.09	1.537495	0.27475	.	.	ENSG00000123395	ENST00000336854;ENST00000553049;ENST00000548915;ENST00000550984	.	.	.	5.01	4.07	0.47477	.	0.000000	0.85682	D	0.000000	T	0.45054	0.1323	L	0.42245	1.32	0.80722	D	1	B	0.26876	0.162	B	0.20955	0.032	T	0.40440	-0.9563	9	0.35671	T	0.21	-12.7953	9.1649	0.37046	0.1594:0.6854:0.1553:0.0	.	66	Q9BSB4	ATGA1_HUMAN	C	66	.	ENSP00000338990:R66C	R	+	1	0	C12orf44	50753897	1.000000	0.71417	0.989000	0.46669	0.557000	0.35523	1.288000	0.33296	2.490000	0.84030	0.462000	0.41574	CGT	.	.	none		0.542	C12orf44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405063.1		
TRIM64C	646754	hgsc.bcm.edu	37	11	49075660	49075660	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:49075660A>G	ENST00000530230.1	-	7	949	c.950T>C	c.(949-951)aTg>aCg	p.M317T		NM_001206631.1	NP_001193560.1	A6NLI5	TR64C_HUMAN	tripartite motif containing 64C	317	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|stomach(1)	2						TTGGGGATCCATGGGTGCACT	0.507																																					p.M320T		Atlas-SNP	.											.	TRIM64C	18	.	0			c.T959C						PASS	.																																			SO:0001583	missense	646754	exon6			GGATCCATGGGTG		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.950T>C	11.37:g.49075660A>G	ENSP00000431987:p.Met317Thr	Somatic	506	0	0		WXS	Illumina HiSeq	Phase_I	505	136	0.269307	NM_001206631		Missense_Mutation	SNP	ENST00000530230.1	37		.	.	.	.	.	.	.	.	.	.	g	0.017	-1.505270	0.00992	.	.	ENSG00000214891	ENST00000530230	T	0.60171	0.21	1.55	-3.11	0.05299	.	.	.	.	.	T	0.40145	0.1105	L	0.47190	1.495	0.09310	N	1	.	.	.	.	.	.	T	0.35276	-0.9795	7	0.09843	T	0.71	.	3.3465	0.07137	0.4129:0.3395:0.0:0.2476	.	.	.	.	T	317	ENSP00000431987:M317T	ENSP00000431987:M317T	M	-	2	0	TRIM64C	49032236	0.000000	0.05858	0.000000	0.03702	0.066000	0.16364	-0.014000	0.12656	-2.733000	0.00383	0.155000	0.16302	ATG	.	.	none		0.507	TRIM64C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000391366.1		
CARD10	29775	hgsc.bcm.edu	37	22	37912258	37912258	+	Nonsense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr22:37912258G>A	ENST00000403299.1	-	4	637	c.421C>T	c.(421-423)Cga>Tga	p.R141*	CARD10_ENST00000494166.1_5'Flank|CARD10_ENST00000251973.5_Nonsense_Mutation_p.R141*			Q9BWT7	CAR10_HUMAN	caspase recruitment domain family, member 10	141					activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein complex assembly (GO:0006461)|regulation of apoptotic process (GO:0042981)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)	receptor signaling complex scaffold activity (GO:0030159)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	17	Melanoma(58;0.0574)					CGCAGCCGTCGCACCTCTGTC	0.647																																					p.R141X		Atlas-SNP	.											CARD10,NS,carcinoma,+1,1	CARD10	55	1	0			c.C421T						scavenged	.						14.0	15.0	14.0					22																	37912258		2191	4291	6482	SO:0001587	stop_gained	29775	exon3			GCCGTCGCACCTC	AF086324	CCDS13948.1	22q13.1	2008-05-22			ENSG00000100065	ENSG00000100065			16422	protein-coding gene	gene with protein product		607209				11259443, 11356195	Standard	NM_014550		Approved	CARMA3, BIMP1	uc003asu.1	Q9BWT7	OTTHUMG00000150592	ENST00000403299.1:c.421C>T	22.37:g.37912258G>A	ENSP00000384570:p.Arg141*	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	33	2	0.0606061	NM_014550	Q14CQ8|Q5TFG6|Q8NC81|Q9UGR5|Q9UGR6|Q9Y3H0	Nonsense_Mutation	SNP	ENST00000403299.1	37	CCDS13948.1	.	.	.	.	.	.	.	.	.	.	G	37	6.491763	0.97612	.	.	ENSG00000100065	ENST00000403299;ENST00000251973	.	.	.	5.27	4.16	0.48862	.	0.143577	0.44483	D	0.000451	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07175	T	0.84	-28.1082	11.0124	0.47669	0.0:0.0:0.5985:0.4015	.	.	.	.	X	141	.	ENSP00000251973:R141X	R	-	1	2	CARD10	36242204	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.304000	0.59104	2.610000	0.88304	0.563000	0.77884	CGA	.	.	none		0.647	CARD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318997.1	NM_014550	
FOXD4	2298	hgsc.bcm.edu	37	9	117789	117789	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr9:117789C>T	ENST00000382500.2	-	1	628	c.331G>A	c.(331-333)Gcg>Acg	p.A111T		NM_207305.4	NP_997188.2	Q12950	FOXD4_HUMAN	forkhead box D4	111					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding, bending (GO:0008301)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A111T(1)		endometrium(5)|large_intestine(2)|lung(3)|prostate(1)|skin(3)	14	all_lung(41;0.218)	all_cancers(5;0.0395)|Acute lymphoblastic leukemia(5;1.91e-07)|all_hematologic(5;1.95e-06)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)		GTGATGAGCGCGATGTACGAG	0.647																																					p.A111T		Atlas-SNP	.											FOXD4,NS,carcinoma,0,1	FOXD4	75	1	1	Substitution - Missense(1)	prostate(1)	c.G331A						scavenged	.						68.0	95.0	86.0					9																	117789		2199	4298	6497	SO:0001583	missense	2298	exon1			TGAGCGCGATGTA	U13223	CCDS34975.1	9p24.3	2014-09-17			ENSG00000170122	ENSG00000170122		"""Forkhead boxes"""	3805	protein-coding gene	gene with protein product		601092		FKHL9		7957066, 8825632, 12234674	Standard	NM_207305		Approved	FREAC5, FOXD4a	uc003zfz.4	Q12950	OTTHUMG00000021015	ENST00000382500.2:c.331G>A	9.37:g.117789C>T	ENSP00000371940:p.Ala111Thr	Somatic	263	1	0.00380228		WXS	Illumina HiSeq	Phase_I	227	3	0.0132159	NM_207305	B2RN05|B9EGL7|Q5VVK1|Q8WXT6	Missense_Mutation	SNP	ENST00000382500.2	37	CCDS34975.1	.	.	.	.	.	.	.	.	.	.	.	17.99	3.523975	0.64747	.	.	ENSG00000170122	ENST00000382500	D	0.95554	-3.74	2.24	2.24	0.28232	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (4);	0.000000	0.37219	U	0.002197	D	0.96546	0.8873	L	0.61218	1.895	0.54753	D	0.999989	D	0.89917	1.0	D	0.85130	0.997	D	0.96248	0.9181	10	0.87932	D	0	.	11.6185	0.51104	0.0:1.0:0.0:0.0	.	111	Q12950	FOXD4_HUMAN	T	111	ENSP00000371940:A111T	ENSP00000371940:A111T	A	-	1	0	FOXD4	107789	1.000000	0.71417	1.000000	0.80357	0.678000	0.39670	5.492000	0.66893	1.253000	0.44018	0.291000	0.19559	GCG	.	.	none		0.647	FOXD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055433.1	NM_207305	
DNAH14	127602	hgsc.bcm.edu	37	1	225332227	225332227	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:225332227G>A	ENST00000445597.2	+	18	3434	c.3434G>A	c.(3433-3435)cGa>cAa	p.R1145Q	DNAH14_ENST00000430092.1_Missense_Mutation_p.R1529Q|DNAH14_ENST00000439375.2_Missense_Mutation_p.R1529Q			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	1145					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						CTCACAGACCGATGCTGGCTG	0.473																																					p.R1529Q		Atlas-SNP	.											.	DNAH14	300	.	0			c.G4586A						PASS	.						112.0	94.0	100.0					1																	225332227		692	1591	2283	SO:0001583	missense	127602	exon28			CAGACCGATGCTG	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.3434G>A	1.37:g.225332227G>A	ENSP00000409472:p.Arg1145Gln	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	111	20	0.18018	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		.	.	.	.	.	.	.	.	.	.	G	23.1	4.371908	0.82573	.	.	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375;ENST00000328556	T;T;T;T	0.14516	2.5;2.5;2.5;2.5	5.31	5.31	0.75309	.	.	.	.	.	T	0.49236	0.1545	M	0.92077	3.27	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.61322	-0.7086	9	0.87932	D	0	.	18.1143	0.89546	0.0:0.0:1.0:0.0	.	1529	Q0VDD8-4	.	Q	1145;1529;1529;624	ENSP00000409472:R1145Q;ENSP00000414402:R1529Q;ENSP00000392061:R1529Q;ENSP00000332424:R624Q	ENSP00000332424:R624Q	R	+	2	0	DNAH14	223398850	1.000000	0.71417	0.007000	0.13788	0.718000	0.41266	8.074000	0.89500	2.639000	0.89480	0.508000	0.49915	CGA	.	.	none		0.473	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
FDX1L	112812	hgsc.bcm.edu	37	19	10428229	10428229	+	5'Flank	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:10428229C>T	ENST00000393708.3	-	0	0				CTD-2369P2.10_ENST00000452032.2_5'Flank|FDX1L_ENST00000541276.1_5'Flank|FDX1L_ENST00000494368.1_5'Flank|RAVER1_ENST00000293677.6_Silent_p.S724S|CTD-2369P2.12_ENST00000586529.1_Silent_p.S125S|FDX1L_ENST00000492239.1_5'Flank	NM_001031734.2	NP_001026904.1	Q6P4F2	ADXL_HUMAN	ferredoxin 1-like						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)			TGGGCTCGGGCGAGGGCAGCA	0.701																																					p.S724S		Atlas-SNP	.											.	RAVER1	67	.	0			c.G2172A						PASS	.						31.0	33.0	33.0					19																	10428229		2002	4163	6165	SO:0001631	upstream_gene_variant	125950	exon13			CTCGGGCGAGGGC	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		19.37:g.10428229C>T	Exception_encountered	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	67	4	0.0597015	NM_133452	Q8N8B8	Silent	SNP	ENST00000393708.3	37	CCDS32905.1	.	.	.	.	.	.	.	.	.	.	C	6.949	0.544861	0.13312	.	.	ENSG00000161847	ENST00000331131	.	.	.	5.15	-10.3	0.00346	.	.	.	.	.	T	0.37183	0.0994	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.13361	-1.0512	7	0.54805	T	0.06	-0.625	5.394	0.16259	0.0732:0.1836:0.2306:0.5125	.	581	Q8IY67	RAVR1_HUMAN	H	581	.	ENSP00000327543:R581H	R	-	2	0	RAVER1	10289229	0.000000	0.05858	0.057000	0.19452	0.729000	0.41735	-5.027000	0.00158	-2.789000	0.00357	-2.358000	0.00240	CGC	.	.	none		0.701	FDX1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280567.2		
PRG4	10216	hgsc.bcm.edu	37	1	186276961	186276961	+	Missense_Mutation	SNP	A	A	C	rs145338869	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:186276961A>C	ENST00000445192.2	+	7	2155	c.2110A>C	c.(2110-2112)Act>Cct	p.T704P	PRG4_ENST00000367486.3_Missense_Mutation_p.T661P|PRG4_ENST00000367483.4_Missense_Mutation_p.T663P|PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367485.4_Missense_Mutation_p.T611P	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	704	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						CCCTAAGGAGACTGCTCCAAC	0.597																																					p.T704P		Atlas-SNP	.											PRG4,NS,malignant_melanoma,0,1	PRG4	259	1	0			c.A2110C						scavenged	.	A	PRO/THR,PRO/THR,PRO/THR,PRO/THR	15,4391		0,15,2188	137.0	152.0	147.0		2110,1708,1831,1987	-5.2	0.0	1	dbSNP_134	147	0,8600		0,0,4300	no	missense,missense,missense,missense	PRG4	NM_005807.3,NM_001127710.1,NM_001127709.1,NM_001127708.1	38,38,38,38	0,15,6488	CC,CA,AA		0.0,0.3404,0.1153	benign,benign,benign,benign	704/1405,570/1271,611/1312,663/1364	186276961	15,12991	2203	4300	6503	SO:0001583	missense	10216	exon7			AAGGAGACTGCTC	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.2110A>C	1.37:g.186276961A>C	ENSP00000399679:p.Thr704Pro	Somatic	141	3	0.0212766		WXS	Illumina HiSeq	Phase_I	164	7	0.0426829	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Missense_Mutation	SNP	ENST00000445192.2	37	CCDS1369.1	.	.	.	.	.	.	.	.	.	.	-	2.283	-0.364165	0.05103	0.003404	0.0	ENSG00000116690	ENST00000367486;ENST00000367482;ENST00000367483;ENST00000367485;ENST00000445192	T;T;T;T	0.05025	3.55;3.65;3.51;3.65	2.61	-5.23	0.02798	.	0.580677	0.14221	N	0.333433	T	0.01627	0.0052	N	0.02011	-0.69	0.09310	N	0.999999	B;B;B;B	0.06786	0.001;0.001;0.0;0.001	B;B;B;B	0.04013	0.001;0.001;0.0;0.001	T	0.39623	-0.9605	9	.	.	.	.	4.4579	0.11652	0.3649:0.3368:0.0:0.2984	.	570;611;704;663	Q92954-4;Q92954-3;Q92954;Q92954-2	.;.;PRG4_HUMAN;.	P	661;570;663;611;704	ENSP00000356456:T661P;ENSP00000356453:T663P;ENSP00000356455:T611P;ENSP00000399679:T704P	.	T	+	1	0	PRG4	184543584	0.005000	0.15991	0.000000	0.03702	0.060000	0.15804	0.317000	0.19487	-1.717000	0.01385	0.138000	0.15974	ACT	A|0.996;C|0.004	0.004	strong		0.597	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807	
PBDC1	51260	hgsc.bcm.edu	37	X	75395309	75395309	+	Splice_Site	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:75395309T>C	ENST00000373358.3	+	4	361	c.158T>C	c.(157-159)cTg>cCg	p.L53P	PBDC1_ENST00000373357.3_Splice_Site_p.L53P	NM_016500.3	NP_057584.2	Q9BVG4	PBDC1_HUMAN	polysaccharide biosynthesis domain containing 1	53																	GTTTCGCAGCTGATTTCATCA	0.413																																					p.L53P		Atlas-SNP	.											.	.	.	.	0			c.T158C						PASS	.						86.0	75.0	79.0					X																	75395309		2203	4300	6503	SO:0001630	splice_region_variant	51260	exon4			CGCAGCTGATTTC	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.157-1T>C	X.37:g.75395309T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	99	28	0.282828	NM_016500		Missense_Mutation	SNP	ENST00000373358.3	37	CCDS14432.1	.	.	.	.	.	.	.	.	.	.	T	19.75	3.885632	0.72410	.	.	ENSG00000102390	ENST00000373358;ENST00000373357	.	.	.	4.77	4.77	0.60923	Yst0336-like domain (1);	0.000000	0.85682	D	0.000000	T	0.81767	0.4892	M	0.91561	3.22	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.85370	0.1113	9	0.87932	D	0	-8.4595	11.3241	0.49438	0.0:0.0:0.0:1.0	.	53	Q9BVG4	CX026_HUMAN	P	53	.	ENSP00000362455:L53P	L	+	2	0	CXorf26	75311711	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	5.748000	0.68697	1.875000	0.54330	0.486000	0.48141	CTG	.	.	none		0.413	PBDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057294.1	NM_016500	Missense_Mutation
PIEZO1	9780	hgsc.bcm.edu	37	16	88800422	88800422	+	Nonsense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr16:88800422G>A	ENST00000301015.9	-	17	2467	c.2221C>T	c.(2221-2223)Cag>Tag	p.Q741*	RP5-1142A6.2_ENST00000567968.1_RNA|RP5-1142A6.2_ENST00000440406.2_RNA	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	741					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						tgctcctgctgctcctcccgc	0.657																																					p.Q741X		Atlas-SNP	.											.	PIEZO1	79	.	0			c.C2221T						PASS	.						8.0	11.0	10.0					16																	88800422		688	1580	2268	SO:0001587	stop_gained	9780	exon17			CCTGCTGCTCCTC	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.2221C>T	16.37:g.88800422G>A	ENSP00000301015:p.Gln741*	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	73	38	0.520548	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	Nonsense_Mutation	SNP	ENST00000301015.9	37	CCDS54058.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.40|14.40	2.524756|2.524756	0.44969|0.44969	.|.	.|.	ENSG00000103335|ENSG00000103335	ENST00000451779|ENST00000301015	.|.	.|.	.|.	2.16|2.16	-0.768|-0.768	0.11013|0.11013	.|.	.|0.867490	.|0.09707	.|N	.|0.766227	T|.	0.09423|.	0.0232|.	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.35475|.	-0.9787|.	4|.	.|0.05833	.|T	.|0.94	.|.	3.7221|3.7221	0.08460|0.08460	0.0:0.2087:0.3757:0.4157|0.0:0.2087:0.3757:0.4157	.|.	.|.	.|.	.|.	V|X	686|741	.|.	.|ENSP00000301015:Q741X	A|Q	-|-	2|1	0|0	FAM38A|FAM38A	87327923|87327923	0.002000|0.002000	0.14202|0.14202	0.002000|0.002000	0.10522|0.10522	0.002000|0.002000	0.02628|0.02628	0.136000|0.136000	0.15974|0.15974	0.144000|0.144000	0.18951|0.18951	0.462000|0.462000	0.41574|0.41574	GCA|CAG	.	.	none		0.657	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
HBS1L	10767	hgsc.bcm.edu	37	6	135358694	135358694	+	Intron	SNP	G	G	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr6:135358694G>C	ENST00000367837.5	-	4	637				HBS1L_ENST00000367826.2_Intron|HBS1L_ENST00000445176.2_Intron|HBS1L_ENST00000415177.2_Intron|HBS1L_ENST00000314674.3_Intron|HBS1L_ENST00000367820.2_Intron|HBS1L_ENST00000367824.4_Intron|HBS1L_ENST00000367822.5_Missense_Mutation_p.Q301E	NM_001145158.1|NM_006620.3	NP_001138630.1|NP_006611.1	Q9Y450	HBS1L_HUMAN	HBS1-like translational GTPase						signal transduction (GO:0007165)|translation (GO:0006412)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation elongation factor activity (GO:0003746)			NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	20	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0046)|GBM - Glioblastoma multiforme(68;0.00702)		GAATTATTTTGAATATATAAA	0.313																																					p.Q301E		Atlas-SNP	.											.	HBS1L	75	.	0			c.C901G						PASS	.						36.0	32.0	33.0					6																	135358694		692	1590	2282	SO:0001627	intron_variant	10767	exon5			TATTTTGAATATA	U87791	CCDS5173.1, CCDS47479.1, CCDS47480.1	6q23.3	2014-04-30	2014-04-30		ENSG00000112339	ENSG00000112339			4834	protein-coding gene	gene with protein product	"""eRF3 family member"""	612450	"""HBS1 (S. cerevisiae)-like"", ""HBS1-like (S. cerevisiae)"""			9872408, 23667253	Standard	NM_006620		Approved	ERFS, HBS1, HSPC276, KIAA1038, DKFZp434g247, EF-1a, eRF3c	uc003qez.2	Q9Y450	OTTHUMG00000015626	ENST00000367837.5:c.430+2016C>G	6.37:g.135358694G>C		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	92	38	0.413043	NM_001145207	B7Z365|Q4VX89|Q4VX90|Q5T7G3|Q8NDW9|Q9UPW3	Missense_Mutation	SNP	ENST00000367837.5	37	CCDS5173.1	.	.	.	.	.	.	.	.	.	.	G	0.406	-0.915705	0.02415	.	.	ENSG00000112339	ENST00000367822	.	.	.	4.82	2.91	0.33838	.	.	.	.	.	T	0.10723	0.0262	.	.	.	0.25267	N	0.989545	B	0.28636	0.218	B	0.25291	0.059	T	0.10613	-1.0622	7	0.62326	D	0.03	.	4.5597	0.12154	0.0899:0.1409:0.6046:0.1646	.	301	Q9Y450-2	.	E	301	.	ENSP00000356796:Q301E	Q	-	1	0	HBS1L	135400387	0.001000	0.12720	0.257000	0.24404	0.077000	0.17291	0.204000	0.17335	2.382000	0.81193	0.655000	0.94253	CAA	.	.	none		0.313	HBS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042339.2		
CHL1	10752	hgsc.bcm.edu	37	3	391167	391167	+	Missense_Mutation	SNP	G	G	A	rs201671256		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:391167G>A	ENST00000256509.2	+	10	1616	c.974G>A	c.(973-975)cGc>cAc	p.R325H	CHL1_ENST00000397491.2_Missense_Mutation_p.R309H	NM_001253387.1|NM_001253388.1|NM_006614.3	NP_001240316.1|NP_001240317.1|NP_006605.2	Q96FC9	DDX11_HUMAN	cell adhesion molecule L1-like	0	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			NS(1)|central_nervous_system(5)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|lung(31)|ovary(1)|prostate(4)|skin(10)|stomach(1)	93		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)		GGAAATTATCGCTGCACAGCC	0.398																																					p.R325H		Atlas-SNP	.											CHL1,caecum,carcinoma,-1,1	CHL1	242	1	0			c.G974A						scavenged	.						107.0	109.0	108.0					3																	391167		2203	4300	6503	SO:0001583	missense	10752	exon8			ATTATCGCTGCAC	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.974G>A	3.37:g.391167G>A	ENSP00000256509:p.Arg325His	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	99	3	0.030303	NM_001253388	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000256509.2	37	CCDS2556.1	.	.	.	.	.	.	.	.	.	.	G	14.51	2.556977	0.45590	.	.	ENSG00000134121	ENST00000256509;ENST00000397491	T;T	0.30981	1.51;1.51	5.46	2.52	0.30459	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.353536	0.32952	N	0.005445	T	0.18130	0.0435	L	0.43757	1.38	0.33529	D	0.593424	B;B;B	0.26708	0.157;0.157;0.021	B;B;B	0.25614	0.062;0.062;0.013	T	0.09684	-1.0663	10	0.12766	T	0.61	.	2.624	0.04924	0.2815:0.0:0.4946:0.2239	.	309;309;325	B3KX75;O00533;O00533-2	.;CHL1_HUMAN;.	H	325;309	ENSP00000256509:R325H;ENSP00000380628:R309H	ENSP00000256509:R325H	R	+	2	0	CHL1	366167	1.000000	0.71417	0.998000	0.56505	0.971000	0.66376	1.710000	0.37920	1.444000	0.47605	0.650000	0.86243	CGC	G|0.999;A|0.001	0.001	weak		0.398	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614	
MYOCD	93649	hgsc.bcm.edu	37	17	12647709	12647709	+	Silent	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr17:12647709G>A	ENST00000343344.4	+	8	927	c.927G>A	c.(925-927)caG>caA	p.Q309Q	MYOCD_ENST00000395988.1_3'UTR|AC005358.1_ENST00000609971.1_Silent_p.Q213Q|MYOCD_ENST00000425538.1_Silent_p.Q309Q			Q8IZQ8	MYCD_HUMAN	myocardin	309	Gln-rich.				cardiac muscle cell differentiation (GO:0055007)|cardiac ventricle development (GO:0003231)|cardiocyte differentiation (GO:0035051)|cell growth involved in cardiac muscle cell development (GO:0061049)|cellular component maintenance (GO:0043954)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hypoxia (GO:0071456)|digestive tract development (GO:0048565)|ductus arteriosus closure (GO:0097070)|hepatic stellate cell activation (GO:0035733)|lung alveolus development (GO:0048286)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of skeletal muscle cell differentiation (GO:2001015)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of cardiac vascular smooth muscle cell differentiation (GO:2000724)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of cell growth by extracellular stimulus (GO:0001560)|regulation of histone acetylation (GO:0035065)|regulation of myoblast differentiation (GO:0045661)|regulation of smooth muscle cell differentiation (GO:0051150)|response to hypoxia (GO:0001666)|smooth muscle cell differentiation (GO:0051145)|urinary bladder development (GO:0060157)|uterus development (GO:0060065)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|protein domain specific binding (GO:0019904)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.Q309Q(1)		breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(2)|lung(33)|ovary(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	70				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)		agcagcagcagcaacaCCGAT	0.587																																					p.Q309Q		Atlas-SNP	.											MYOCD,colon,carcinoma,0,1	MYOCD	291	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G927A						scavenged	.						42.0	30.0	34.0					17																	12647709		2203	4300	6503	SO:0001819	synonymous_variant	93649	exon8			GCAGCAGCAACAC	AF532596	CCDS11163.1, CCDS54091.1	17p11.2	2004-03-01			ENSG00000141052	ENSG00000141052			16067	protein-coding gene	gene with protein product		606127				11439182, 12397177	Standard	XM_005256863		Approved	MYCD	uc002gno.2	Q8IZQ8	OTTHUMG00000058767	ENST00000343344.4:c.927G>A	17.37:g.12647709G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	115	2	0.0173913	NM_001146312	Q5UBU5|Q8N7Q1	Silent	SNP	ENST00000343344.4	37	CCDS11163.1																																																																																			.	.	none		0.587	MYOCD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129950.1	NM_153604	
NEFH	4744	hgsc.bcm.edu	37	22	29885562	29885562	+	Missense_Mutation	SNP	G	G	A	rs370929798		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr22:29885562G>A	ENST00000310624.6	+	4	1966	c.1933G>A	c.(1933-1935)Gaa>Aaa	p.E645K		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	645	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AACGAAGGAGGAAGCAAAGTC	0.562																																					p.E645K		Atlas-SNP	.											NEFH,rectum,carcinoma,-2,1	NEFH	178	1	0			c.G1933A						scavenged	.						82.0	88.0	86.0					22																	29885562		2203	4300	6503	SO:0001583	missense	4744	exon4			AAGGAGGAAGCAA		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1933G>A	22.37:g.29885562G>A	ENSP00000311997:p.Glu645Lys	Somatic	64	1	0.015625		WXS	Illumina HiSeq	Phase_I	64	9	0.140625	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Missense_Mutation	SNP	ENST00000310624.6	37	CCDS13858.1	.	.	.	.	.	.	.	.	.	.	G	9.212	1.031217	0.19590	.	.	ENSG00000100285	ENST00000328842;ENST00000310624	D	0.83914	-1.78	4.97	4.97	0.65823	.	0.115504	0.38778	N	0.001569	D	0.87783	0.6264	L	0.61218	1.895	0.29104	N	0.881289	P	0.36712	0.566	P	0.52267	0.694	D	0.83526	0.0088	10	0.44086	T	0.13	.	16.1111	0.81263	0.0:0.0:1.0:0.0	.	645	P12036	NFH_HUMAN	K	645	ENSP00000311997:E645K	ENSP00000311997:E645K	E	+	1	0	NEFH	28215562	0.001000	0.12720	0.367000	0.25926	0.091000	0.18340	0.923000	0.28757	2.745000	0.94114	0.491000	0.48974	GAA	.	.	weak		0.562	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
JAKMIP3	282973	hgsc.bcm.edu	37	10	133962951	133962951	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr10:133962951C>T	ENST00000298622.4	+	14	2022	c.1884C>T	c.(1882-1884)caC>caT	p.H628H	JAKMIP3_ENST00000477275.1_3'UTR	NM_001105521.2	NP_001098991.1	Q5VZ66	JKIP3_HUMAN	Janus kinase and microtubule interacting protein 3	628						Golgi apparatus (GO:0005794)				breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	31		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)		TCAGCTTCCACCACACGCCCT	0.657																																					p.H628H		Atlas-SNP	.											.	JAKMIP3	69	.	0			c.C1884T						PASS	.						71.0	51.0	58.0					10																	133962951		2184	4286	6470	SO:0001819	synonymous_variant	282973	exon14			CTTCCACCACACG	AL832756	CCDS44494.1	10q26.3	2009-04-23	2009-04-23	2008-01-28	ENSG00000188385	ENSG00000188385			23523	protein-coding gene	gene with protein product	"""neuroendocrine long coiled-coil 2"""	611198	"""chromosome 10 open reading frame 39"", ""chromosome 10 open reading frame 14"""	C10orf39, C10orf14		15277531, 17572408	Standard	NM_001105521		Approved	FLJ37857, NECC2, KIAA4091, bA140A10.5	uc001lkx.4	Q5VZ66	OTTHUMG00000150167	ENST00000298622.4:c.1884C>T	10.37:g.133962951C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	64	29	0.453125	NM_001105521	A6PW00|Q69YM6|Q6ZT29	Silent	SNP	ENST00000298622.4	37	CCDS44494.1																																																																																			.	.	none		0.657	JAKMIP3-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051049.3	NM_194303	
DUSP2	1844	hgsc.bcm.edu	37	2	96810595	96810595	+	Missense_Mutation	SNP	A	A	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:96810595A>C	ENST00000288943.4	-	2	500	c.415T>G	c.(415-417)Tgt>Ggt	p.C139G	AC012307.2_ENST00000449242.1_lincRNA	NM_004418.3	NP_004409.1	Q05923	DUS2_HUMAN	dual specificity phosphatase 2	139	Rhodanese. {ECO:0000255|PROSITE- ProRule:PRU00173}.				endoderm formation (GO:0001706)|inactivation of MAPK activity (GO:0000188)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	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)			NS(1)|breast(1)|lung(2)|skin(1)	5		Ovarian(717;0.0228)				AGATCGGGACAGCAGCCCTGG	0.692																																					p.C139G		Atlas-SNP	.											.	DUSP2	20	.	0			c.T415G						PASS	.						15.0	21.0	19.0					2																	96810595		2119	4214	6333	SO:0001583	missense	1844	exon2			CGGGACAGCAGCC	L11329	CCDS2016.1	2q11	2011-06-09			ENSG00000158050	ENSG00000158050		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	3068	protein-coding gene	gene with protein product		603068				7806236, 7590752, 12673251	Standard	NM_004418		Approved	PAC-1	uc002svk.4	Q05923	OTTHUMG00000130456	ENST00000288943.4:c.415T>G	2.37:g.96810595A>C	ENSP00000288943:p.Cys139Gly	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	98	37	0.377551	NM_004418	Q53T45	Missense_Mutation	SNP	ENST00000288943.4	37	CCDS2016.1	.	.	.	.	.	.	.	.	.	.	A	11.95	1.791720	0.31685	.	.	ENSG00000158050	ENST00000288943	T	0.35421	1.31	4.31	4.31	0.51392	Rhodanese-like (4);	0.305675	0.32258	N	0.006346	T	0.27933	0.0688	L	0.49778	1.585	0.35359	D	0.788057	P	0.38335	0.627	B	0.28916	0.096	T	0.47947	-0.9077	10	0.66056	D	0.02	.	9.8111	0.40824	1.0:0.0:0.0:0.0	.	139	Q05923	DUS2_HUMAN	G	139	ENSP00000288943:C139G	ENSP00000288943:C139G	C	-	1	0	DUSP2	96174322	0.132000	0.22450	0.778000	0.31720	0.171000	0.22731	3.037000	0.49775	1.812000	0.52913	0.374000	0.22700	TGT	.	.	none		0.692	DUSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252847.1	NM_004418	
ZNF750	79755	hgsc.bcm.edu	37	17	80789538	80789538	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr17:80789538A>G	ENST00000269394.3	-	2	1626	c.793T>C	c.(793-795)Tcg>Ccg	p.S265P	ZNF750_ENST00000572562.1_Intron|TBCD_ENST00000397466.2_Intron|TBCD_ENST00000539345.2_Intron|TBCD_ENST00000355528.4_Intron	NM_024702.2	NP_078978.2	Q32MQ0	ZN750_HUMAN	zinc finger protein 750	265					cell differentiation (GO:0030154)|epidermis development (GO:0008544)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(3)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(4)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	31	Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0514)|all_epithelial(8;0.0748)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.149)			CACTCAGGCGAGCTCCCAGCC	0.612																																					p.S265P		Atlas-SNP	.											ZNF750,colon,carcinoma,0,1	ZNF750	60	1	0			c.T793C						scavenged	.						74.0	80.0	78.0					17																	80789538		2203	4300	6503	SO:0001583	missense	79755	exon2			CAGGCGAGCTCCC	AK023903	CCDS11819.1	17q25.3	2008-05-02				ENSG00000141579			25843	protein-coding gene	gene with protein product		610226				16751772	Standard	NM_024702		Approved	FLJ13841, Zfp750	uc002kga.3	Q32MQ0		ENST00000269394.3:c.793T>C	17.37:g.80789538A>G	ENSP00000269394:p.Ser265Pro	Somatic	141	2	0.0141844		WXS	Illumina HiSeq	Phase_I	164	3	0.0182927	NM_024702	Q9H899	Missense_Mutation	SNP	ENST00000269394.3	37	CCDS11819.1	.	.	.	.	.	.	.	.	.	.	A	7.963	0.747384	0.15710	.	.	ENSG00000141579	ENST00000269394	T	0.15372	2.43	5.34	-10.7	0.00240	.	0.864820	0.10068	N	0.720061	T	0.10294	0.0252	L	0.55481	1.735	0.09310	N	0.999998	B	0.11235	0.004	B	0.11329	0.006	T	0.10941	-1.0608	9	.	.	.	-0.0571	3.6201	0.08092	0.1851:0.3862:0.3201:0.1085	.	265	Q32MQ0	ZN750_HUMAN	P	265	ENSP00000269394:S265P	.	S	-	1	0	ZNF750	78382827	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-0.687000	0.05156	-3.177000	0.00223	-0.250000	0.11733	TCG	.	.	none		0.612	ZNF750-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439074.2	NM_024702	
MUC4	4585	hgsc.bcm.edu	37	3	195505858	195505858	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:195505858G>A	ENST00000463781.3	-	2	13052	c.12593C>T	c.(12592-12594)aCt>aTt	p.T4198I	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T4198I|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGCTGAGGAAGTGTCGGTGAC	0.602																																					p.T4198I		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-1,3	MUC4	1505	3	0			c.C12593T						scavenged	.						19.0	15.0	16.0					3																	195505858		689	1576	2265	SO:0001583	missense	4585	exon2			GAGGAAGTGTCGG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12593C>T	3.37:g.195505858G>A	ENSP00000417498:p.Thr4198Ile	Somatic	145	2	0.0137931		WXS	Illumina HiSeq	Phase_I	138	7	0.0507246	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	4.623	0.115726	0.08831	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.35605	1.38;1.3	.	.	.	.	.	.	.	.	T	0.19485	0.0468	N	0.14661	0.345	0.21105	N	0.999787	P	0.44090	0.826	B	0.40782	0.34	T	0.09975	-1.0650	7	.	.	.	.	6.6097	0.22745	2.0E-4:0.0:0.9998:0.0	.	4070	E7ESK3	.	I	4198	ENSP00000417498:T4198I;ENSP00000420243:T4198I	.	T	-	2	0	MUC4	196990637	0.000000	0.05858	0.017000	0.16124	0.032000	0.12392	0.289000	0.18957	0.452000	0.26830	0.074000	0.15403	ACT	.	.	none		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
HLA-C	3107	hgsc.bcm.edu	37	6	31238853	31238853	+	Missense_Mutation	SNP	C	C	T	rs17849598		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr6:31238853C>T	ENST00000376228.5	-	3	630	c.616G>A	c.(616-618)Gca>Aca	p.A206T	HLA-C_ENST00000383329.3_Missense_Mutation_p.A206T	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	206	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						CTGGTACCTGCGCGCTGCAGC	0.647																																					p.A206T		Atlas-SNP	.											HLA-C_ENST00000383329,NS,carcinoma,0,2	HLA-C	92	2	0			c.G616A						scavenged	.						47.0	42.0	44.0					6																	31238853		2202	4300	6502	SO:0001583	missense	3107	exon3			TACCTGCGCGCTG	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.616G>A	6.37:g.31238853C>T	ENSP00000365402:p.Ala206Thr	Somatic	220	4	0.0181818		WXS	Illumina HiSeq	Phase_I	160	7	0.04375	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	9.192|9.192	1.026185|1.026185	0.19512|0.19512	.|.	.|.	ENSG00000204525|ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307|ENST00000415537	T;T|T	0.00695|0.00235	5.84;5.83|8.48	2.55|2.55	-4.93|-4.93	0.03066|0.03066	MHC class I-like antigen recognition (1);|.	0.959209|.	0.08469|.	N|.	0.941313|.	T|T	0.00039|0.00039	0.0001|0.0001	N|N	0.25060|0.25060	0.705|0.705	0.21290|0.21290	N|N	0.999739|0.999739	B;B;B;B|.	0.21905|.	0.062;0.002;0.008;0.004|.	B;B;B;B|.	0.18263|.	0.021;0.005;0.005;0.007|.	T|T	0.18555|0.18555	-1.0333|-1.0333	10|7	0.30078|0.87932	T|D	0.28|0	.|.	6.1502|6.1502	0.20308|0.20308	0.1486:0.2084:0.0:0.643|0.1486:0.2084:0.0:0.643	rs17849598;rs17850340|rs17849598;rs17850340	206;206;206;206|.	A2AEA4;A6H578;A2AEA2;P10321|.	.;.;.;1C07_HUMAN|.	T|H	206;206;206;243|205	ENSP00000365402:A206T;ENSP00000372819:A206T|ENSP00000400410:R205H	ENSP00000365402:A206T|ENSP00000400410:R205H	A|R	-|-	1|2	0|0	HLA-C|HLA-C	31346832|31346832	0.000000|0.000000	0.05858|0.05858	0.261000|0.261000	0.24466|0.24466	0.005000|0.005000	0.04900|0.04900	-0.679000|-0.679000	0.05203|0.05203	-1.431000|-1.431000	0.01982|0.01982	-0.704000|-0.704000	0.03662|0.03662	GCA|CGC	.	.	weak		0.647	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
PAK2	5062	hgsc.bcm.edu	37	3	196534708	196534708	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:196534708T>C	ENST00000327134.3	+	7	954	c.632T>C	c.(631-633)gTt>gCt	p.V211A		NM_002577.4	NP_002568.2	Q13177	PAK2_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 2	211					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis (GO:2001271)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-serine phosphorylation (GO:0018105)|phosphorylation (GO:0016310)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of defense response to virus by virus (GO:0050690)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activator activity (GO:0030296)	p.V211G(1)		breast(1)|cervix(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)	12	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.07e-23)|all cancers(36;6.38e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00405)		GATTCACATGTTGATGGTGCT	0.373																																					p.V211A		Atlas-SNP	.											PAK2,NS,carcinoma,0,1	PAK2	113	1	1	Substitution - Missense(1)	lung(1)	c.T632C						scavenged	.						122.0	115.0	117.0					3																	196534708		2203	4300	6503	SO:0001583	missense	5062	exon7			CACATGTTGATGG	U24153	CCDS3321.1	3q29	2008-06-17	2008-06-17			ENSG00000180370	2.7.11.1		8591	protein-coding gene	gene with protein product	"""S6/H4 kinase"""	605022	"""p21 (CDKN1A)-activated kinase 2"""			7744004, 7618083	Standard	NM_002577		Approved	PAK65, PAKgamma	uc003fwy.4	Q13177		ENST00000327134.3:c.632T>C	3.37:g.196534708T>C	ENSP00000314067:p.Val211Ala	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	188	2	0.0106383	NM_002577	Q13154|Q6ISC3	Missense_Mutation	SNP	ENST00000327134.3	37	CCDS3321.1	.	.	.	.	.	.	.	.	.	.	T	0.015	-1.547244	0.00926	.	.	ENSG00000180370	ENST00000327134	T	0.67171	-0.25	5.62	4.46	0.54185	.	0.319855	0.34133	N	0.004223	T	0.41766	0.1173	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.33163	-0.9879	10	0.02654	T	1	.	5.6673	0.17702	0.0:0.1522:0.1442:0.7037	.	211	Q13177	PAK2_HUMAN	A	211	ENSP00000314067:V211A	ENSP00000314067:V211A	V	+	2	0	PAK2	198019105	0.976000	0.34144	0.087000	0.20705	0.121000	0.20230	1.491000	0.35583	0.970000	0.38263	0.460000	0.39030	GTT	.	.	none		0.373	PAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340548.1	NM_002577	
GRAMD3	65983	hgsc.bcm.edu	37	5	125813449	125813449	+	Silent	SNP	C	C	T	rs375006587		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:125813449C>T	ENST00000285689.3	+	6	1013	c.552C>T	c.(550-552)aaC>aaT	p.N184N	GRAMD3_ENST00000511134.1_Silent_p.N168N|GRAMD3_ENST00000502348.1_Silent_p.N75N|GRAMD3_ENST00000543198.1_Silent_p.N161N|RP11-517I3.1_ENST00000515808.1_RNA|GRAMD3_ENST00000542322.1_Silent_p.N192N|GRAMD3_ENST00000515200.1_Silent_p.N161N|GRAMD3_ENST00000513040.1_Silent_p.N199N|RP11-517I3.1_ENST00000512500.1_RNA|GRAMD3_ENST00000544396.1_Silent_p.N80N	NM_023927.2	NP_076416.2	Q96HH9	GRAM3_HUMAN	GRAM domain containing 3	184						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)		TAGTGCCAAACGCCCTGATCA	0.488																																					p.N199N		Atlas-SNP	.											.	GRAMD3	30	.	0			c.C597T						PASS	.	C	,,,,	1,4405	2.1+/-5.4	0,1,2202	114.0	116.0	115.0		597,240,576,504,552	-0.1	1.0	5		115	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GRAMD3	NM_001146319.1,NM_001146320.1,NM_001146321.1,NM_001146322.1,NM_023927.2	,,,,	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	,,,,	199/448,80/329,192/441,168/417,184/433	125813449	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	65983	exon6			GCCAAACGCCCTG	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.552C>T	5.37:g.125813449C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	146	35	0.239726	NM_001146319	B7Z1F2|B7Z3R1|B7Z6D8|B7Z8T2|D3DSZ3|Q9H753	Silent	SNP	ENST00000285689.3	37	CCDS4136.1																																																																																			.	.	weak		0.488	GRAMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250922.2	NM_023927	
CACNA1F	778	hgsc.bcm.edu	37	X	49061779	49061779	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:49061779C>T	ENST00000376265.2	-	48	5813	c.5752G>A	c.(5752-5754)Gtg>Atg	p.V1918M	SYP-AS1_ENST00000433499.1_RNA|CACNA1F_ENST00000376251.1_Missense_Mutation_p.V1853M|AF196779.1_ENST00000583131.1_RNA|CACNA1F_ENST00000323022.5_Missense_Mutation_p.V1907M	NM_005183.2	NP_005174.2	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type, alpha 1F subunit	1918					axonogenesis (GO:0007409)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|dendrite morphogenesis (GO:0048813)|detection of light stimulus involved in visual perception (GO:0050908)|membrane depolarization during action potential (GO:0086010)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|perikaryon (GO:0043204)|photoreceptor outer segment (GO:0001750)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			autonomic_ganglia(1)|breast(8)|central_nervous_system(3)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(4)|urinary_tract(1)	85					Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	GCCAGGGCCACGAAACGTGGG	0.597																																					p.V1918M		Atlas-SNP	.											.	CACNA1F	218	.	0			c.G5752A						PASS	.						65.0	39.0	47.0					X																	49061779		2203	4300	6503	SO:0001583	missense	778	exon48			GGGCCACGAAACG	AA019975	CCDS35253.1, CCDS59166.1, CCDS59167.1	Xp11.23	2013-01-23	2007-02-16		ENSG00000102001	ENSG00000102001		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1393	protein-coding gene	gene with protein product		300110	"""Aland island eye disease (Forsius-Eriksson ocular albinism, ocular albinism type 2)"""	CSNB2, AIED		9344658, 9662400, 16382099, 12111638, 17525176	Standard	NM_005183		Approved	Cav1.4, JM8, JMC8, CSNBX2, CORDX3, CSNB2A, OA2	uc010nip.3	O60840	OTTHUMG00000022703	ENST00000376265.2:c.5752G>A	X.37:g.49061779C>T	ENSP00000365441:p.Val1918Met	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	137	65	0.474453	NM_005183	A6NI29|F5CIQ9|O43901|O95226|Q9UHB1	Missense_Mutation	SNP	ENST00000376265.2	37	CCDS35253.1	.	.	.	.	.	.	.	.	.	.	C	17.08	3.297889	0.60086	.	.	ENSG00000102001	ENST00000376251;ENST00000323022;ENST00000376265	T;T;T	0.60548	0.18;0.18;0.18	4.95	4.02	0.46733	.	0.000000	0.64402	D	0.000001	T	0.69052	0.3068	M	0.74467	2.265	0.48452	D	0.999656	D;D	0.76494	0.999;0.997	P;P	0.57057	0.812;0.654	T	0.74349	-0.3694	10	0.87932	D	0	.	12.3113	0.54929	0.1697:0.8303:0.0:0.0	.	1907;1918	F5CIQ9;O60840	.;CAC1F_HUMAN	M	1853;1907;1918	ENSP00000365427:V1853M;ENSP00000321618:V1907M;ENSP00000365441:V1918M	ENSP00000321618:V1907M	V	-	1	0	CACNA1F	48948723	0.999000	0.42202	0.915000	0.36163	0.519000	0.34347	3.722000	0.54948	2.178000	0.69098	0.529000	0.55759	GTG	.	.	none		0.597	CACNA1F-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358157.1	NM_005183	
FOXA3	3171	hgsc.bcm.edu	37	19	46375713	46375713	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:46375713C>T	ENST00000302177.2	+	2	647	c.450C>T	c.(448-450)ctC>ctT	p.L150L		NM_004497.2	NP_004488.2	P55318	FOXA3_HUMAN	forkhead box A3	150					cell differentiation (GO:0030154)|cellular glucose homeostasis (GO:0001678)|cellular response to starvation (GO:0009267)|chromatin modification (GO:0016568)|endocrine pancreas development (GO:0031018)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(2)|large_intestine(2)|lung(4)|ovary(2)|pancreas(1)|prostate(1)	13		Ovarian(192;0.0308)|all_neural(266;0.0476)		OV - Ovarian serous cystadenocarcinoma(262;0.00453)|GBM - Glioblastoma multiforme(486;0.0518)|Epithelial(262;0.236)		TCATGGACCTCTTCCCTTACT	0.552																																					p.L150L		Atlas-SNP	.											FOXA3,NS,carcinoma,+2,1	FOXA3	19	1	0			c.C450T						scavenged	.						114.0	109.0	111.0					19																	46375713		2203	4300	6503	SO:0001819	synonymous_variant	3171	exon2			GGACCTCTTCCCT	L12141	CCDS12677.1	19q13.32	2014-09-11		2002-09-20	ENSG00000170608	ENSG00000170608		"""Forkhead boxes"""	5023	protein-coding gene	gene with protein product		602295	"""hepatocyte nuclear factor 3, gamma"""	HNF3G		9119385	Standard	NM_004497		Approved		uc002pdr.3	P55318	OTTHUMG00000182484	ENST00000302177.2:c.450C>T	19.37:g.46375713C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	141	3	0.0212766	NM_004497	A9LYI5|Q53F16|Q9UMW9	Silent	SNP	ENST00000302177.2	37	CCDS12677.1																																																																																			.	.	none		0.552	FOXA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461682.1		
PDGFB	5155	hgsc.bcm.edu	37	22	39627798	39627798	+	Silent	SNP	G	G	A	rs147036196		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr22:39627798G>A	ENST00000331163.6	-	4	1072	c.285C>T	c.(283-285)gcC>gcT	p.A95A	PDGFB_ENST00000381551.4_Silent_p.A80A	NM_002608.2	NP_002599.1	P01127	PDGFB_HUMAN	platelet-derived growth factor beta polypeptide	95					actin cytoskeleton organization (GO:0030036)|activation of protein kinase activity (GO:0032147)|activation of protein kinase B activity (GO:0032148)|blood coagulation (GO:0007596)|blood vessel morphogenesis (GO:0048514)|branching involved in salivary gland morphogenesis (GO:0060445)|cell chemotaxis (GO:0060326)|cell growth (GO:0016049)|cell projection assembly (GO:0030031)|cellular response to growth factor stimulus (GO:0071363)|cellular response to mycophenolic acid (GO:0071506)|DNA replication (GO:0006260)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|extracellular matrix organization (GO:0030198)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|metanephric glomerular endothelium development (GO:0072264)|metanephric glomerular mesangial cell development (GO:0072255)|metanephric glomerular mesangial cell proliferation involved in metanephros development (GO:0072262)|monocyte chemotaxis (GO:0002548)|negative regulation of cell migration (GO:0030336)|negative regulation of phosphatidylinositol biosynthetic process (GO:0010512)|negative regulation of platelet activation (GO:0010544)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|paracrine signaling (GO:0038001)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of calcium ion import (GO:0090280)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemotaxis (GO:0050921)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of DNA replication (GO:0045740)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of glomerular filtration (GO:0003104)|positive regulation of glomerular mesangial cell proliferation (GO:0072126)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of metanephric mesenchymal cell migration (GO:2000591)|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 peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein tyrosine kinase activity (GO:0061098)|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)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|response to wounding (GO:0009611)|substrate-dependent cell migration (GO:0006929)|transforming growth factor beta receptor signaling pathway (GO:0007179)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi membrane (GO:0000139)|platelet alpha granule lumen (GO:0031093)	chemoattractant activity (GO:0042056)|collagen binding (GO:0005518)|growth factor activity (GO:0008083)|identical protein binding (GO:0042802)|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)|superoxide-generating NADPH oxidase activator activity (GO:0016176)		COL1A1/PDGFB(429)	central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(2)	7	Melanoma(58;0.04)					TCTTGCACTCGGCGATCATGG	0.647			T	COL1A1	DFSP								G|||	1	0.000199681	0.0008	0.0	5008	,	,		14561	0.0		0.0	False		,,,				2504	0.0				p.A95A		Atlas-SNP	.		Dom	yes		22	22q12.3-q13.1	5155	platelet-derived growth factor beta polypeptide (simian sarcoma viral (v-sis) oncogene homolog)		M	.	PDGFB	91	.	0			c.C285T						PASS	.	G	,	5,4401	11.4+/-27.6	0,5,2198	46.0	39.0	41.0		285,240	-4.0	1.0	22	dbSNP_134	41	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	PDGFB	NM_002608.2,NM_033016.2	,	0,5,6498	AA,AG,GG		0.0,0.1135,0.0384	,	95/242,80/227	39627798	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	5155	exon4			GCACTCGGCGATC		CCDS13987.1, CCDS33650.1	22q13.1	2012-10-02	2011-05-19		ENSG00000100311	ENSG00000100311			8800	protein-coding gene	gene with protein product	"""oncogene SIS"", ""becaplermin"""	190040	"""platelet-derived growth factor beta polypeptide (simian sarcoma viral (v-sis) oncogene homolog)"""	SIS		2991848, 1661670	Standard	NM_002608		Approved	SSV	uc003axf.3	P01127	OTTHUMG00000151029	ENST00000331163.6:c.285C>T	22.37:g.39627798G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	61	31	0.508197	NM_002608	G3XAG8|P78431|Q15354|Q6FHE7|Q9UF23	Silent	SNP	ENST00000331163.6	37	CCDS13987.1																																																																																			G|1.000;A|0.000	0.000	weak		0.647	PDGFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321043.1	NM_002608	
SLC35F1	222553	hgsc.bcm.edu	37	6	118596682	118596682	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr6:118596682C>T	ENST00000360388.4	+	5	899	c.698C>T	c.(697-699)tCt>tTt	p.S233F		NM_001029858.3	NP_001025029.2	Q5T1Q4	S35F1_HUMAN	solute carrier family 35, member F1	233					transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(3)|kidney(1)|large_intestine(7)|lung(21)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(226;0.217)		TATGGTATTTCTAACGTCTGG	0.448																																					p.S233F		Atlas-SNP	.											SLC35F1,NS,carcinoma,0,1	SLC35F1	65	1	0			c.C698T						scavenged	.						107.0	107.0	107.0					6																	118596682		2203	4300	6503	SO:0001583	missense	222553	exon5			GTATTTCTAACGT	BC028615	CCDS34524.1	6q22.31	2013-05-22			ENSG00000196376	ENSG00000196376		"""Solute carriers"""	21483	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 169"""	C6orf169			Standard	NM_001029858		Approved	dJ230I3.1	uc003pxx.4	Q5T1Q4	OTTHUMG00000015460	ENST00000360388.4:c.698C>T	6.37:g.118596682C>T	ENSP00000353557:p.Ser233Phe	Somatic	134	1	0.00746269		WXS	Illumina HiSeq	Phase_I	133	2	0.0150376	NM_001029858	E1P564|Q1RMG1|Q4G0U9|Q4G167|Q6N007	Missense_Mutation	SNP	ENST00000360388.4	37	CCDS34524.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.882251	0.91740	.	.	ENSG00000196376	ENST00000360388	.	.	.	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	T	0.81541	0.4844	M	0.84433	2.695	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.79827	-0.1639	9	0.39692	T	0.17	.	19.2178	0.93785	0.0:1.0:0.0:0.0	.	233	Q5T1Q4	S35F1_HUMAN	F	233	.	ENSP00000353557:S233F	S	+	2	0	SLC35F1	118703375	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.239000	0.78182	2.836000	0.97738	0.655000	0.94253	TCT	.	.	none		0.448	SLC35F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041991.2	XM_167044	
APOBEC3D	140564	hgsc.bcm.edu	37	22	39421654	39421654	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr22:39421654C>T	ENST00000216099.8	+	4	990	c.583C>T	c.(583-585)Cgc>Tgc	p.R195C	APOBEC3D_ENST00000381568.4_Missense_Mutation_p.R195C|APOBEC3D_ENST00000427494.2_Intron	NM_152426.3	NP_689639.2	Q96AK3	ABC3D_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3D	195					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)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines (GO:0016814)|zinc ion binding (GO:0008270)	p.R264C(1)|p.R195C(1)		breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)	11	Melanoma(58;0.04)					ATCCCTGCACCGCACGCTAAA	0.532																																					p.R195C		Atlas-SNP	.											APOBEC3D_ENST00000381568,NS,carcinoma,0,4	APOBEC3D	61	4	2	Substitution - Missense(2)	endometrium(2)	c.C583T						scavenged	.						290.0	251.0	264.0					22																	39421654		2203	4300	6503	SO:0001583	missense	140564	exon4			CTGCACCGCACGC	BF832090	CCDS46709.1	22q13.1	2012-10-19	2008-05-01		ENSG00000243811	ENSG00000243811		"""Apolipoprotein B mRNA editing enzymes"""	17354	protein-coding gene	gene with protein product		609900	"""apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3D (putative)"", ""apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3E pseudogene"""	APOBEC3E		11863358	Standard	NM_152426		Approved	ARP6, APOBEC3DE	uc003awt.4	Q96AK3	OTTHUMG00000151084	ENST00000216099.8:c.583C>T	22.37:g.39421654C>T	ENSP00000216099:p.Arg195Cys	Somatic	300	0	0		WXS	Illumina HiSeq	Phase_I	298	5	0.0167785	NM_152426	Q5JZ91|Q7Z2N2|Q7Z2N5|Q7Z2N6	Missense_Mutation	SNP	ENST00000216099.8	37	CCDS46709.1	.	.	.	.	.	.	.	.	.	.	.	1.037	-0.679932	0.03353	.	.	ENSG00000243811	ENST00000381568;ENST00000216099	T;T	0.66280	-0.2;-0.2	2.44	-4.88	0.03113	.	.	.	.	.	T	0.36358	0.0964	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.06698	-1.0812	9	0.40728	T	0.16	.	0.797	0.01068	0.1922:0.128:0.2869:0.3929	.	195	Q96AK3	ABC3D_HUMAN	C	195	ENSP00000370980:R195C;ENSP00000216099:R195C	ENSP00000216099:R195C	R	+	1	0	APOBEC3D	37751600	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.246000	0.00138	-3.006000	0.00274	-1.827000	0.00596	CGC	.	.	none		0.532	APOBEC3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321232.2	NM_152426	
MUC4	4585	hgsc.bcm.edu	37	3	195505867	195505867	+	Missense_Mutation	SNP	A	A	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:195505867A>T	ENST00000463781.3	-	2	13043	c.12584T>A	c.(12583-12585)gTc>gAc	p.V4195D	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.V4195D|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.V4195D(6)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGTGTCGGTGACAGGAAGAGG	0.607																																					p.V4195D		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,8	MUC4	1505	8	6	Substitution - Missense(6)	endometrium(3)|kidney(3)	c.T12584A						scavenged	.																																			SO:0001583	missense	4585	exon2			TCGGTGACAGGAA	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12584T>A	3.37:g.195505867A>T	ENSP00000417498:p.Val4195Asp	Somatic	125	1	0.008		WXS	Illumina HiSeq	Phase_I	124	2	0.016129	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	a	0.384	-0.927152	0.02377	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.36157	1.42;1.27	.	.	.	.	.	.	.	.	T	0.34513	0.0900	N	0.19112	0.55	0.29126	N	0.879938	D	0.67145	0.996	D	0.69479	0.964	T	0.27938	-1.0059	7	.	.	.	.	4.4413	0.11575	0.3374:0.0:0.6626:0.0	.	4067	E7ESK3	.	D	4195	ENSP00000417498:V4195D;ENSP00000420243:V4195D	.	V	-	2	0	MUC4	196990646	0.000000	0.05858	0.033000	0.17914	0.055000	0.15305	-2.347000	0.01095	-0.475000	0.06852	0.063000	0.15292	GTC	.	.	none		0.607	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
BIRC8	112401	hgsc.bcm.edu	37	19	53793269	53793269	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:53793269C>T	ENST00000426466.1	-	1	1606	c.359G>A	c.(358-360)cGa>cAa	p.R120Q		NM_033341.4	NP_203127.3	Q96P09	BIRC8_HUMAN	baculoviral IAP repeat containing 8	120					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)	p.R120Q(1)		NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(10)|urinary_tract(1)	19				GBM - Glioblastoma multiforme(134;0.00304)		AAATCCCATTCGTATAGCTTC	0.383																																					p.R120Q		Atlas-SNP	.											BIRC8,colon,carcinoma,0,9	BIRC8	54	9	1	Substitution - Missense(1)	NS(1)	c.G359A						scavenged	.						189.0	185.0	187.0					19																	53793269		2203	4300	6503	SO:0001583	missense	112401	exon1			CCCATTCGTATAG	AF164682	CCDS12863.1	19q13.3-q13.4	2011-01-25	2011-01-25			ENSG00000163098		"""Baculoviral IAP repeat containing"""	14878	protein-coding gene	gene with protein product	"""IAP-like protein 2"", ""inhibitor of apoptosis-like protein 2"""		"""baculoviral IAP repeat-containing 8"""			11390657	Standard	NM_033341		Approved	ILP-2, hILP2	uc002qbk.3	Q96P09		ENST00000426466.1:c.359G>A	19.37:g.53793269C>T	ENSP00000412957:p.Arg120Gln	Somatic	237	1	0.00421941		WXS	Illumina HiSeq	Phase_I	276	3	0.0108696	NM_033341	Q6IPY1|Q96RW5	Missense_Mutation	SNP	ENST00000426466.1	37	CCDS12863.1	.	.	.	.	.	.	.	.	.	.	C	0.204	-1.042575	0.01997	.	.	ENSG00000163098	ENST00000426466	T	0.33654	1.4	0.502	-1.0	0.10196	.	.	.	.	.	T	0.15955	0.0384	L	0.34521	1.04	0.09310	N	1	B	0.30511	0.282	B	0.14578	0.011	T	0.32025	-0.9922	9	0.06625	T	0.88	-16.4135	1.9268	0.03319	0.2682:0.25:0.0:0.4818	.	120	Q96P09	BIRC8_HUMAN	Q	120	ENSP00000412957:R120Q	ENSP00000412957:R120Q	R	-	2	0	BIRC8	58485081	0.639000	0.27234	0.000000	0.03702	0.001000	0.01503	0.452000	0.21795	-1.280000	0.02402	-0.851000	0.03033	CGA	.	.	none		0.383	BIRC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464357.1	NM_033341	
OR52I2	143502	hgsc.bcm.edu	37	11	4608393	4608393	+	Silent	SNP	A	A	G	rs56002758	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:4608393A>G	ENST00000312614.4	+	1	373	c.351A>G	c.(349-351)tcA>tcG	p.S117S		NM_001005170.2	NP_001005170.1	Q8NH67	O52I2_HUMAN	olfactory receptor, family 52, subfamily I, member 2	117						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|pancreas(1)|skin(1)	19		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;8.45e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		TCTTCTGCTCAGGAGACAGCT	0.512													A|||	138	0.0275559	0.0915	0.0029	5008	,	,		24334	0.0109		0.0	False		,,,				2504	0.0041				p.S117S		Atlas-SNP	.											OR52I2,NS,carcinoma,0,1	OR52I2	50	1	0			c.A351G						scavenged	.						202.0	191.0	195.0					11																	4608393		2201	4298	6499	SO:0001819	synonymous_variant	143502	exon1			CTGCTCAGGAGAC	BK004264	CCDS31355.1	11p15.4	2012-08-09			ENSG00000226288	ENSG00000226288		"""GPCR / Class A : Olfactory receptors"""	15221	protein-coding gene	gene with protein product							Standard	NM_001005170		Approved		uc010qyh.2	Q8NH67	OTTHUMG00000165721	ENST00000312614.4:c.351A>G	11.37:g.4608393A>G		Somatic	384	13	0.0338542		WXS	Illumina HiSeq	Phase_I	363	16	0.0440771	NM_001005170	B2RNJ5|B9EKV8|Q6IFJ8	Silent	SNP	ENST00000312614.4	37	CCDS31355.1																																																																																			A|0.972;G|0.028	0.028	strong		0.512	OR52I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385946.1	NM_001005170	
RYR3	6263	hgsc.bcm.edu	37	15	34064327	34064327	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr15:34064327T>C	ENST00000389232.4	+	63	9093	c.9023T>C	c.(9022-9024)gTc>gCc	p.V3008A	RYR3_ENST00000415757.3_Missense_Mutation_p.V3008A	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	3008					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)		TTTGAGCACGTCACTCAGCAT	0.488																																					p.V3008A		Atlas-SNP	.											RYR3,NS,carcinoma,+1,1	RYR3	760	1	0			c.T9023C						scavenged	.						82.0	76.0	78.0					15																	34064327		1993	4177	6170	SO:0001583	missense	6263	exon63			AGCACGTCACTCA		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.9023T>C	15.37:g.34064327T>C	ENSP00000373884:p.Val3008Ala	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	190	2	0.0105263	NM_001243996	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	T	18.46	3.628276	0.67015	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	D;D	0.96885	-4.16;-4.16	5.65	5.65	0.86999	.	0.367090	0.27172	N	0.020595	D	0.92645	0.7663	N	0.19112	0.55	0.31972	N	0.607035	B;B	0.19817	0.008;0.039	B;B	0.22601	0.006;0.04	D	0.91591	0.5287	10	0.62326	D	0.03	.	16.0399	0.80667	0.0:0.0:0.0:1.0	.	3008;3008	Q15413-2;Q15413	.;RYR3_HUMAN	A	3008	ENSP00000373884:V3008A;ENSP00000399610:V3008A	ENSP00000354735:V3008A	V	+	2	0	RYR3	31851619	1.000000	0.71417	0.231000	0.23993	0.993000	0.82548	7.825000	0.86693	2.371000	0.80710	0.533000	0.62120	GTC	.	.	none		0.488	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
MAP3K13	9175	hgsc.bcm.edu	37	3	185190894	185190894	+	Missense_Mutation	SNP	G	G	A	rs555365583		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:185190894G>A	ENST00000265026.3	+	11	2109	c.1775G>A	c.(1774-1776)cGa>cAa	p.R592Q	MAP3K13_ENST00000446828.1_Missense_Mutation_p.R385Q|MAP3K13_ENST00000424227.1_Missense_Mutation_p.R592Q|MAP3K13_ENST00000443863.1_Missense_Mutation_p.R448Q|MAP3K13_ENST00000535426.1_Missense_Mutation_p.R448Q	NM_004721.4	NP_004712.1			mitogen-activated protein kinase kinase kinase 13											NS(1)|biliary_tract(1)|breast(3)|endometrium(3)|kidney(1)|large_intestine(13)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54	all_cancers(143;7.21e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)			CGCCACCGCCGAGGGAATAGC	0.537													G|||	1	0.000199681	0.0	0.0	5008	,	,		17515	0.0		0.001	False		,,,				2504	0.0				p.R592Q		Atlas-SNP	.											MAP3K13_ENST00000424227,colon,carcinoma,+1,4	MAP3K13	209	4	0			c.G1775A						scavenged	.						220.0	243.0	235.0					3																	185190894		2203	4300	6503	SO:0001583	missense	9175	exon11			ACCGCCGAGGGAA	BC031677	CCDS3270.1, CCDS56298.1	3q27	2011-06-09			ENSG00000073803	ENSG00000073803		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6852	protein-coding gene	gene with protein product	"""leucine zipper-bearing kinase"""	604915				9353328	Standard	NM_004721		Approved	LZK, MEKK13	uc003fpi.3	O43283	OTTHUMG00000156673	ENST00000265026.3:c.1775G>A	3.37:g.185190894G>A	ENSP00000265026:p.Arg592Gln	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	162	3	0.0185185	NM_004721		Missense_Mutation	SNP	ENST00000265026.3	37	CCDS3270.1	.	.	.	.	.	.	.	.	.	.	G	34	5.392422	0.96009	.	.	ENSG00000073803	ENST00000446828;ENST00000424227;ENST00000443863;ENST00000535426;ENST00000265026	T;T;T;T;T	0.38401	1.14;1.14;1.14;1.14;1.14	5.47	5.47	0.80525	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.50990	0.1648	L	0.29908	0.895	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.996;0.992	T	0.50717	-0.8795	10	0.52906	T	0.07	.	19.3275	0.94268	0.0:0.0:1.0:0.0	.	448;385;592	O43283-4;O43283-5;O43283	.;.;M3K13_HUMAN	Q	385;592;448;448;592	ENSP00000411483:R385Q;ENSP00000399910:R592Q;ENSP00000409325:R448Q;ENSP00000439257:R448Q;ENSP00000265026:R592Q	ENSP00000265026:R592Q	R	+	2	0	MAP3K13	186673588	1.000000	0.71417	0.991000	0.47740	0.911000	0.54048	9.559000	0.98135	2.552000	0.86080	0.561000	0.74099	CGA	.	.	none		0.537	MAP3K13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345268.1	NM_004721	
ADAMTSL1	92949	hgsc.bcm.edu	37	9	18889701	18889701	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr9:18889701C>T	ENST00000380548.4	+	25	4937	c.4598C>T	c.(4597-4599)cCt>cTt	p.P1533L	ADAMTSL1_ENST00000380545.5_Missense_Mutation_p.P234L	NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1	1533						proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(2)|lung(17)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(50;1.29e-17)		AAGGTTCGCCCTGCGGTGCAG	0.667																																					p.P1533L		Atlas-SNP	.											ADAMTSL1_ENST00000380548,right_upper_lobe,carcinoma,+1,1	ADAMTSL1	306	1	0			c.C4598T						scavenged	.						24.0	29.0	27.0					9																	18889701		2080	4214	6294	SO:0001583	missense	92949	exon25			TTCGCCCTGCGGT	AF176313	CCDS6485.1, CCDS47954.1	9p21.3	2013-01-11			ENSG00000178031	ENSG00000178031		"""Immunoglobulin superfamily / I-set domain containing"""	14632	protein-coding gene	gene with protein product	"""punctin"""	609198	"""chromosome 9 open reading frame 94"""	C9orf94		9628581, 11805097	Standard	NM_001040272		Approved	ADAMTSR1, FLJ35283	uc003zne.4	Q8N6G6	OTTHUMG00000019604	ENST00000380548.4:c.4598C>T	9.37:g.18889701C>T	ENSP00000369921:p.Pro1533Leu	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	114	2	0.0175439	NM_001040272	A6PVN1|A8K7E1|Q496M6|Q496M8|Q5T708|Q5VZT8|Q8NAI9|Q96RW4|Q9BXY3	Missense_Mutation	SNP	ENST00000380548.4	37	CCDS47954.1	.	.	.	.	.	.	.	.	.	.	C	16.42	3.118516	0.56505	.	.	ENSG00000178031	ENST00000380548;ENST00000380545;ENST00000316239;ENST00000380541;ENST00000380538	T;T;T	0.60672	0.17;0.17;0.17	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.78786	0.4338	M	0.79805	2.47	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.91635	0.961;0.999	T	0.77991	-0.2379	10	0.46703	T	0.11	.	19.9928	0.97374	0.0:1.0:0.0:0.0	.	234;1533	Q8N6G6-6;Q8N6G6	.;ATL1_HUMAN	L	1533;234;237;237;135	ENSP00000369921:P1533L;ENSP00000369918:P234L;ENSP00000369911:P135L	ENSP00000325584:P237L	P	+	2	0	ADAMTSL1	18879701	0.999000	0.42202	0.976000	0.42696	0.071000	0.16799	5.298000	0.65710	2.745000	0.94114	0.650000	0.86243	CCT	.	.	none		0.667	ADAMTSL1-012	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401206.1		
KCNT2	343450	hgsc.bcm.edu	37	1	196342346	196342346	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:196342346C>T	ENST00000294725.9	-	14	2242	c.1327G>A	c.(1327-1329)Gcc>Acc	p.A443T	KCNT2_ENST00000498426.1_5'UTR|KCNT2_ENST00000367431.4_Missense_Mutation_p.A443T|KCNT2_ENST00000367433.5_Missense_Mutation_p.A443T|KCNT2_ENST00000609185.1_Missense_Mutation_p.A443T|KCNT2_ENST00000451324.2_Missense_Mutation_p.A54T			Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	443	RCK N-terminal.				potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(16)|lung(43)|ovary(5)|pancreas(1)|prostate(1)|skin(11)|stomach(2)|upper_aerodigestive_tract(1)	97						GCTAACATGGCGTATTTAAAC	0.289																																					p.A443T		Atlas-SNP	.											KCNT2,NS,carcinoma,+2,1	KCNT2	243	1	0			c.G1327A						scavenged	.						89.0	90.0	90.0					1																	196342346		2203	4294	6497	SO:0001583	missense	343450	exon14			ACATGGCGTATTT	BX647852, AY359444, AK127807	CCDS1384.1, CCDS72994.1, CCDS72995.1	1q31.3	2012-07-05			ENSG00000162687	ENSG00000162687		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	18866	protein-coding gene	gene with protein product	"""sodium and chloride activated ATP sensitive potassium channel"""	610044				16382103	Standard	NM_198503		Approved	KCa4.2, SLICK, SLO2.1	uc001gtd.1	Q6UVM3	OTTHUMG00000035611	ENST00000294725.9:c.1327G>A	1.37:g.196342346C>T	ENSP00000294725:p.Ala443Thr	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	187	2	0.0106952	NM_198503	Q3SY59|Q5VTN1|Q6ZMT3	Missense_Mutation	SNP	ENST00000294725.9	37	CCDS1384.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.988851	0.93106	.	.	ENSG00000162687	ENST00000367433;ENST00000367431;ENST00000535608;ENST00000451324;ENST00000294725	T;T;T;T	0.46819	0.86;0.86;0.86;0.86	5.74	5.74	0.90152	Potassium channel, calcium-activated, BK, alpha subunit (1);NAD(P)-binding domain (1);	0.000000	0.64402	D	0.000006	T	0.71821	0.3385	M	0.80982	2.52	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;0.968;1.0	D;D;P;D	0.79108	0.992;0.931;0.56;0.992	T	0.74503	-0.3644	10	0.72032	D	0.01	-12.1203	18.4944	0.90860	0.0:1.0:0.0:0.0	.	443;443;443;443	A9LNM6;Q6UVM3-2;Q6UVM3-3;Q6UVM3	.;.;.;KCNT2_HUMAN	T	443;443;264;54;443	ENSP00000356403:A443T;ENSP00000356401:A443T;ENSP00000405474:A54T;ENSP00000294725:A443T	ENSP00000294725:A443T	A	-	1	0	KCNT2	194608969	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.106000	0.77039	2.728000	0.93425	0.650000	0.86243	GCC	.	.	none		0.289	KCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086418.2	NM_198503	
HSP90B1	7184	hgsc.bcm.edu	37	12	104335448	104335448	+	Silent	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:104335448T>C	ENST00000299767.5	+	10	1454	c.1272T>C	c.(1270-1272)gaT>gaC	p.D424D		NM_003299.2	NP_003290.1	P14625	ENPL_HUMAN	heat shock protein 90kDa beta (Grp94), member 1	424					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)	ACTTCCATGATATGATGCCTA	0.408																																					p.D424D		Atlas-SNP	.											HSP90B1,NS,carcinoma,+1,1	HSP90B1	72	1	0			c.T1272C						scavenged	.						133.0	125.0	128.0					12																	104335448		2203	4300	6503	SO:0001819	synonymous_variant	7184	exon10			CCATGATATGATG	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.1272T>C	12.37:g.104335448T>C		Somatic	300	0	0		WXS	Illumina HiSeq	Phase_I	363	4	0.0110193	NM_003299	Q96A97	Silent	SNP	ENST00000299767.5	37	CCDS9094.1																																																																																			.	.	none		0.408	HSP90B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407349.1	NM_003299	
DUOX2	50506	hgsc.bcm.edu	37	15	45403769	45403769	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr15:45403769C>T	ENST00000603300.1	-	6	730	c.528G>A	c.(526-528)acG>acA	p.T176T	DUOX2_ENST00000389039.6_Silent_p.T176T|DUOXA2_ENST00000323030.5_5'Flank	NM_014080.4	NP_054799.4	Q9NRD8	DUOX2_HUMAN	dual oxidase 2	176	Peroxidase-like; mediates peroxidase activity. {ECO:0000250}.				adenohypophysis morphogenesis (GO:0048855)|bone mineralization (GO:0030282)|cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|fertilization (GO:0009566)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|inner ear development (GO:0048839)|multicellular organism growth (GO:0035264)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|response to virus (GO:0009615)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|peroxidase activity (GO:0004601)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	63		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)		CCAGCCAGCCCGTCACCTGGT	0.781																																					p.T176T		Atlas-SNP	.											.	DUOX2	137	.	0			c.G528A						PASS	.						4.0	4.0	4.0					15																	45403769		1903	3798	5701	SO:0001819	synonymous_variant	50506	exon6			CCAGCCCGTCACC	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.528G>A	15.37:g.45403769C>T		Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	7	6	0.857143	NM_014080	A8MQ13|D2XI64|Q9NR02|Q9UHF9	Silent	SNP	ENST00000603300.1	37	CCDS10117.1																																																																																			.	.	none		0.781	DUOX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_014080	
MYCBP2	23077	hgsc.bcm.edu	37	13	77657173	77657173	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr13:77657173G>A	ENST00000544440.2	-	63	10933	c.10916C>T	c.(10915-10917)gCc>gTc	p.A3639V	MYCBP2_ENST00000357337.6_Missense_Mutation_p.A3639V|MYCBP2-AS1_ENST00000422231.2_RNA|MYCBP2-AS1_ENST00000448470.2_RNA|MYCBP2-AS1_ENST00000593933.1_RNA|MYCBP2_ENST00000407578.2_Missense_Mutation_p.A3677V|MYCBP2-AS2_ENST00000428716.2_RNA|MYCBP2-AS1_ENST00000450627.2_RNA					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)		TTACCTCAGGGCCATTTGCTG	0.423																																					p.A3677V		Atlas-SNP	.											.	MYCBP2	1029	.	0			c.C11030T						PASS	.						130.0	126.0	127.0					13																	77657173		2203	4300	6503	SO:0001583	missense	23077	exon63			CTCAGGGCCATTT	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.10916C>T	13.37:g.77657173G>A	ENSP00000444596:p.Ala3639Val	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	141	56	0.397163	NM_015057		Missense_Mutation	SNP	ENST00000544440.2	37		.	.	.	.	.	.	.	.	.	.	G	27.0	4.795732	0.90453	.	.	ENSG00000005810	ENST00000357337;ENST00000407578;ENST00000544440	T;T;T	0.69806	-0.43;-0.43;-0.43	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	T	0.79281	0.4419	L	0.55213	1.73	0.80722	D	1	D	0.63880	0.993	D	0.68192	0.956	T	0.80879	-0.1185	10	0.87932	D	0	.	19.165	0.93553	0.0:0.0:1.0:0.0	.	3639	O75592	MYCB2_HUMAN	V	3639;3677;3639	ENSP00000349892:A3639V;ENSP00000384288:A3677V;ENSP00000444596:A3639V	ENSP00000349892:A3639V	A	-	2	0	MYCBP2	76555174	1.000000	0.71417	1.000000	0.80357	0.537000	0.34900	9.869000	0.99810	2.504000	0.84457	0.650000	0.86243	GCC	.	.	none		0.423	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057	
SPATA31A6	389730	hgsc.bcm.edu	37	9	43626815	43626815	+	Silent	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr9:43626815G>A	ENST00000332857.6	-	4	1900	c.1872C>T	c.(1870-1872)gaC>gaT	p.D624D	SPATA31A6_ENST00000496386.1_5'Flank	NM_001145196.1	NP_001138668.1	Q5VVP1	S31A6_HUMAN	SPATA31 subfamily A, member 6	624					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CTGGTGATTCGTCCCGAAGCT	0.547																																					p.D624D		Atlas-SNP	.											FAM75A6,NS,carcinoma,0,3	.	.	3	0			c.C1872T						scavenged	.																																			SO:0001819	synonymous_variant	389730	exon4			TGATTCGTCCCGA		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.1872C>T	9.37:g.43626815G>A		Somatic	46	1	0.0217391		WXS	Illumina HiSeq	Phase_I	41	4	0.097561	NM_001145196		Silent	SNP	ENST00000332857.6	37	CCDS47973.1																																																																																			A|1.000;|0.000	1.000	weak		0.547	SPATA31A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036987.1	NM_001145196	
DCP1A	55802	hgsc.bcm.edu	37	3	53353455	53353455	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:53353455C>T	ENST00000607628.1	-	4	459	c.350G>A	c.(349-351)cGc>cAc	p.R117H	DCP1A_ENST00000606822.1_Missense_Mutation_p.R117H|DCP1A_ENST00000480258.1_5'UTR|DCP1A_ENST00000294241.6_Missense_Mutation_p.R117H	NM_018403.5	NP_060873.4	Q9NPI6	DCP1A_HUMAN	decapping mRNA 1A	117					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	hydrolase activity (GO:0016787)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	10				BRCA - Breast invasive adenocarcinoma(193;0.000164)|KIRC - Kidney renal clear cell carcinoma(197;0.00525)|Kidney(197;0.00579)|OV - Ovarian serous cystadenocarcinoma(275;0.0647)		TTTTGCTATGCGGTGACAGTC	0.333																																					p.R117H		Atlas-SNP	.											DCP1A,colon,carcinoma,-1,2	DCP1A	30	2	0			c.G350A						scavenged	.						66.0	58.0	60.0					3																	53353455		1818	4072	5890	SO:0001583	missense	55802	exon4			GCTATGCGGTGAC	AJ275986	CCDS74946.1	3p21.1	2013-05-02	2013-05-02		ENSG00000162290	ENSG00000272886			18714	protein-coding gene	gene with protein product		607010	"""DCP1 decapping enzyme homolog A (S. cerevisiae)"""				Standard	XM_005278360		Approved	HSA275986, SMIF, SMAD4IP1	uc021wzi.1	Q9NPI6	OTTHUMG00000158193	ENST00000607628.1:c.350G>A	3.37:g.53353455C>T	ENSP00000475920:p.Arg117His	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	158	3	0.0189873	NM_018403	B4DHN9|U3KQM8	Missense_Mutation	SNP	ENST00000607628.1	37																																																																																				.	.	none		0.333	DCP1A-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_018403	
MAML3	55534	hgsc.bcm.edu	37	4	140811125	140811125	+	Missense_Mutation	SNP	G	G	T	rs62344940		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr4:140811125G>T	ENST00000509479.2	-	2	2321	c.1465C>A	c.(1465-1467)Caa>Aaa	p.Q489K	MAML3_ENST00000398940.1_Missense_Mutation_p.Q28K|MAML3_ENST00000327122.5_Missense_Mutation_p.Q333K	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)					tgctgctgttgctgttgctgt	0.552																																					p.Q489K		Atlas-SNP	.											MAML3_ENST00000509479,colon,carcinoma,+2,2	MAML3	192	2	0			c.C1465A						scavenged	.						17.0	20.0	19.0					4																	140811125		2194	4294	6488	SO:0001583	missense	55534	exon2			GCTGTTGCTGTTG	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.1465C>A	4.37:g.140811125G>T	ENSP00000421180:p.Gln489Lys	Somatic	69	4	0.057971		WXS	Illumina HiSeq	Phase_I	88	11	0.125	NM_018717		Missense_Mutation	SNP	ENST00000509479.2	37	CCDS54805.1	.	.	.	.	.	.	.	.	.	.	G	3.000	-0.206260	0.06180	.	.	ENSG00000196782	ENST00000509479;ENST00000327122;ENST00000398940	T;T	0.76448	0.83;-1.02	2.61	2.61	0.31194	.	0.000000	0.64402	D	0.000001	T	0.66607	0.2806	N	0.08118	0	0.31344	N	0.683255	P	0.43392	0.805	P	0.59424	0.857	T	0.64106	-0.6485	10	0.05436	T	0.98	.	8.8799	0.35367	0.0:0.0:1.0:0.0	rs62344940	489	Q96JK9	MAML3_HUMAN	K	489;333;28	ENSP00000421180:Q489K;ENSP00000313316:Q333K	ENSP00000313316:Q333K	Q	-	1	0	MAML3	141030575	1.000000	0.71417	1.000000	0.80357	0.631000	0.37964	3.291000	0.51764	1.788000	0.52465	0.484000	0.47621	CAA	.	.	weak		0.552	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2		
IFITM3	10410	hgsc.bcm.edu	37	11	320723	320723	+	Missense_Mutation	SNP	C	C	T	rs199582787	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:320723C>T	ENST00000399808.4	-	1	327	c.91G>A	c.(91-93)Gtg>Atg	p.V31M	RP11-326C3.11_ENST00000602756.1_RNA|RP11-326C3.11_ENST00000508004.2_RNA|IFITM3_ENST00000602735.1_Missense_Mutation_p.V10M|RP11-326C3.14_ENST00000602809.1_lincRNA|RP11-326C3.10_ENST00000534271.1_RNA|IFITM3_ENST00000526811.1_Missense_Mutation_p.V10M|RP11-326C3.11_ENST00000602429.1_RNA	NM_021034.2	NP_066362.2	Q01628	IFM3_HUMAN	interferon induced transmembrane protein 3	31					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|immune response (GO:0006955)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral genome replication (GO:0045071)|negative regulation of viral transcription (GO:0032897)|response to interferon-alpha (GO:0035455)|response to interferon-beta (GO:0035456)|response to interferon-gamma (GO:0034341)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)				central_nervous_system(7)|endometrium(7)|kidney(2)|large_intestine(1)|lung(1)	18		all_cancers(49;2e-09)|all_epithelial(84;3.36e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;8.85e-28)|Epithelial(43;5.52e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)		GCCCCCAGCACAGCCACCTCG	0.612																																					p.V31M		Atlas-SNP	.											IFITM3,brain,glioma,0,1	IFITM3	132	1	0			c.G91A						scavenged	.						87.0	98.0	95.0					11																	320723		1967	4140	6107	SO:0001583	missense	10410	exon1			CCAGCACAGCCAC	X57352	CCDS41585.1	11p15.5	2011-05-24	2011-05-24		ENSG00000142089	ENSG00000142089			5414	protein-coding gene	gene with protein product		605579	"""interferon induced transmembrane protein 3 (1-8U)"""			1906403, 16326387	Standard	NM_021034		Approved	1-8U	uc001lpa.2	Q01628		ENST00000399808.4:c.91G>A	11.37:g.320723C>T	ENSP00000382707:p.Val31Met	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	88	3	0.0340909	NM_021034	Q53Y76|Q96HK8|Q96J15	Missense_Mutation	SNP	ENST00000399808.4	37	CCDS41585.1	.	.	.	.	.	.	.	.	.	.	C	11.06	1.526447	0.27299	.	.	ENSG00000142089	ENST00000399808;ENST00000270031;ENST00000526811	T;T	0.79454	-1.03;-1.27	4.61	-4.91	0.03085	.	11.488500	0.02440	N	0.084490	T	0.64516	0.2605	L	0.39147	1.195	0.09310	N	1	B	0.16802	0.019	B	0.15484	0.013	T	0.46400	-0.9194	10	0.13108	T	0.6	0.9022	6.4601	0.21952	0.1231:0.361:0.0:0.5159	.	31	Q01628	IFM3_HUMAN	M	31;15;10	ENSP00000382707:V31M;ENSP00000432108:V10M	ENSP00000372047:V15M	V	-	1	0	IFITM3	310723	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-1.638000	0.02013	-0.562000	0.06086	-1.790000	0.00627	GTG	.	.	weak		0.612	IFITM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384765.1	NM_021034	
PCDHB7	56129	hgsc.bcm.edu	37	5	140554429	140554429	+	Silent	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:140554429G>A	ENST00000231137.3	+	1	2187	c.2013G>A	c.(2011-2013)ctG>ctA	p.L671L	PCDHB8_ENST00000239444.2_5'Flank	NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	671	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(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)			AGCCCTACCTGCGGCTCCCGG	0.692																																					p.L671L		Atlas-SNP	.											.	PCDHB7	231	.	0			c.G2013A						PASS	.						49.0	78.0	69.0					5																	140554429		2170	4274	6444	SO:0001819	synonymous_variant	56129	exon1			CTACCTGCGGCTC	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.2013G>A	5.37:g.140554429G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	37	19	0.513514	NM_018940	A1L3Y8	Silent	SNP	ENST00000231137.3	37	CCDS4249.1																																																																																			.	.	none		0.692	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940	
PLET1	349633	hgsc.bcm.edu	37	11	112123070	112123070	+	Splice_Site	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:112123070C>T	ENST00000338832.2	-	3	719		c.e3+1			NM_001145024.1	NP_001138496.1	Q6UQ28	PLET1_HUMAN							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						AAGGAACTCACGTTTTTCTCT	0.463																																					.		Atlas-SNP	.											.	C11orf34	6	.	0			c.448+1G>A						PASS	.						153.0	131.0	138.0					11																	112123070		692	1591	2283	SO:0001630	splice_region_variant	349633	exon4			AACTCACGTTTTT																												ENST00000338832.2:c.448+1G>A	11.37:g.112123070C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	84	33	0.392857	NM_001145024	Q6UQ24|Q6UQ25|Q6UQ27	Splice_Site	SNP	ENST00000338832.2	37		.	.	.	.	.	.	.	.	.	.	C	13.88	2.368899	0.42003	.	.	ENSG00000188771	ENST00000338832	.	.	.	3.77	3.77	0.43336	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.4137	0.49939	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	C11orf34	111628280	0.974000	0.33945	0.819000	0.32651	0.174000	0.22865	3.066000	0.50002	2.420000	0.82092	0.650000	0.86243	.	.	.	none		0.463	C11orf34-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			Intron
TUBA3C	7278	hgsc.bcm.edu	37	13	19751196	19751196	+	Silent	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr13:19751196G>A	ENST00000400113.3	-	4	1031	c.927C>T	c.(925-927)caC>caT	p.H309H		NM_006001.2	NP_005992.1	Q13748	TBA3C_HUMAN	tubulin, alpha 3c	309					'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.H309H(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)		TGTACTTGCCGTGGCGAGGGT	0.587																																					p.H309H		Atlas-SNP	.											TUBA3C,NS,carcinoma,0,1	TUBA3C	166	1	1	Substitution - coding silent(1)	prostate(1)	c.C927T						scavenged	.						171.0	145.0	154.0					13																	19751196		2203	4300	6503	SO:0001819	synonymous_variant	7278	exon4			CTTGCCGTGGCGA	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.927C>T	13.37:g.19751196G>A		Somatic	226	2	0.00884956		WXS	Illumina HiSeq	Phase_I	255	6	0.0235294	NM_006001	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Silent	SNP	ENST00000400113.3	37	CCDS9284.1																																																																																			.	.	none		0.587	TUBA3C-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044007.2	NM_006001	
HECW2	57520	hgsc.bcm.edu	37	2	197298113	197298113	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:197298113A>G	ENST00000260983.3	-	2	217	c.35T>C	c.(34-36)gTg>gCg	p.V12A		NM_020760.1	NP_065811.1	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	12					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(24)|lung(45)|ovary(5)|pancreas(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	113						TCGACGCCTCACAAAAAGCAG	0.547																																					p.V12A		Atlas-SNP	.											.	HECW2	239	.	0			c.T35C						PASS	.						63.0	58.0	60.0					2																	197298113		2203	4300	6503	SO:0001583	missense	57520	exon2			CGCCTCACAAAAA	AL390186	CCDS33354.1	2q32.3	2004-12-13			ENSG00000138411	ENSG00000138411			29853	protein-coding gene	gene with protein product						10718198, 12890487	Standard	NM_020760		Approved	KIAA1301, NEDL2	uc002utm.1	Q9P2P5	OTTHUMG00000154435	ENST00000260983.3:c.35T>C	2.37:g.197298113A>G	ENSP00000260983:p.Val12Ala	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	225	84	0.373333	NM_020760	B8ZZB4|Q17RT5|Q68DF8|Q9NPS9	Missense_Mutation	SNP	ENST00000260983.3	37	CCDS33354.1	.	.	.	.	.	.	.	.	.	.	A	7.043	0.563022	0.13498	.	.	ENSG00000138411	ENST00000260983;ENST00000452031;ENST00000427457	T	0.30714	1.52	5.27	5.27	0.74061	.	0.214433	0.39759	N	0.001275	T	0.26484	0.0647	L	0.51422	1.61	0.41396	D	0.987641	P	0.38767	0.646	B	0.35770	0.21	T	0.05435	-1.0885	10	0.13853	T	0.58	.	13.9092	0.63855	1.0:0.0:0.0:0.0	.	12	Q9P2P5	HECW2_HUMAN	A	12	ENSP00000260983:V12A	ENSP00000260983:V12A	V	-	2	0	HECW2	197006358	0.999000	0.42202	1.000000	0.80357	0.878000	0.50629	2.801000	0.47908	2.209000	0.71365	0.459000	0.35465	GTG	.	.	none		0.547	HECW2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335199.3	NM_020760	
ARMC3	219681	hgsc.bcm.edu	37	10	23287301	23287301	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr10:23287301C>T	ENST00000298032.5	+	11	1484	c.1400C>T	c.(1399-1401)gCg>gTg	p.A467V	ARMC3_ENST00000376528.4_Missense_Mutation_p.A204V|ARMC3_ENST00000409049.3_Missense_Mutation_p.A467V|RNA5SP304_ENST00000411199.1_RNA|ARMC3_ENST00000409983.3_Missense_Mutation_p.A467V	NM_173081.3	NP_775104.2	Q5W041	ARMC3_HUMAN	armadillo repeat containing 3	467						extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(24)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						ACCGCAACTGCGTGTGACGTT	0.458																																					p.A467V		Atlas-SNP	.											ARMC3,NS,carcinoma,-1,1	ARMC3	102	1	0			c.C1400T						scavenged	.						59.0	57.0	57.0					10																	23287301		2203	4300	6503	SO:0001583	missense	219681	exon11			CAACTGCGTGTGA	AK057389	CCDS7142.1, CCDS60499.1, CCDS60500.1, CCDS73073.1	10p12.31	2013-02-14			ENSG00000165309	ENSG00000165309		"""Armadillo repeat containing"""	30964	protein-coding gene	gene with protein product	"""cancer/testis antigen 81"""	611226					Standard	XM_005252380		Approved	FLJ32827, CT81	uc001irm.4	Q5W041	OTTHUMG00000017811	ENST00000298032.5:c.1400C>T	10.37:g.23287301C>T	ENSP00000298032:p.Ala467Val	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	85	2	0.0235294	NM_173081	A0PG76|A6NH64|B4DZL3|B7ZBN6|B7ZBN7|Q8IXS5|Q8N7B0|Q96M49	Missense_Mutation	SNP	ENST00000298032.5	37	CCDS7142.1	.	.	.	.	.	.	.	.	.	.	C	10.61	1.397573	0.25205	.	.	ENSG00000165309	ENST00000298032;ENST00000409983;ENST00000376523;ENST00000409049;ENST00000376528	T;T;T;T	0.65916	-0.18;-0.18;1.41;0.6	5.44	4.44	0.53790	Armadillo-like helical (1);Armadillo-type fold (1);	0.341113	0.33092	N	0.005283	T	0.52419	0.1733	L	0.52759	1.655	0.35458	D	0.796233	B;B	0.18310	0.006;0.027	B;B	0.13407	0.009;0.004	T	0.55302	-0.8162	10	0.22706	T	0.39	-18.7917	9.9229	0.41474	0.0:0.74:0.173:0.087	.	467;467	Q5W041-4;Q5W041	.;ARMC3_HUMAN	V	467;467;403;467;204	ENSP00000298032:A467V;ENSP00000386943:A467V;ENSP00000387288:A467V;ENSP00000365711:A204V	ENSP00000298032:A467V	A	+	2	0	ARMC3	23327307	0.824000	0.29247	0.034000	0.17996	0.010000	0.07245	1.449000	0.35123	1.128000	0.42052	0.467000	0.42956	GCG	.	.	none		0.458	ARMC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047197.2	NM_173081	
AIMP1	9255	hgsc.bcm.edu	37	4	107246152	107246152	+	5'UTR	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr4:107246152C>T	ENST00000442366.1	+	0	38				AIMP1_ENST00000394701.4_Missense_Mutation_p.R20C|AIMP1_ENST00000358008.3_5'UTR	NM_001142415.1	NP_001135887.1	Q12904	AIMP1_HUMAN	aminoacyl tRNA synthetase complex-interacting multifunctional protein 1						angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|chemotaxis (GO:0006935)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|inflammatory response (GO:0006954)|leukocyte migration (GO:0050900)|negative regulation of endothelial cell proliferation (GO:0001937)|response to wounding (GO:0009611)|signal transduction (GO:0007165)|tRNA aminoacylation for protein translation (GO:0006418)	aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|protein homodimerization activity (GO:0042803)|tRNA binding (GO:0000049)			breast(1)|endometrium(2)|kidney(1)|lung(5)|skin(1)|urinary_tract(1)	11						GATTTTCTGCCGTCTCTTGGC	0.358																																					p.R20C		Atlas-SNP	.											.	AIMP1	20	.	0			c.C58T						PASS	.						42.0	41.0	41.0					4																	107246152		2202	4300	6502	SO:0001623	5_prime_UTR_variant	9255	exon2			TTCTGCCGTCTCT	U10117	CCDS3674.1, CCDS47121.1	4q24	2009-05-20	2009-05-20	2009-05-20	ENSG00000164022	ENSG00000164022			10648	protein-coding gene	gene with protein product	"""EMAP II"", ""ARS-interacting multifunctional protein 1"""	603605	"""small inducible cytokine subfamily E, member 1 (endothelial monocyte-activating)"""	SCYE1		7929199, 7545917	Standard	NM_004757		Approved	EMAPII, EMAP-2, p43	uc011cfg.2	Q12904	OTTHUMG00000131217	ENST00000442366.1:c.-15C>T	4.37:g.107246152C>T		Somatic	349	0	0		WXS	Illumina HiSeq	Phase_I	295	69	0.233898	NM_001142416	B3KTR2|B4E1S7|Q6FG28|Q96CQ9	Missense_Mutation	SNP	ENST00000442366.1	37	CCDS3674.1	.	.	.	.	.	.	.	.	.	.	C	7.740	0.701160	0.15172	.	.	ENSG00000164022	ENST00000394701	T	0.26223	1.75	5.06	2.42	0.29668	.	0.253283	0.34268	U	0.004120	T	0.38401	0.1039	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.11324	-1.0592	7	0.59425	D	0.04	-8.449	10.7435	0.46166	0.0:0.7985:0.0:0.2015	.	.	.	.	C	20	ENSP00000378191:R20C	ENSP00000378191:R20C	R	+	1	0	AIMP1	107465601	1.000000	0.71417	0.985000	0.45067	0.115000	0.19883	2.116000	0.41930	0.195000	0.20347	-0.964000	0.02622	CGT	.	.	none		0.358	AIMP1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253961.1	NM_004757	
MUC4	4585	hgsc.bcm.edu	37	3	195512665	195512665	+	Missense_Mutation	SNP	G	G	A	rs79300100	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:195512665G>A	ENST00000463781.3	-	2	6245	c.5786C>T	c.(5785-5787)gCa>gTa	p.A1929V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A1929V|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.A1929V(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)		ACCTGTGGATGCTGAGGAAAG	0.582																																					p.A1929V		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - Missense(1)	kidney(1)	c.C5786T						scavenged	.						37.0	33.0	34.0					3																	195512665		686	1586	2272	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.5786C>T	3.37:g.195512665G>A	ENSP00000417498:p.Ala1929Val	Somatic	410	9	0.0219512		WXS	Illumina HiSeq	Phase_I	425	15	0.0352941	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	6.513	0.462935	0.12402	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.26810	1.72;1.71	.	.	.	.	.	.	.	.	T	0.15478	0.0373	N	0.19112	0.55	0.09310	N	1	P	0.43392	0.805	P	0.45506	0.483	T	0.09997	-1.0649	7	.	.	.	.	5.4001	0.16291	0.2688:0.0:0.7312:0.0	.	1929	E7ESK3	.	V	1929	ENSP00000417498:A1929V;ENSP00000420243:A1929V	.	A	-	2	0	MUC4	196997060	.	.	0.001000	0.08648	0.008000	0.06430	.	.	-1.752000	0.01325	-2.092000	0.00371	GCA	G|0.993;A|0.007	0.007	strong		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PYHIN1	149628	hgsc.bcm.edu	37	1	158911833	158911833	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:158911833A>G	ENST00000368140.1	+	5	891	c.646A>G	c.(646-648)Atc>Gtc	p.I216V	PYHIN1_ENST00000392254.2_Missense_Mutation_p.I216V|PYHIN1_ENST00000485134.1_3'UTR|PYHIN1_ENST00000392252.3_Missense_Mutation_p.I207V|PYHIN1_ENST00000368138.3_Missense_Mutation_p.I207V	NM_152501.4|NM_198928.4|NM_198929.4	NP_689714.2|NP_945146.1|NP_945147.1	Q6K0P9	IFIX_HUMAN	pyrin and HIN domain family, member 1	216	HIN-200. {ECO:0000255|PROSITE- ProRule:PRU00106}.				cell cycle (GO:0007049)	nucleus (GO:0005634)				breast(2)|endometrium(3)|large_intestine(10)|lung(32)|ovary(3)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_hematologic(112;0.0378)					AGACCCAATAATCGCGATGGT	0.383																																					p.I216V		Atlas-SNP	.											PYHIN1_ENST00000392254,NS,carcinoma,-2,2	PYHIN1	208	2	0			c.A646G						scavenged	.						66.0	67.0	66.0					1																	158911833		2203	4300	6503	SO:0001583	missense	149628	exon5			CCAATAATCGCGA	AY185344	CCDS1178.1, CCDS1179.1, CCDS30907.1, CCDS30908.1	1q23.1	2008-02-05			ENSG00000163564	ENSG00000163564			28894	protein-coding gene	gene with protein product		612677				15122330	Standard	NM_152501		Approved	IFIX, MGC23885	uc001ftb.3	Q6K0P9	OTTHUMG00000037109	ENST00000368140.1:c.646A>G	1.37:g.158911833A>G	ENSP00000357122:p.Ile216Val	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	88	2	0.0227273	NM_152501	Q5T3W6|Q6K0P6|Q6K0P7|Q6K0P8|Q8WW65	Missense_Mutation	SNP	ENST00000368140.1	37	CCDS1178.1	.	.	.	.	.	.	.	.	.	.	A	2.353	-0.348425	0.05208	.	.	ENSG00000163564	ENST00000368140;ENST00000368138;ENST00000392254;ENST00000392252	T;T;T;T	0.13778	2.56;2.56;2.56;2.56	2.85	-3.74	0.04385	HIN-200/IF120x (2);Nucleic acid-binding, OB-fold (1);	.	.	.	.	T	0.03053	0.0090	L	0.34521	1.04	0.09310	N	1	B;B;B;B	0.16603	0.006;0.003;0.006;0.018	B;B;B;B	0.13407	0.005;0.007;0.005;0.009	T	0.43376	-0.9395	9	0.45353	T	0.12	.	9.4454	0.38695	0.3169:0.0:0.6831:0.0	.	207;216;207;216	Q6K0P9-4;Q6K0P9-3;Q6K0P9-2;Q6K0P9	.;.;.;IFIX_HUMAN	V	216;207;216;207	ENSP00000357122:I216V;ENSP00000357120:I207V;ENSP00000376083:I216V;ENSP00000376082:I207V	ENSP00000357120:I207V	I	+	1	0	PYHIN1	157178457	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.668000	0.01959	-0.863000	0.04084	-0.290000	0.09829	ATC	.	.	none		0.383	PYHIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090110.1	NM_152501	
SLFN11	91607	hgsc.bcm.edu	37	17	33680037	33680037	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr17:33680037C>T	ENST00000394566.1	-	7	2316	c.2044G>A	c.(2044-2046)Ggg>Agg	p.G682R	SLFN11_ENST00000308377.4_Missense_Mutation_p.G682R	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	682					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)	p.G682R(2)		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)		TTTGCCTTCCCATACCAGTCC	0.468																																					p.G682R		Atlas-SNP	.											SLFN11,NS,carcinoma,0,1	SLFN11	112	1	2	Substitution - Missense(2)	prostate(1)|lung(1)	c.G2044A						scavenged	.						152.0	149.0	150.0					17																	33680037		2203	4300	6503	SO:0001583	missense	91607	exon5			CCTTCCCATACCA	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.2044G>A	17.37:g.33680037C>T	ENSP00000378067:p.Gly682Arg	Somatic	130	1	0.00769231		WXS	Illumina HiSeq	Phase_I	176	2	0.0113636	NM_152270	E1P643|Q8N3S8|Q8N762|Q8TEE0	Missense_Mutation	SNP	ENST00000394566.1	37	CCDS11294.1	.	.	.	.	.	.	.	.	.	.	c	7.153	0.584094	0.13749	.	.	ENSG00000172716	ENST00000308377;ENST00000394566	T;T	0.80909	-1.43;-1.43	4.0	-1.57	0.08506	.	1.460060	0.04413	N	0.366411	T	0.68742	0.3034	L	0.33485	1.01	0.19575	N	0.999964	B	0.09022	0.002	B	0.12156	0.007	T	0.48570	-0.9024	10	0.16420	T	0.52	.	7.3033	0.26432	0.0:0.4518:0.0:0.5482	.	682	Q7Z7L1	SLN11_HUMAN	R	682	ENSP00000312402:G682R;ENSP00000378067:G682R	ENSP00000312402:G682R	G	-	1	0	SLFN11	30704150	0.000000	0.05858	0.303000	0.25071	0.313000	0.28021	-2.684000	0.00835	-0.118000	0.11851	-0.140000	0.14226	GGG	.	.	none		0.468	SLFN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256480.1	NM_152270	
BTBD3	22903	hgsc.bcm.edu	37	20	11903884	11903884	+	Missense_Mutation	SNP	C	C	T	rs535169870		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr20:11903884C>T	ENST00000405977.1	+	5	1764	c.1139C>T	c.(1138-1140)tCg>tTg	p.S380L	BTBD3_ENST00000378226.2_Missense_Mutation_p.S380L|BTBD3_ENST00000399006.2_Missense_Mutation_p.S319L|BTBD3_ENST00000254977.3_Missense_Mutation_p.S319L	NM_001282550.1|NM_001282552.1|NM_001282554.1	NP_001269479.1|NP_001269481.1|NP_001269483.1	Q9Y2F9	BTBD3_HUMAN	BTB (POZ) domain containing 3	380					cerebral cortex development (GO:0021987)|dendrite morphogenesis (GO:0048813)	cytosol (GO:0005829)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(18)|ovary(3)|skin(2)	34						CGTTTCCAGTCGTGTGCCTAT	0.512																																					p.S380L		Atlas-SNP	.											BTBD3,NS,carcinoma,0,2	BTBD3	92	2	0			c.C1139T						scavenged	.						84.0	71.0	76.0					20																	11903884		2203	4300	6503	SO:0001583	missense	22903	exon4			TCCAGTCGTGTGC	AB023169	CCDS13113.1, CCDS13114.1	20p12.2	2013-01-08			ENSG00000132640	ENSG00000132640		"""BTB/POZ domain containing"""	15854	protein-coding gene	gene with protein product		615566					Standard	NM_001282551		Approved	KIAA0952, dJ742J24.1	uc002wnz.3	Q9Y2F9	OTTHUMG00000031889	ENST00000405977.1:c.1139C>T	20.37:g.11903884C>T	ENSP00000384545:p.Ser380Leu	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	169	2	0.0118343	NM_014962	D3DW19|Q5JY73	Missense_Mutation	SNP	ENST00000405977.1	37	CCDS13113.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.752141	0.89753	.	.	ENSG00000132640	ENST00000254977;ENST00000399006;ENST00000405977;ENST00000378226	T;T;T;T	0.79940	-1.28;-1.28;-1.32;-1.32	6.16	6.16	0.99307	PHR (1);	0.000000	0.85682	D	0.000000	D	0.91195	0.7226	M	0.87827	2.91	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	D	0.89715	0.3915	10	0.40728	T	0.16	.	19.848	0.96722	0.0:1.0:0.0:0.0	.	380	Q9Y2F9	BTBD3_HUMAN	L	319;319;380;380	ENSP00000254977:S319L;ENSP00000381971:S319L;ENSP00000384545:S380L;ENSP00000367471:S380L	ENSP00000254977:S319L	S	+	2	0	BTBD3	11851884	1.000000	0.71417	0.973000	0.42090	0.924000	0.55760	7.818000	0.86416	2.937000	0.99478	0.650000	0.86243	TCG	.	.	none		0.512	BTBD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078021.3		
ZNF597	146434	hgsc.bcm.edu	37	16	3490834	3490834	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr16:3490834C>T	ENST00000301744.4	-	3	368	c.133G>A	c.(133-135)Gag>Aag	p.E45K	NAA60_ENST00000407558.4_5'Flank|NAA60_ENST00000608722.1_5'Flank|NAA60_ENST00000424546.2_5'Flank|NAA60_ENST00000573580.1_5'Flank	NM_152457.1	NP_689670.1	Q96LX8	ZN597_HUMAN	zinc finger protein 597	45	KRAB.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	13						TCCAAAGACTCTTTTGTACCA	0.463																																					p.E45K		Atlas-SNP	.											ZNF597,NS,carcinoma,0,1	ZNF597	41	1	0			c.G133A						scavenged	.						107.0	90.0	96.0					16																	3490834		2197	4300	6497	SO:0001583	missense	146434	exon3			AAGACTCTTTTGT	AK057633	CCDS10505.1	16p13.3	2013-01-08			ENSG00000167981	ENSG00000167981		"""Zinc fingers, C2H2-type"", ""-"""	26573	protein-coding gene	gene with protein product		614685				12477932	Standard	NM_152457		Approved	FLJ33071	uc002cvd.3	Q96LX8	OTTHUMG00000129359	ENST00000301744.4:c.133G>A	16.37:g.3490834C>T	ENSP00000301744:p.Glu45Lys	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	70	3	0.0428571	NM_152457		Missense_Mutation	SNP	ENST00000301744.4	37	CCDS10505.1	.	.	.	.	.	.	.	.	.	.	C	5.452	0.268558	0.10349	.	.	ENSG00000167981	ENST00000301744	T	0.04234	3.67	4.07	3.12	0.35913	Krueppel-associated box (3);	0.418161	0.17752	N	0.163194	T	0.10337	0.0253	M	0.89095	3.005	0.09310	N	1	B	0.23937	0.094	B	0.24269	0.052	T	0.12426	-1.0548	10	0.87932	D	0	-5.0167	7.5987	0.28063	0.0:0.8832:0.0:0.1168	.	45	Q96LX8	ZN597_HUMAN	K	45	ENSP00000301744:E45K	ENSP00000301744:E45K	E	-	1	0	ZNF597	3430835	0.067000	0.21026	0.031000	0.17742	0.023000	0.10783	2.230000	0.42999	1.058000	0.40530	0.563000	0.77884	GAG	.	.	none		0.463	ZNF597-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251511.2	NM_152457	
COL7A1	1294	hgsc.bcm.edu	37	3	48613080	48613080	+	Silent	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:48613080T>C	ENST00000328333.8	-	72	6065	c.5958A>G	c.(5956-5958)gaA>gaG	p.E1986E	COL7A1_ENST00000454817.1_Silent_p.E1954E	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	1986	Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		GGGGGCCCTGTTCGCCTGAGT	0.637																																					p.E1986E		Atlas-SNP	.											COL7A1,rectum,carcinoma,-2,1	COL7A1	320	1	0			c.A5958G						scavenged	.						55.0	58.0	57.0					3																	48613080		2203	4300	6503	SO:0001819	synonymous_variant	1294	exon72			GCCCTGTTCGCCT	L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"""Collagens"", ""Fibronectin type III domain containing"""	2214	protein-coding gene	gene with protein product	"""collagen VII, alpha-1 polypeptide"", ""LC collagen"""	120120	"""epidermolysis bullosa, dystrophic, dominant and recessive"""	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.5958A>G	3.37:g.48613080T>C		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	117	3	0.025641	NM_000094	Q14054|Q16507	Silent	SNP	ENST00000328333.8	37	CCDS2773.1																																																																																			.	.	none		0.637	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094	
SSX3	10214	hgsc.bcm.edu	37	X	48209473	48209473	+	Silent	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:48209473G>A	ENST00000298396.2	-	6	467	c.415C>T	c.(415-417)Ctg>Ttg	p.L139L	SSX3_ENST00000376893.3_Silent_p.L139L|SSX3_ENST00000376895.1_Silent_p.L51L	NM_021014.2	NP_066294.1	Q99909	SSX3_HUMAN	synovial sarcoma, X breakpoint 3	139					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			endometrium(3)|large_intestine(1)|lung(9)	13						GGGGGGCACAGCTGTTTCCCA	0.488																																					p.L139L	Colon(37;227 826 19399 40970 48007)	Atlas-SNP	.											.	SSX3	64	.	0			c.C415T						PASS	.						251.0	230.0	237.0					X																	48209473		2203	4300	6503	SO:0001819	synonymous_variant	10214	exon6			GGCACAGCTGTTT	U90840	CCDS14291.1	Xp11.23	2009-06-17			ENSG00000165584	ENSG00000165584			11337	protein-coding gene	gene with protein product		300325				8697803, 9378559	Standard	NM_021014		Approved	CT5.3	uc004djd.1	Q99909	OTTHUMG00000021489	ENST00000298396.2:c.415C>T	X.37:g.48209473G>A		Somatic	858	1	0.0011655		WXS	Illumina HiSeq	Phase_I	825	350	0.424242	NM_021014	O60223|Q5JQZ3|Q9BRW7	Silent	SNP	ENST00000298396.2	37	CCDS14291.1																																																																																			.	.	none		0.488	SSX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056486.1	NM_021014	
THG1L	54974	hgsc.bcm.edu	37	5	157161623	157161623	+	Missense_Mutation	SNP	C	C	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:157161623C>G	ENST00000231198.7	+	3	652	c.408C>G	c.(406-408)agC>agG	p.S136R	AC026407.1_ENST00000599823.1_Missense_Mutation_p.A35P	NM_017872.3	NP_060342.2	Q9NWX6	THG1_HUMAN	tRNA-histidine guanylyltransferase 1-like (S. cerevisiae)	136					protein homotetramerization (GO:0051289)|tRNA modification (GO:0006400)|tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|tRNA binding (GO:0000049)|tRNA guanylyltransferase activity (GO:0008193)			NS(1)|central_nervous_system(2)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)|skin(1)	13	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TTGCCTCCAGCTATGTGTTTT	0.458																																					p.S136R		Atlas-SNP	.											.	THG1L	31	.	0			c.C408G						PASS	.						160.0	158.0	158.0					5																	157161623		2203	4300	6503	SO:0001583	missense	54974	exon3			CTCCAGCTATGTG	AK223119	CCDS4341.1	5q33.3	2008-02-05			ENSG00000113272	ENSG00000113272			26053	protein-coding gene	gene with protein product	"""interphase cytoplasmic foci protein 45"""					11230166	Standard	XM_005265939		Approved	ICF45, FLJ11601, FLJ20546	uc003lxd.3	Q9NWX6	OTTHUMG00000130254	ENST00000231198.7:c.408C>G	5.37:g.157161623C>G	ENSP00000231198:p.Ser136Arg	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	209	82	0.392345	NM_017872	D3DQJ5|Q53G12|Q7L5R3|Q9H0S2	Missense_Mutation	SNP	ENST00000231198.7	37	CCDS4341.1	.	.	.	.	.	.	.	.	.	.	C	15.80	2.940943	0.52972	.	.	ENSG00000113272	ENST00000231198;ENST00000448153	T	0.46063	0.88	5.95	3.8	0.43715	.	0.203335	0.64402	N	0.000017	T	0.54549	0.1865	M	0.83483	2.645	0.58432	D	0.999995	D	0.60160	0.987	P	0.57468	0.821	T	0.53851	-0.8380	10	0.21540	T	0.41	-19.4724	6.4975	0.22150	0.1369:0.669:0.0:0.1941	.	136	Q9NWX6	THG1_HUMAN	R	136;11	ENSP00000231198:S136R	ENSP00000231198:S136R	S	+	3	2	THG1L	157094201	0.992000	0.36948	1.000000	0.80357	0.997000	0.91878	0.323000	0.19593	0.583000	0.29574	0.650000	0.86243	AGC	.	.	none		0.458	THG1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252579.2	NM_017872	
FRG1	2483	hgsc.bcm.edu	37	4	190873379	190873379	+	Missense_Mutation	SNP	A	A	G	rs112612436		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr4:190873379A>G	ENST00000226798.4	+	3	418	c.196A>G	c.(196-198)Aag>Gag	p.K66E	FRG1_ENST00000514482.1_3'UTR	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1	66			K -> E (in dbSNP:rs17406826).		mRNA splicing, via spliceosome (GO:0000398)|muscle organ development (GO:0007517)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.K66E(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1)	32		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		TGAAATGGATAAGGGAACCTA	0.383																																					p.K66E		Atlas-SNP	.											FRG1,arm,malignant_melanoma,0,1	FRG1	76	1	1	Substitution - Missense(1)	skin(1)	c.A196G						scavenged	.						101.0	115.0	110.0					4																	190873379		2203	4298	6501	SO:0001583	missense	2483	exon3			ATGGATAAGGGAA	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.196A>G	4.37:g.190873379A>G	ENSP00000226798:p.Lys66Glu	Somatic	135	16	0.118519		WXS	Illumina HiSeq	Phase_I	119	24	0.201681	NM_004477	A8K775	Missense_Mutation	SNP	ENST00000226798.4	37	CCDS34121.1	.	.	.	.	.	.	.	.	.	.	.	11.33	1.608104	0.28623	.	.	ENSG00000109536	ENST00000226798;ENST00000531991	T;T	0.44083	2.07;0.93	3.47	2.23	0.28157	Actin cross-linking (1);	0.148940	0.64402	D	0.000013	T	0.29288	0.0729	L	0.52011	1.625	0.42341	D	0.992332	B	0.02656	0.0	B	0.04013	0.001	T	0.10314	-1.0635	10	0.06757	T	0.87	-8.6418	8.2577	0.31766	0.7983:0.2017:0.0:0.0	rs17406826	66	Q14331	FRG1_HUMAN	E	66;3	ENSP00000226798:K66E;ENSP00000435943:K3E	ENSP00000226798:K66E	K	+	1	0	FRG1	191110373	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	2.931000	0.48932	0.668000	0.31126	0.441000	0.28932	AAG	.	.	weak		0.383	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359622.4	NM_004477	
OBSCN	84033	hgsc.bcm.edu	37	1	228434398	228434398	+	Silent	SNP	G	G	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:228434398G>T	ENST00000422127.1	+	13	3971	c.3927G>T	c.(3925-3927)gcG>gcT	p.A1309A	OBSCN_ENST00000570156.2_Silent_p.A1401A|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Silent_p.A1309A	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	1309	Ig-like 13.				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)				TAGAGGCTGCGGGCTGCATGC	0.637																																					p.A1401A		Atlas-SNP	.											OBSCN_ENST00000570156,NS,carcinoma,0,6	OBSCN	2142	6	0			c.G4203T						scavenged	.						76.0	82.0	80.0					1																	228434398		2050	4201	6251	SO:0001819	synonymous_variant	84033	exon14			GGCTGCGGGCTGC	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.3927G>T	1.37:g.228434398G>T		Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	256	3	0.0117188	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		0.637	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
MED26	9441	hgsc.bcm.edu	37	19	16687806	16687806	+	Missense_Mutation	SNP	G	G	A	rs201182566		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:16687806G>A	ENST00000263390.3	-	3	1097	c.835C>T	c.(835-837)Cgg>Tgg	p.R279W	CTC-429P9.4_ENST00000593962.1_5'Flank|CTD-3222D19.2_ENST00000409035.1_Missense_Mutation_p.R287W	NM_004831.3	NP_004822.2	O95402	MED26_HUMAN	mediator complex subunit 26	279	Pro-rich.				gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|RNA polymerase II transcription cofactor activity (GO:0001104)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|skin(1)	8						CCCTCATGCCGTGAGTTCCGA	0.662																																					p.R279W		Atlas-SNP	.											MED26,colon,carcinoma,+1,1	MED26	25	1	0			c.C835T						PASS	.						31.0	33.0	32.0					19																	16687806		2203	4300	6503	SO:0001583	missense	9441	exon3			CATGCCGTGAGTT	AF104253	CCDS12347.1	19p13.11	2008-02-05	2007-07-30	2007-07-30		ENSG00000105085			2376	protein-coding gene	gene with protein product		605043	"""cofactor required for Sp1 transcriptional activation, subunit 7, 70kDa"""	CRSP7		9989412	Standard	NM_004831		Approved	CRSP70	uc002nen.1	O95402		ENST00000263390.3:c.835C>T	19.37:g.16687806G>A	ENSP00000263390:p.Arg279Trp	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	103	18	0.174757	NM_004831	A1A4S3|Q0VGB6	Missense_Mutation	SNP	ENST00000263390.3	37	CCDS12347.1	.	.	.	.	.	.	.	.	.	.	G	14.24	2.475948	0.44044	.	.	ENSG00000105085	ENST00000263390	.	.	.	4.74	3.61	0.41365	.	0.198170	0.41294	D	0.000907	T	0.63331	0.2502	L	0.57536	1.79	0.29237	N	0.87285	D	0.89917	1.0	D	0.87578	0.998	T	0.60801	-0.7191	9	0.72032	D	0.01	-30.7651	13.7896	0.63131	0.0:0.0:0.803:0.197	.	279	O95402	MED26_HUMAN	W	279	.	ENSP00000263390:R279W	R	-	1	2	MED26	16548806	1.000000	0.71417	1.000000	0.80357	0.129000	0.20672	2.921000	0.48852	2.194000	0.70268	0.555000	0.69702	CGG	G|0.999;A|0.001	0.001	weak		0.662	MED26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461178.1	NM_004831	
PRG4	10216	hgsc.bcm.edu	37	1	186276981	186276981	+	Silent	SNP	A	A	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:186276981A>G	ENST00000445192.2	+	7	2175	c.2130A>G	c.(2128-2130)aaA>aaG	p.K710K	PRG4_ENST00000367486.3_Silent_p.K667K|PRG4_ENST00000367483.4_Silent_p.K669K|PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367485.4_Silent_p.K617K	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	710	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						CTACCCCTAAAGGGACTGCTC	0.582																																					p.K710K		Atlas-SNP	.											PRG4,NS,carcinoma,0,6	PRG4	259	6	0			c.A2130G						scavenged	.						162.0	175.0	171.0					1																	186276981		2203	4300	6503	SO:0001819	synonymous_variant	10216	exon7			CCCTAAAGGGACT	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.2130A>G	1.37:g.186276981A>G		Somatic	179	2	0.0111732		WXS	Illumina HiSeq	Phase_I	198	10	0.050505	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Silent	SNP	ENST00000445192.2	37	CCDS1369.1																																																																																			.	.	none		0.582	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807	
ZNF804B	219578	hgsc.bcm.edu	37	7	88966043	88966043	+	Silent	SNP	G	G	T	rs371801451		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr7:88966043G>T	ENST00000333190.4	+	4	4356	c.3747G>T	c.(3745-3747)tcG>tcT	p.S1249S		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	1249							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)			TTTCATTTTCGACTCTGACTC	0.458										HNSCC(36;0.09)																											p.S1249S		Atlas-SNP	.											ZNF804B,bladder,carcinoma,+1,2	ZNF804B	322	2	0			c.G3747T						scavenged	.						216.0	181.0	193.0					7																	88966043		2203	4300	6503	SO:0001819	synonymous_variant	219578	exon4			ATTTTCGACTCTG	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.3747G>T	7.37:g.88966043G>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	145	2	0.0137931	NM_181646	B2RTV2|Q7Z714|Q96MN7	Silent	SNP	ENST00000333190.4	37	CCDS5613.1																																																																																			.	.	alt		0.458	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646	
ZNF880	400713	hgsc.bcm.edu	37	19	52887146	52887146	+	Nonsense_Mutation	SNP	A	A	T	rs398101268|rs34470614		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	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	89	1	0.011236		WXS	Illumina HiSeq	Phase_I	144	3	0.0208333	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	
INO80D	54891	hgsc.bcm.edu	37	2	206872127	206872127	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:206872127G>A	ENST00000403263.1	-	10	2203	c.1799C>T	c.(1798-1800)cCg>cTg	p.P600L	Vault_ENST00000516676.1_RNA	NM_017759.4	NP_060229.3	Q53TQ3	IN80D_HUMAN	INO80 complex subunit D	600					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				NS(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	26						AATGTCATCCGGCAACTCATC	0.493																																					p.P600L		Atlas-SNP	.											INO80D_ENST00000403263,NS,carcinoma,+1,2	INO80D	134	2	0			c.C1799T						scavenged	.						129.0	129.0	129.0					2																	206872127		2062	4217	6279	SO:0001583	missense	54891	exon10			TCATCCGGCAACT		CCDS46500.1	2q33.3	2011-07-06			ENSG00000114933	ENSG00000114933		"""INO80 complex subunits"""	25997	protein-coding gene	gene with protein product						16230350	Standard	NM_017759		Approved	FLJ20309	uc002vaz.4	Q53TQ3	OTTHUMG00000154649	ENST00000403263.1:c.1799C>T	2.37:g.206872127G>A	ENSP00000384198:p.Pro600Leu	Somatic	280	0	0		WXS	Illumina HiSeq	Phase_I	341	4	0.0117302	NM_017759	B3KU68|B9EG77|Q6PJC6|Q6PJU1|Q6PKA1|Q9NXD5	Missense_Mutation	SNP	ENST00000403263.1	37	CCDS46500.1	.	.	.	.	.	.	.	.	.	.	G	35	5.548155	0.96488	.	.	ENSG00000114933	ENST00000403263;ENST00000233270	T	0.38560	1.13	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.63212	0.2492	L	0.54323	1.7	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.63157	-0.6700	10	0.72032	D	0.01	.	19.918	0.97070	0.0:0.0:1.0:0.0	.	600	Q53TQ3-2	.	L	600	ENSP00000384198:P600L	ENSP00000233270:P600L	P	-	2	0	INO80D	206580372	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.476000	0.97823	2.716000	0.92895	0.561000	0.74099	CCG	.	.	none		0.493	INO80D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336459.1	NM_017759	
EPHA3	2042	hgsc.bcm.edu	37	3	89391088	89391088	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:89391088G>A	ENST00000336596.2	+	5	1379	c.1154G>A	c.(1153-1155)cGa>cAa	p.R385Q	EPHA3_ENST00000452448.2_Missense_Mutation_p.R385Q|EPHA3_ENST00000494014.1_Missense_Mutation_p.R385Q	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	385	Fibronectin type-III 1. {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)		TTCCTCCCTCGACAGTTTGGA	0.478										TSP Lung(6;0.00050)																											p.R385Q		Atlas-SNP	.											EPHA3_ENST00000452448,colon,carcinoma,+1,2	EPHA3	501	2	0			c.G1154A						scavenged	.						106.0	93.0	98.0					3																	89391088		2203	4300	6503	SO:0001583	missense	2042	exon5			TCCCTCGACAGTT	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.1154G>A	3.37:g.89391088G>A	ENSP00000337451:p.Arg385Gln	Somatic	145	3	0.0206897		WXS	Illumina HiSeq	Phase_I	154	2	0.012987	NM_005233	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	37	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	G	11.95	1.793051	0.31685	.	.	ENSG00000044524	ENST00000336596;ENST00000452448;ENST00000494014	T;T;T	0.59224	0.28;0.28;0.28	5.66	4.79	0.61399	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.68879	0.3049	L	0.45698	1.435	0.80722	D	1	D;P	0.76494	0.999;0.764	D;B	0.80764	0.994;0.095	T	0.67933	-0.5542	9	.	.	.	.	14.9169	0.70805	0.0687:0.0:0.9313:0.0	.	385;385	P29320;P29320-2	EPHA3_HUMAN;.	Q	385	ENSP00000337451:R385Q;ENSP00000399926:R385Q;ENSP00000419190:R385Q	.	R	+	2	0	EPHA3	89473778	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.813000	0.99286	1.538000	0.49270	0.655000	0.94253	CGA	.	.	none		0.478	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233	
RGS18	64407	hgsc.bcm.edu	37	1	192153517	192153517	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:192153517T>C	ENST00000367460.3	+	5	722	c.541T>C	c.(541-543)Tat>Cat	p.Y181H		NM_130782.2	NP_570138.1	Q9NS28	RGS18_HUMAN	regulator of G-protein signaling 18	181	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				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						AAGCAGAGTGTATCAGCTCAT	0.398																																					p.Y181H		Atlas-SNP	.											RGS18,right_upper_lobe,carcinoma,-2,1	RGS18	54	1	0			c.T541C						scavenged	.						145.0	136.0	139.0					1																	192153517		2203	4300	6503	SO:0001583	missense	64407	exon5			AGAGTGTATCAGC	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.541T>C	1.37:g.192153517T>C	ENSP00000356430:p.Tyr181His	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	144	3	0.0208333	NM_130782	B2RD23	Missense_Mutation	SNP	ENST00000367460.3	37	CCDS1374.1	.	.	.	.	.	.	.	.	.	.	T	19.12	3.765516	0.69878	.	.	ENSG00000150681	ENST00000367460	T	0.66280	-0.2	5.62	5.62	0.85841	Regulator of G protein signalling (4);Regulator of G protein signalling superfamily (1);	0.053083	0.85682	D	0.000000	T	0.80675	0.4668	M	0.86573	2.825	0.80722	D	1	D	0.55605	0.972	D	0.68039	0.955	T	0.82784	-0.0286	10	0.48119	T	0.1	.	14.661	0.68870	0.0:0.0:0.0:1.0	.	181	Q9NS28	RGS18_HUMAN	H	181	ENSP00000356430:Y181H	ENSP00000356430:Y181H	Y	+	1	0	RGS18	190420140	1.000000	0.71417	0.710000	0.30468	0.963000	0.63663	7.534000	0.82004	2.140000	0.66376	0.460000	0.39030	TAT	.	.	none		0.398	RGS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086382.1	NM_130782	
CDC27	996	hgsc.bcm.edu	37	17	45234386	45234386	+	Silent	SNP	G	G	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr17:45234386G>T	ENST00000066544.3	-	7	828	c.735C>A	c.(733-735)gtC>gtA	p.V245V	CDC27_ENST00000531206.1_Silent_p.V245V|CDC27_ENST00000527547.1_Silent_p.V245V|CDC27_ENST00000528748.1_5'Flank|CDC27_ENST00000446365.2_Silent_p.V184V	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	245					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)	p.V245V(9)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TTCCCAGTGGGACAGTATCAG	0.358																																					p.V245V		Atlas-SNP	.											CDC27_ENST00000531206,NS,carcinoma,0,8	CDC27	337	8	9	Substitution - coding silent(9)	prostate(9)	c.C735A						scavenged	.						48.0	53.0	51.0					17																	45234386		2196	4292	6488	SO:0001819	synonymous_variant	996	exon7			CAGTGGGACAGTA	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.735C>A	17.37:g.45234386G>T		Somatic	45	1	0.0222222		WXS	Illumina HiSeq	Phase_I	63	8	0.126984	NM_001114091	G3V1C4|Q16349|Q96F35	Silent	SNP	ENST00000066544.3	37	CCDS11509.1																																																																																			.	.	none		0.358	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
BUB1B	701	hgsc.bcm.edu	37	15	40453452	40453452	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr15:40453452C>T	ENST00000287598.6	+	1	226	c.31C>T	c.(31-33)Ctg>Ttg	p.L11L	BUB1B_ENST00000560120.1_3'UTR|BUB1B_ENST00000412359.3_Silent_p.L11L	NM_001211.5	NP_001202	O60566	BUB1B_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase B	11					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|protein localization to chromosome, centromeric region (GO:0071459)|protein localization to kinetochore (GO:0034501)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|condensed chromosome kinetochore (GO:0000777)|condensed chromosome outer kinetochore (GO:0000940)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|perinuclear region of cytoplasm (GO:0048471)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(1)|stomach(2)|urinary_tract(2)	36		all_cancers(109;1.12e-18)|all_epithelial(112;1.61e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0556)		AGGGGGTGCTCTGAGGTAGGT	0.637			"""Mis, N, F, S"""			rhabdomyosarcoma			Mosaic Variegated Aneuploidy Syndrome																												p.L11L		Atlas-SNP	.	yes	Rec		Mosaic variegated aneuploidy	15	15q15	701	BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast)		M	.	BUB1B	71	.	0			c.C31T						PASS	.						66.0	54.0	58.0					15																	40453452		2202	4298	6500	SO:0001819	synonymous_variant	701	exon1	Familial Cancer Database	MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division	GGTGCTCTGAGGT	AF107297	CCDS10053.1	15q15	2014-09-17	2013-01-17		ENSG00000156970	ENSG00000156970			1149	protein-coding gene	gene with protein product		602860	"""budding uninhibited by benzimidazoles 1 (yeast homolog), beta"", ""budding uninhibited by benzimidazoles 1 homolog beta (yeast)"""			9889005	Standard	NM_001211		Approved	BUBR1, MAD3L, Bub1A, SSK1	uc001zkx.4	O60566	OTTHUMG00000129877	ENST00000287598.6:c.31C>T	15.37:g.40453452C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	78	17	0.217949	NM_001211	B2R6U0|B4DL09|B4DLG3|O60501|O60627|O60758|O75389|Q59HH6|Q8WV50|Q96KM4	Silent	SNP	ENST00000287598.6	37	CCDS10053.1																																																																																			.	.	none		0.637	BUB1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252122.4		
TMC5	79838	hgsc.bcm.edu	37	16	19488796	19488796	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr16:19488796C>T	ENST00000396229.2	+	13	2874	c.2125C>T	c.(2125-2127)Ctt>Ttt	p.L709F	TMC5_ENST00000381414.4_Missense_Mutation_p.L709F|TMC5_ENST00000541464.1_Missense_Mutation_p.L657F|TMC5_ENST00000219821.5_Missense_Mutation_p.L463F|TMC5_ENST00000564959.1_Missense_Mutation_p.L392F|TMC5_ENST00000561503.1_Missense_Mutation_p.L350F|CTA-363E6.6_ENST00000561762.1_RNA|TMC5_ENST00000542583.2_Missense_Mutation_p.L709F	NM_001105248.1	NP_001098718.1	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5	709					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|liver(2)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						CATTGGCATTCTTTGTTACTA	0.388																																					p.L709F		Atlas-SNP	.											TMC5_ENST00000396229,NS,carcinoma,0,2	TMC5	169	2	0			c.C2125T						scavenged	.						247.0	229.0	235.0					16																	19488796		2197	4300	6497	SO:0001583	missense	79838	exon13			GGCATTCTTTGTT	AY263164	CCDS10577.1, CCDS42126.1, CCDS45431.1	16p13.11	2008-02-05			ENSG00000103534	ENSG00000103534			22999	protein-coding gene	gene with protein product						12812529, 12906855	Standard	NM_024780		Approved	FLJ13593	uc010var.2	Q6UXY8	OTTHUMG00000131458	ENST00000396229.2:c.2125C>T	16.37:g.19488796C>T	ENSP00000379531:p.Leu709Phe	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	183	2	0.010929	NM_001105249	Q68DK8|Q8IY20|Q8NHV6|Q9H8I7	Missense_Mutation	SNP	ENST00000396229.2	37	CCDS45431.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.256030	0.80246	.	.	ENSG00000103534	ENST00000541464;ENST00000381414;ENST00000396229;ENST00000542583;ENST00000219821;ENST00000440743	T;T;T;T;T	0.75050	-0.69;-0.9;-0.9;-0.9;-0.9	4.33	4.33	0.51752	.	0.000000	0.64402	D	0.000001	D	0.86406	0.5925	M	0.82823	2.61	0.47308	D	0.99938	D;D;D;D;D;D	0.89917	0.997;0.994;0.997;0.984;0.995;1.0	D;P;P;P;P;D	0.91635	0.927;0.882;0.895;0.788;0.847;0.999	D	0.86258	0.1653	10	0.33141	T	0.24	-15.0845	16.7528	0.85490	0.0:1.0:0.0:0.0	.	657;392;463;463;709;709	F5GYU8;E7EU57;Q6UXY8-3;B3KUQ8;Q6UXY8;Q6UXY8-2	.;.;.;.;TMC5_HUMAN;.	F	657;709;709;709;463;392	ENSP00000441227:L657F;ENSP00000370822:L709F;ENSP00000379531:L709F;ENSP00000446274:L709F;ENSP00000219821:L463F	ENSP00000219821:L463F	L	+	1	0	TMC5	19396297	1.000000	0.71417	1.000000	0.80357	0.744000	0.42396	2.683000	0.46943	2.112000	0.64535	0.655000	0.94253	CTT	.	.	none		0.388	TMC5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435888.1	NM_024780	
FSIP1	161835	hgsc.bcm.edu	37	15	40068702	40068702	+	Silent	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr15:40068702T>C	ENST00000350221.3	-	2	233	c.24A>G	c.(22-24)ctA>ctG	p.L8L	RP11-37C7.1_ENST00000558616.1_RNA	NM_152597.4	NP_689810.3	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	8										NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	23		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)		AAATTCCATCTAGGTTTCCCT	0.348																																					p.L8L		Atlas-SNP	.											FSIP1,NS,carcinoma,-2,1	FSIP1	53	1	0			c.A24G						scavenged	.						112.0	110.0	111.0					15																	40068702		2203	4300	6503	SO:0001819	synonymous_variant	161835	exon2			TCCATCTAGGTTT	BC045191	CCDS10050.1	15q14	2012-11-19			ENSG00000150667	ENSG00000150667			21674	protein-coding gene	gene with protein product		615795				14702039	Standard	NM_152597		Approved	FLJ35989	uc001zki.3	Q8NA03	OTTHUMG00000172456	ENST00000350221.3:c.24A>G	15.37:g.40068702T>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	110	3	0.0272727	NM_152597	Q6X2C8|Q86Y89	Silent	SNP	ENST00000350221.3	37	CCDS10050.1																																																																																			.	.	none		0.348	FSIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252118.2	NM_152597	
DYRK1A	1859	hgsc.bcm.edu	37	21	38845022	38845022	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr21:38845022G>A	ENST00000398960.2	+	2	122	c.47G>A	c.(46-48)cGg>cAg	p.R16Q	DYRK1A_ENST00000338785.3_Missense_Mutation_p.R16Q|DYRK1A_ENST00000398956.2_Missense_Mutation_p.R16Q|DYRK1A_ENST00000321219.8_Missense_Mutation_p.R16Q|DYRK1A_ENST00000462274.1_3'UTR|DYRK1A_ENST00000451934.1_Missense_Mutation_p.R16Q|DYRK1A_ENST00000339659.4_Missense_Mutation_p.R16Q	NM_001396.3|NM_130438.2	NP_001387.2|NP_569122.1	Q13627	DYR1A_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A	16					circadian rhythm (GO:0007623)|mitotic cell cycle (GO:0000278)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|nervous system development (GO:0007399)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of protein deacetylation (GO:0090312)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|tau protein binding (GO:0048156)			breast(4)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						TCATCTGTTCGGCTTGCACCG	0.438																																					p.R16Q	Melanoma(114;464 1602 31203 43785 45765)	Atlas-SNP	.											DYRK1A,NS,carcinoma,+1,1	DYRK1A	85	1	0			c.G47A						scavenged	.						115.0	110.0	111.0					21																	38845022		2203	4300	6503	SO:0001583	missense	1859	exon2			CTGTTCGGCTTGC	U52373	CCDS13653.1, CCDS13654.1, CCDS42925.1, CCDS42926.1	21q22.13	2010-04-21			ENSG00000157540	ENSG00000157540			3091	protein-coding gene	gene with protein product		600855		DYRK1, DYRK, MNBH		9284911	Standard	NM_130436		Approved		uc002ywk.3	Q13627	OTTHUMG00000086657	ENST00000398960.2:c.47G>A	21.37:g.38845022G>A	ENSP00000381932:p.Arg16Gln	Somatic	142	1	0.00704225		WXS	Illumina HiSeq	Phase_I	233	4	0.0171674	NM_001396	O60769|Q92582|Q92810|Q9UNM5	Missense_Mutation	SNP	ENST00000398960.2	37	CCDS42925.1	.	.	.	.	.	.	.	.	.	.	G	35	5.554137	0.96501	.	.	ENSG00000157540	ENST00000338785;ENST00000455097;ENST00000426672;ENST00000339659;ENST00000321219;ENST00000451934;ENST00000398960;ENST00000398956	T;T;T;T;T;T;T	0.59502	0.36;0.43;0.27;0.4;0.36;0.26;0.4	6.16	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.51398	0.1672	L	0.43152	1.355	0.80722	D	1	B;B;B;B;B	0.23490	0.086;0.086;0.052;0.086;0.086	B;B;B;B;B	0.12837	0.008;0.008;0.002;0.005;0.008	T	0.50659	-0.8802	10	0.66056	D	0.02	.	15.4253	0.75045	0.066:0.0:0.934:0.0	.	16;16;16;16;16	Q13627-3;Q13627-4;Q13627;Q13627-2;Q13627-5	.;.;DYR1A_HUMAN;.;.	Q	16	ENSP00000342690:R16Q;ENSP00000412269:R16Q;ENSP00000340373:R16Q;ENSP00000319032:R16Q;ENSP00000416089:R16Q;ENSP00000381932:R16Q;ENSP00000381929:R16Q	ENSP00000319032:R16Q	R	+	2	0	DYRK1A	37766892	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.476000	0.97823	1.623000	0.50342	0.650000	0.86243	CGG	.	.	none		0.438	DYRK1A-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194804.1	NM_001396	
FLG2	388698	hgsc.bcm.edu	37	1	152325925	152325925	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:152325925G>A	ENST00000388718.5	-	3	4409	c.4337C>T	c.(4336-4338)aCt>aTt	p.T1446I	FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	1446					establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TTGGCCATGAGTTTGTTCTTG	0.527																																					p.T1446I		Atlas-SNP	.											.	FLG2	431	.	0			c.C4337T						PASS	.						366.0	329.0	341.0					1																	152325925		2203	4300	6503	SO:0001583	missense	388698	exon3			CCATGAGTTTGTT	AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"""EF-hand domain containing"""	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.4337C>T	1.37:g.152325925G>A	ENSP00000373370:p.Thr1446Ile	Somatic	307	0	0		WXS	Illumina HiSeq	Phase_I	314	149	0.474522	NM_001014342	Q9H4U1	Missense_Mutation	SNP	ENST00000388718.5	37	CCDS30861.1	.	.	.	.	.	.	.	.	.	.	G	4.655	0.121725	0.08931	.	.	ENSG00000143520	ENST00000388718	T	0.40476	1.03	3.22	-6.43	0.01926	.	.	.	.	.	T	0.11965	0.0291	M	0.68593	2.085	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.13229	-1.0517	9	0.52906	T	0.07	3.444	0.1468	0.00089	0.2725:0.2261:0.1625:0.3389	.	1446	Q5D862	FILA2_HUMAN	I	1446	ENSP00000373370:T1446I	ENSP00000373370:T1446I	T	-	2	0	FLG2	150592549	0.029000	0.19370	0.000000	0.03702	0.001000	0.01503	-0.043000	0.12043	-2.658000	0.00420	-0.913000	0.02753	ACT	.	.	none		0.527	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342	
LILRB1	10859	hgsc.bcm.edu	37	19	55148031	55148031	+	Silent	SNP	T	T	C	rs41308746	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:55148031T>C	ENST00000396331.1	+	15	2091	c.1734T>C	c.(1732-1734)ccT>ccC	p.P578P	AC009892.10_ENST00000456337.1_Intron|LILRB1_ENST00000396332.4_Silent_p.P579P|LILRB1_ENST00000448689.1_3'UTR|LILRB1_ENST00000462628.1_3'UTR|LILRB1_ENST00000396321.2_Silent_p.P578P|LILRB1_ENST00000427581.2_Silent_p.P629P|LILRB1_ENST00000324602.7_Silent_p.P580P|LILRB1_ENST00000396315.1_Silent_p.P580P|LILRB1_ENST00000434867.2_Silent_p.P578P|LILRB1_ENST00000396327.3_Silent_p.P579P|LILRB1_ENST00000396317.1_Silent_p.P562P|LILRB1_ENST00000418536.2_Silent_p.P562P	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	578					cellular response to lipopolysaccharide (GO:0071222)|defense response to virus (GO:0051607)|dendritic cell differentiation (GO:0097028)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma production (GO:0032609)|interferon-gamma secretion (GO:0072643)|negative regulation of alpha-beta T cell activation (GO:0046636)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of CD8-positive, alpha-beta T cell activation (GO:2001186)|negative regulation of cell cycle (GO:0045786)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of endocytosis (GO:0045806)|negative regulation of interferon-beta secretion (GO:0035548)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-12 secretion (GO:2001183)|negative regulation of mononuclear cell proliferation (GO:0032945)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|negative regulation of osteoclast development (GO:2001205)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001189)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transforming growth factor-beta secretion (GO:2001202)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of gamma-delta T cell activation involved in immune response (GO:2001193)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor internalization (GO:0031623)|regulation of immune response (GO:0050776)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation involved in immune response (GO:0002309)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	HLA-A specific inhibitory MHC class I receptor activity (GO:0030107)|HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)|MHC class I protein binding (GO:0042288)|MHC class I receptor activity (GO:0032393)|protein homodimerization activity (GO:0042803)|protein phosphatase 1 binding (GO:0008157)|SH2 domain binding (GO:0042169)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(38)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	74				GBM - Glioblastoma multiforme(193;0.0188)		CCTCTCCTCCTTCCCCACTGT	0.582										HNSCC(37;0.09)			t|||	554	0.110623	0.1785	0.0893	5008	,	,		16680	0.0139		0.1491	False		,,,				2504	0.0941				p.P580P		Atlas-SNP	.											LILRB1,NS,carcinoma,+2,1	LILRB1	140	1	0			c.T1740C						scavenged	.						111.0	95.0	100.0					19																	55148031		2200	4295	6495	SO:0001819	synonymous_variant	10859	exon14			TCCTCCTTCCCCA	AF009220	CCDS42614.1, CCDS42615.1, CCDS42616.1, CCDS42617.1, CCDS62803.1	19q13.4	2013-01-11						"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6605	protein-coding gene	gene with protein product		604811				9285411, 9382880	Standard	XM_006726246		Approved	LIR-1, ILT2, MIR-7, CD85, LIR1, CD85j	uc002qgm.3	Q8NHL6		ENST00000396331.1:c.1734T>C	19.37:g.55148031T>C		Somatic	345	5	0.0144928		WXS	Illumina HiSeq	Phase_I	460	14	0.0304348	NM_001081637	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Silent	SNP	ENST00000396331.1	37	CCDS42617.1																																																																																			.	.	weak		0.582	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4		
HMMR	3161	hgsc.bcm.edu	37	5	162910330	162910330	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:162910330G>A	ENST00000358715.3	+	15	1775	c.1739G>A	c.(1738-1740)cGt>cAt	p.R580H	HMMR_ENST00000393915.4_Missense_Mutation_p.R581H|RP11-80G7.1_ENST00000514724.2_RNA|RP11-80G7.1_ENST00000521666.1_RNA|HMMR_ENST00000432118.2_Missense_Mutation_p.R494H|HMMR_ENST00000353866.3_Missense_Mutation_p.R565H			O75330	HMMR_HUMAN	hyaluronan-mediated motility receptor (RHAMM)	580					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)			cervix(1)|kidney(3)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	23	Renal(175;0.000281)	Medulloblastoma(196;0.00853)|all_neural(177;0.0408)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0296)|OV - Ovarian serous cystadenocarcinoma(192;0.0423)|Epithelial(171;0.0848)	Hyaluronan(DB08818)	AACAAGTGGCGTCTCCTCTAT	0.303																																					p.R581H		Atlas-SNP	.											HMMR,NS,carcinoma,+1,1	HMMR	64	1	0			c.G1742A						scavenged	.						53.0	59.0	57.0					5																	162910330		2193	4297	6490	SO:0001583	missense	3161	exon15			AGTGGCGTCTCCT	U29343	CCDS4362.1, CCDS4363.1, CCDS47334.1, CCDS47335.1	5q34	2013-09-19			ENSG00000072571	ENSG00000072571		"""CD molecules"""	5012	protein-coding gene	gene with protein product		600936					Standard	NM_001142556		Approved	RHAMM, CD168	uc003lzh.3	O75330	OTTHUMG00000130381	ENST00000358715.3:c.1739G>A	5.37:g.162910330G>A	ENSP00000351554:p.Arg580His	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	164	2	0.0121951	NM_001142556	A8K3G2|B4E114|D3DQK9|D3DQL0|E9PCS0|Q32N02|Q92767	Missense_Mutation	SNP	ENST00000358715.3	37	CCDS4362.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.170091	0.78452	.	.	ENSG00000072571	ENST00000416990;ENST00000353866;ENST00000393915;ENST00000426586;ENST00000432118;ENST00000358715	T;T;T;T;T	0.28666	1.6;1.6;1.6;1.6;1.6	5.55	5.55	0.83447	.	0.044947	0.85682	D	0.000000	T	0.38268	0.1034	M	0.74258	2.255	0.47065	D	0.999309	P;B;P;P	0.50156	0.593;0.36;0.761;0.932	B;B;B;B	0.38954	0.14;0.042;0.286;0.286	T	0.45991	-0.9223	10	0.56958	D	0.05	-9.757	19.8764	0.96873	0.0:0.0:1.0:0.0	.	494;581;565;580	O75330-4;O75330-3;O75330-2;O75330	.;.;.;HMMR_HUMAN	H	466;565;581;557;494;580	ENSP00000400527:R466H;ENSP00000185942:R565H;ENSP00000377492:R581H;ENSP00000402673:R494H;ENSP00000351554:R580H	ENSP00000185942:R565H	R	+	2	0	HMMR	162842908	1.000000	0.71417	1.000000	0.80357	0.753000	0.42808	1.742000	0.38248	2.768000	0.95171	0.655000	0.94253	CGT	.	.	none		0.303	HMMR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252752.1	NM_012484	
MED26	9441	hgsc.bcm.edu	37	19	16687805	16687805	+	Missense_Mutation	SNP	C	C	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:16687805C>A	ENST00000263390.3	-	3	1098	c.836G>T	c.(835-837)cGg>cTg	p.R279L	CTC-429P9.4_ENST00000593962.1_5'Flank|CTD-3222D19.2_ENST00000409035.1_Missense_Mutation_p.R287L	NM_004831.3	NP_004822.2	O95402	MED26_HUMAN	mediator complex subunit 26	279	Pro-rich.				gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|RNA polymerase II transcription cofactor activity (GO:0001104)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|skin(1)	8						GCCCTCATGCCGTGAGTTCCG	0.667																																					p.R279L		Atlas-SNP	.											MED26,colon,carcinoma,0,1	MED26	25	1	0			c.G836T						PASS	.						30.0	32.0	32.0					19																	16687805		2203	4299	6502	SO:0001583	missense	9441	exon3			TCATGCCGTGAGT	AF104253	CCDS12347.1	19p13.11	2008-02-05	2007-07-30	2007-07-30		ENSG00000105085			2376	protein-coding gene	gene with protein product		605043	"""cofactor required for Sp1 transcriptional activation, subunit 7, 70kDa"""	CRSP7		9989412	Standard	NM_004831		Approved	CRSP70	uc002nen.1	O95402		ENST00000263390.3:c.836G>T	19.37:g.16687805C>A	ENSP00000263390:p.Arg279Leu	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	102	17	0.166667	NM_004831	A1A4S3|Q0VGB6	Missense_Mutation	SNP	ENST00000263390.3	37	CCDS12347.1	.	.	.	.	.	.	.	.	.	.	C	13.81	2.349489	0.41599	.	.	ENSG00000105085	ENST00000263390	.	.	.	4.74	3.69	0.42338	.	0.198170	0.41294	D	0.000907	T	0.61652	0.2364	L	0.57536	1.79	0.30471	N	0.773314	D	0.76494	0.999	D	0.79784	0.993	T	0.61797	-0.6989	9	0.28530	T	0.3	-30.7651	13.3549	0.60623	0.1589:0.8411:0.0:0.0	.	279	O95402	MED26_HUMAN	L	279	.	ENSP00000263390:R279L	R	-	2	0	MED26	16548805	1.000000	0.71417	0.997000	0.53966	0.076000	0.17211	4.328000	0.59253	0.977000	0.38444	-0.324000	0.08512	CGG	.	.	none		0.667	MED26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461178.1	NM_004831	
P2RY8	286530	hgsc.bcm.edu	37	X	1584574	1584574	+	Missense_Mutation	SNP	T	T	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:1584574T>A	ENST00000381297.4	-	2	1088	c.878A>T	c.(877-879)tAt>tTt	p.Y293F	P2RY8_ENST00000460672.1_5'Flank	NM_178129.4	NP_835230.1	Q86VZ1	P2RY8_HUMAN	purinergic receptor P2Y, G-protein coupled, 8	293						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|lung(13)|prostate(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)				CGCAAAGTAATAAACAAACGG	0.592			T	CRLF2	"""B-ALL, Downs associated ALL"""																																p.Y293F		Atlas-SNP	.		Dom	yes		"""X,Y"""	Xp22.3; Yp11.3	286530	"""purinergic receptor P2Y, G-protein coupled, 8"""		L	.	P2RY8	53	.	0			c.A878T						PASS	.						110.0	110.0	110.0					X																	1584574		2203	4296	6499	SO:0001583	missense	286530	exon2			AAGTAATAAACAA	AA804531	CCDS14115.1	Xp22.33 and Yp11.3	2012-08-08			ENSG00000182162	ENSG00000182162		"""Pseudoautosomal regions / PAR1"", ""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	15524	protein-coding gene	gene with protein product		300525				11004484	Standard	NM_178129		Approved	P2Y8	uc004cpz.2	Q86VZ1	OTTHUMG00000021060	ENST00000381297.4:c.878A>T	X.37:g.1584574T>A	ENSP00000370697:p.Tyr293Phe	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	120	74	0.616667	NM_178129		Missense_Mutation	SNP	ENST00000381297.4	37	CCDS14115.1	.	.	.	.	.	.	.	.	.	.	t	14.85	2.658567	0.47467	.	.	ENSG00000182162	ENST00000381297	D	0.92911	-3.13	2.73	2.73	0.32206	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	U	0.000003	D	0.94288	0.8165	M	0.64260	1.97	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	D	0.87643	0.2523	10	0.87932	D	0	.	10.6579	0.45686	0.0:0.0:0.0:1.0	.	293	Q86VZ1	P2RY8_HUMAN	F	293	ENSP00000370697:Y293F	ENSP00000370697:Y293F	Y	-	2	0	P2RY8	1544574	1.000000	0.71417	0.971000	0.41717	0.141000	0.21300	6.181000	0.71988	0.823000	0.34589	0.230000	0.17803	TAT	.	.	none		0.592	P2RY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055602.1	NM_178129	
TNRC6B	23112	hgsc.bcm.edu	37	22	40661027	40661027	+	Missense_Mutation	SNP	G	G	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr22:40661027G>T	ENST00000454349.2	+	5	1004	c.793G>T	c.(793-795)Gct>Tct	p.A265S	TNRC6B_ENST00000335727.9_Missense_Mutation_p.A265S|TNRC6B_ENST00000402203.1_Intron|TNRC6B_ENST00000301923.9_Intron	NM_001162501.1	NP_001155973.1	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B	265	Interaction with argonaute proteins.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)	1						TGACCCTAAGGCTAAATCTGT	0.468																																					p.A265S		Atlas-SNP	.											.	TNRC6B	195	.	0			c.G793T						PASS	.						109.0	105.0	107.0					22																	40661027		1899	4123	6022	SO:0001583	missense	23112	exon5			CCTAAGGCTAAAT	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.793G>T	22.37:g.40661027G>T	ENSP00000401946:p.Ala265Ser	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	71	37	0.521127	NM_001162501	B0QY73|B0QY78|B4DGC0|Q5TH52|Q8TBX2	Missense_Mutation	SNP	ENST00000454349.2	37	CCDS54533.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.104|8.104	0.777317|0.777317	0.16120|0.16120	.|.	.|.	ENSG00000100354|ENSG00000100354	ENST00000454349;ENST00000400140;ENST00000335727|ENST00000446273	T;T|.	0.51574|.	0.7;0.7|.	4.93|4.93	3.77|3.77	0.43336|0.43336	.|.	0.324254|.	0.32769|.	N|.	0.005673|.	T|T	0.30008|0.30008	0.0751|0.0751	N|N	0.16903|0.16903	0.455|0.455	0.31485|0.31485	N|N	0.666686|0.666686	B;B;B|.	0.22683|.	0.044;0.005;0.073|.	B;B;B|.	0.21917|.	0.036;0.01;0.037|.	T|T	0.30822|0.30822	-0.9965|-0.9965	10|5	0.08179|.	T|.	0.78|.	-0.1419|-0.1419	10.9081|10.9081	0.47092|0.47092	0.1037:0.0:0.8963:0.0|0.1037:0.0:0.8963:0.0	.|.	265;265;265|.	Q9UPQ9;A8MYY3;Q9UPQ9-1|.	TNR6B_HUMAN;.;.|.	S|S	265|7	ENSP00000401946:A265S;ENSP00000338371:A265S|.	ENSP00000338371:A265S|.	A|R	+|+	1|3	0|2	TNRC6B|TNRC6B	38990973|38990973	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	1.482000|1.482000	0.35486|0.35486	0.801000|0.801000	0.34066|0.34066	0.650000|0.650000	0.86243|0.86243	GCT|AGG	.	.	none		0.468	TNRC6B-202	KNOWN	basic|CCDS	protein_coding	protein_coding			
ADAM21	8747	hgsc.bcm.edu	37	14	70924812	70924812	+	Missense_Mutation	SNP	C	C	T	rs370238293		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr14:70924812C>T	ENST00000603540.1	+	2	854	c.596C>T	c.(595-597)tCt>tTt	p.S199F	RP11-486O13.4_ENST00000556646.1_lincRNA|ADAM21_ENST00000267499.3_Missense_Mutation_p.S199F	NM_003813.3	NP_003804.2	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21	199					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	31				all cancers(60;0.00326)|BRCA - Breast invasive adenocarcinoma(234;0.00646)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		GAACCAAAATCTGCTGGTGAC	0.448																																					p.S199F		Atlas-SNP	.											ADAM21_ENST00000267499,NS,carcinoma,0,6	ADAM21	181	6	0			c.C596T						scavenged	.						74.0	76.0	75.0					14																	70924812		2203	4300	6503	SO:0001583	missense	8747	exon2			CAAAATCTGCTGG	AF029900	CCDS9804.1	14q24.1	2008-09-05	2005-08-18		ENSG00000139985	ENSG00000139985		"""ADAM metallopeptidase domain containing"""	200	protein-coding gene	gene with protein product		603713	"""a disintegrin and metalloproteinase domain 21"""			9469942	Standard	NM_003813		Approved	ADAM31	uc001xmd.3	Q9UKJ8		ENST00000603540.1:c.596C>T	14.37:g.70924812C>T	ENSP00000474385:p.Ser199Phe	Somatic	205	1	0.00487805		WXS	Illumina HiSeq	Phase_I	213	9	0.0422535	NM_003813	O43507|Q2VPC6|Q32MR0	Missense_Mutation	SNP	ENST00000603540.1	37	CCDS9804.1	.	.	.	.	.	.	.	.	.	.	C	9.262	1.043355	0.19748	.	.	ENSG00000139985	ENST00000267499	T	0.01215	5.16	3.49	3.49	0.39957	.	0.378699	0.19013	U	0.125029	T	0.02230	0.0069	M	0.68593	2.085	0.26948	N	0.966098	B	0.32876	0.388	B	0.37422	0.249	T	0.24764	-1.0151	10	0.40728	T	0.16	.	10.6601	0.45698	0.0:1.0:0.0:0.0	.	199	Q9UKJ8	ADA21_HUMAN	F	199	ENSP00000267499:S199F	ENSP00000267499:S199F	S	+	2	0	ADAM21	69994565	0.001000	0.12720	0.813000	0.32504	0.022000	0.10575	0.380000	0.20602	1.947000	0.56498	0.557000	0.71058	TCT	.	.	weak		0.448	ADAM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413008.3		
PKHD1L1	93035	hgsc.bcm.edu	37	8	110495331	110495331	+	Missense_Mutation	SNP	G	G	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr8:110495331G>T	ENST00000378402.5	+	57	9677	c.9573G>T	c.(9571-9573)tgG>tgT	p.W3191C		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	3191					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)			CTGTGGATTGGCAGGTAGACA	0.368										HNSCC(38;0.096)																											p.W3191C		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.G9573T						PASS	.						75.0	71.0	72.0					8																	110495331		1863	4096	5959	SO:0001583	missense	93035	exon57			GGATTGGCAGGTA	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.9573G>T	8.37:g.110495331G>T	ENSP00000367655:p.Trp3191Cys	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	103	32	0.31068	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.129890	0.77549	.	.	ENSG00000205038	ENST00000378402;ENST00000526472	D;D	0.85339	-1.97;-1.97	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	D	0.94660	0.8278	H	0.94847	3.59	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95742	0.8784	10	0.87932	D	0	.	17.1705	0.86828	0.0:0.0:1.0:0.0	.	3191	Q86WI1	PKHL1_HUMAN	C	3191;119	ENSP00000367655:W3191C;ENSP00000437376:W119C	ENSP00000367655:W3191C	W	+	3	0	PKHD1L1	110564507	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	7.552000	0.82192	2.654000	0.90174	0.585000	0.79938	TGG	.	.	none		0.368	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
CADM3	57863	hgsc.bcm.edu	37	1	159170688	159170688	+	Silent	SNP	C	C	T	rs569300786		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:159170688C>T	ENST00000368125.4	+	9	1330	c.1173C>T	c.(1171-1173)gaC>gaT	p.D391D	CADM3_ENST00000497636.1_3'UTR|CADM3_ENST00000368124.4_Silent_p.D425D|CTA-134P22.2_ENST00000415675.2_RNA|DARC_ENST00000537147.1_5'Flank|CTA-134P22.2_ENST00000609696.1_RNA	NM_001127173.1	NP_001120645.1	Q8N126	CADM3_HUMAN	cell adhesion molecule 3	391					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|protein localization (GO:0008104)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(20)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55	all_hematologic(112;0.0429)					CAGGAGGGGACGACAAGAAGG	0.612													C|||	1	0.000199681	0.0008	0.0	5008	,	,		11580	0.0		0.0	False		,,,				2504	0.0				p.D425D		Atlas-SNP	.											CADM3,NS,carcinoma,0,1	CADM3	118	1	0			c.C1275T						scavenged	.						89.0	85.0	87.0					1																	159170688		2203	4300	6503	SO:0001819	synonymous_variant	57863	exon10			AGGGGACGACAAG	AY046418	CCDS1182.1, CCDS44251.1	1q21.2-q22	2013-01-29	2007-02-07	2007-02-07	ENSG00000162706	ENSG00000162706		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17601	protein-coding gene	gene with protein product	"""nectin-like 1"""	609743	"""immunoglobulin superfamily, member 4B"""	IGSF4B		11536053	Standard	NM_021189		Approved	BIgR, FLJ10698, TSLL1, NECL1, SynCAM3, Necl-1	uc001ftk.2	Q8N126	OTTHUMG00000037177	ENST00000368125.4:c.1173C>T	1.37:g.159170688C>T		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	146	3	0.0205479	NM_021189	Q8IZQ9|Q9NVJ5|Q9UJP1	Silent	SNP	ENST00000368125.4	37	CCDS44251.1																																																																																			.	.	none		0.612	CADM3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090330.1	NM_021189	
DNAJC13	23317	hgsc.bcm.edu	37	3	132245067	132245067	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:132245067T>C	ENST00000260818.6	+	53	6571	c.6323T>C	c.(6322-6324)cTa>cCa	p.L2108P		NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	2108					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						ACTGTTGGTCTAGCCTGTGAA	0.413																																					p.L2108P		Atlas-SNP	.											.	DNAJC13	253	.	0			c.T6323C						PASS	.						118.0	112.0	114.0					3																	132245067		2203	4300	6503	SO:0001583	missense	23317	exon53			TTGGTCTAGCCTG	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.6323T>C	3.37:g.132245067T>C	ENSP00000260818:p.Leu2108Pro	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	94	5	0.0531915	NM_015268	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Missense_Mutation	SNP	ENST00000260818.6	37	CCDS33857.1	.	.	.	.	.	.	.	.	.	.	T	15.62	2.886801	0.51908	.	.	ENSG00000138246	ENST00000260818;ENST00000538066	T	0.50548	0.74	5.58	5.58	0.84498	Armadillo-like helical (1);Armadillo-type fold (1);	0.233516	0.36482	N	0.002575	T	0.49847	0.1581	M	0.76838	2.35	0.80722	D	1	P	0.39131	0.661	B	0.33521	0.165	T	0.57487	-0.7803	10	0.52906	T	0.07	.	16.0439	0.80704	0.0:0.0:0.0:1.0	.	2108	O75165	DJC13_HUMAN	P	2108;755	ENSP00000260818:L2108P	ENSP00000260818:L2108P	L	+	2	0	DNAJC13	133727757	1.000000	0.71417	0.979000	0.43373	0.989000	0.77384	7.864000	0.87037	2.250000	0.74265	0.482000	0.46254	CTA	.	.	none		0.413	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268	
FAT1	2195	hgsc.bcm.edu	37	4	187629904	187629904	+	Missense_Mutation	SNP	A	A	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr4:187629904A>C	ENST00000441802.2	-	2	1287	c.1078T>G	c.(1078-1080)Ttc>Gtc	p.F360V		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	360					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						CCGGCTTTGAACTGTGGAGAA	0.458										HNSCC(5;0.00058)																											p.F360V	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.T1078G						PASS	.						121.0	114.0	116.0					4																	187629904		1864	4103	5967	SO:0001583	missense	2195	exon2			CTTTGAACTGTGG	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.1078T>G	4.37:g.187629904A>C	ENSP00000406229:p.Phe360Val	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	88	19	0.215909	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	A	9.719	1.159141	0.21454	.	.	ENSG00000083857	ENST00000441802;ENST00000260147;ENST00000509647	T;T	0.69306	-0.39;0.54	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.50034	0.1592	N	0.17278	0.47	0.80722	D	1	P	0.43431	0.807	B	0.40940	0.344	T	0.49051	-0.8979	10	0.11485	T	0.65	.	15.4097	0.74908	1.0:0.0:0.0:0.0	.	360	Q14517	FAT1_HUMAN	V	360	ENSP00000406229:F360V;ENSP00000423736:F360V	ENSP00000260147:F360V	F	-	1	0	FAT1	187866898	1.000000	0.71417	0.997000	0.53966	0.958000	0.62258	5.956000	0.70315	2.229000	0.72834	0.482000	0.46254	TTC	.	.	none		0.458	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
MUC4	4585	hgsc.bcm.edu	37	3	195515078	195515078	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:195515078C>T	ENST00000463781.3	-	2	3832	c.3373G>A	c.(3373-3375)Gac>Aac	p.D1125N	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D1125N|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	564					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.D1125N(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)		GAGGAAGTGTCGGTGACAGGA	0.562																																					p.D1125N		Atlas-SNP	.											MUC4_ENST00000463781,bladder,carcinoma,+1,5	MUC4	1505	5	3	Substitution - Missense(3)	endometrium(3)	c.G3373A						scavenged	.																																			SO:0001583	missense	4585	exon2			AAGTGTCGGTGAC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.3373G>A	3.37:g.195515078C>T	ENSP00000417498:p.Asp1125Asn	Somatic	131	2	0.0152672		WXS	Illumina HiSeq	Phase_I	141	6	0.0425532	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	5.951	0.359409	0.11239	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30182	1.56;1.54	0.814	-1.63	0.08345	.	.	.	.	.	T	0.18676	0.0448	N	0.19112	0.55	0.09310	N	1	D	0.59357	0.985	P	0.48738	0.588	T	0.05971	-1.0853	8	.	.	.	.	0.3671	0.00373	0.2014:0.3069:0.2014:0.2903	.	1125	E7ESK3	.	N	1125	ENSP00000417498:D1125N;ENSP00000420243:D1125N	.	D	-	1	0	MUC4	196999473	0.000000	0.05858	0.000000	0.03702	0.150000	0.21749	-3.293000	0.00523	-1.645000	0.01515	0.064000	0.15345	GAC	.	.	none		0.562	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
BAI2	576	hgsc.bcm.edu	37	1	32196967	32196967	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:32196967A>G	ENST00000373658.3	-	29	4155	c.3814T>C	c.(3814-3816)Tcc>Ccc	p.S1272P	BAI2_ENST00000398542.1_Missense_Mutation_p.S1172P|BAI2_ENST00000398547.1_Missense_Mutation_p.S1205P|BAI2_ENST00000440175.2_Missense_Mutation_p.S881P|BAI2_ENST00000465256.1_5'UTR|BAI2_ENST00000373655.2_Missense_Mutation_p.S1272P|BAI2_ENST00000398538.1_Missense_Mutation_p.S1260P|BAI2_ENST00000257070.4_Missense_Mutation_p.S1239P|BAI2_ENST00000527361.1_Missense_Mutation_p.S1239P|BAI2_ENST00000398556.3_Missense_Mutation_p.S1187P	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	1272					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(2)|endometrium(1)|large_intestine(7)|liver(2)|lung(24)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	55		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)		STAD - Stomach adenocarcinoma(196;0.0557)		GACAGGCGGGATAGTGTGCCC	0.622																																					p.S1272P		Atlas-SNP	.											BAI2,NS,haematopoietic_neoplasm,+2,1	BAI2	128	1	0			c.T3814C						scavenged	.						35.0	29.0	31.0					1																	32196967		2202	4299	6501	SO:0001583	missense	576	exon29			GGCGGGATAGTGT	AB005298	CCDS72746.1, CCDS72747.1	1p35	2014-08-08			ENSG00000121753	ENSG00000121753		"""-"", ""GPCR / Class B : Orphans"""	944	protein-coding gene	gene with protein product		602683				9533023	Standard	XM_006710783		Approved		uc001btn.3	O60241	OTTHUMG00000003885	ENST00000373658.3:c.3814T>C	1.37:g.32196967A>G	ENSP00000362762:p.Ser1272Pro	Somatic	247	24	0.097166		WXS	Illumina HiSeq	Phase_I	215	19	0.0883721	NM_001703	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	Missense_Mutation	SNP	ENST00000373658.3	37	CCDS346.2	.	.	.	.	.	.	.	.	.	.	A	18.29	3.590738	0.66219	.	.	ENSG00000121753	ENST00000398556;ENST00000398547;ENST00000373658;ENST00000373655;ENST00000398542;ENST00000257070;ENST00000527361;ENST00000440175;ENST00000398538	T;T;T;T;T;T;T;T;T	0.56611	1.12;1.45;0.62;0.62;1.5;0.45;0.45;1.15;0.64	5.16	5.16	0.70880	.	0.000000	0.42420	D	0.000719	T	0.69378	0.3104	M	0.63843	1.955	0.52501	D	0.999951	D;D;D;D;D;D;D	0.76494	0.999;0.998;0.997;0.999;0.999;0.997;0.997	D;D;D;D;D;D;D	0.91635	0.999;0.974;0.922;0.942;0.999;0.942;0.922	T	0.71024	-0.4712	10	0.51188	T	0.08	.	14.9679	0.71208	1.0:0.0:0.0:0.0	.	1239;1260;881;1187;1272;1272;1260	O60241-4;O60241-3;B4DKC3;A2A3C6;O60241-2;O60241;A2A3C2	.;.;.;.;.;BAI2_HUMAN;.	P	1187;1205;1272;1272;1172;1239;1239;881;1260	ENSP00000381564:S1187P;ENSP00000381555:S1205P;ENSP00000362762:S1272P;ENSP00000362759:S1272P;ENSP00000381550:S1172P;ENSP00000257070:S1239P;ENSP00000435397:S1239P;ENSP00000391071:S881P;ENSP00000381548:S1260P	ENSP00000257070:S1239P	S	-	1	0	BAI2	31969554	1.000000	0.71417	0.910000	0.35882	0.817000	0.46193	5.281000	0.65609	2.074000	0.62210	0.459000	0.35465	TCC	.	.	none		0.622	BAI2-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381838.1	NM_001703	
ANKS1B	56899	hgsc.bcm.edu	37	12	99640284	99640284	+	Silent	SNP	G	G	A	rs367637188		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:99640284G>A	ENST00000547776.2	-	13	2114	c.2115C>T	c.(2113-2115)aaC>aaT	p.N705N	ANKS1B_ENST00000550833.1_5'UTR|ANKS1B_ENST00000547010.1_Silent_p.N285N|ANKS1B_ENST00000329257.7_Silent_p.N705N	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B	705						cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ephrin receptor binding (GO:0046875)	p.N705K(1)		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)		ATCCCCCTGCGTTCATAACCC	0.448																																					p.N705N		Atlas-SNP	.											ANKS1B,NS,carcinoma,0,1	ANKS1B	180	1	1	Substitution - Missense(1)	lung(1)	c.C2115T						scavenged	.	G		0,3802		0,0,1901	125.0	120.0	121.0		2115	0.1	0.1	12		121	1,8241		0,1,4120	no	coding-synonymous	ANKS1B	NM_152788.4		0,1,6021	AA,AG,GG		0.0121,0.0,0.0083		705/1249	99640284	1,12043	1901	4121	6022	SO:0001819	synonymous_variant	56899	exon13			CCCTGCGTTCATA	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.2115C>T	12.37:g.99640284G>A		Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	340	4	0.0117647	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																																																																																			.	.	weak		0.448	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140	
HSPA2	3306	hgsc.bcm.edu	37	14	65008064	65008064	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr14:65008064C>T	ENST00000394709.1	+	2	573	c.497C>T	c.(496-498)aCg>aTg	p.T166M	HSPA2_ENST00000247207.6_Missense_Mutation_p.T166M|HSPA2_ENST00000554883.1_3'UTR|RP11-973N13.4_ENST00000554918.1_RNA			P54652	HSP72_HUMAN	heat shock 70kDa protein 2	166					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)	p.T166M(1)		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)		GGCACCATCACGGGGCTCAAT	0.662																																					p.T166M	Pancreas(136;1211 1835 24894 31984 38227)	Atlas-SNP	.											HSPA2,NS,carcinoma,0,2	HSPA2	83	2	1	Substitution - Missense(1)	endometrium(1)	c.C497T						PASS	.						51.0	52.0	52.0					14																	65008064		2203	4300	6503	SO:0001583	missense	3306	exon1			CCATCACGGGGCT	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.497C>T	14.37:g.65008064C>T	ENSP00000378199:p.Thr166Met	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	81	39	0.481481	NM_021979	Q15508|Q53XM3|Q9UE78	Missense_Mutation	SNP	ENST00000394709.1	37	CCDS9766.1	.	.	.	.	.	.	.	.	.	.	C	19.15	3.772333	0.69992	.	.	ENSG00000126803	ENST00000394709;ENST00000247207	T;T	0.01015	5.44;5.44	5.18	5.18	0.71444	.	0.112431	0.38605	U	0.001623	T	0.01905	0.0060	N	0.08118	0	0.39563	D	0.969168	D	0.71674	0.998	P	0.62014	0.897	T	0.75505	-0.3294	10	0.87932	D	0	-7.4702	18.6851	0.91560	0.0:1.0:0.0:0.0	.	166	P54652	HSP72_HUMAN	M	166	ENSP00000378199:T166M;ENSP00000247207:T166M	ENSP00000247207:T166M	T	+	2	0	HSPA2	64077817	1.000000	0.71417	0.993000	0.49108	0.983000	0.72400	7.818000	0.86416	2.407000	0.81776	0.563000	0.77884	ACG	.	.	none		0.662	HSPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280651.1		
NFKB2	4791	hgsc.bcm.edu	37	10	104160764	104160764	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr10:104160764G>A	ENST00000369966.3	+	18	2279	c.2029G>A	c.(2029-2031)Gga>Aga	p.G677R	NFKB2_ENST00000428099.1_Missense_Mutation_p.G677R|NFKB2_ENST00000189444.6_Missense_Mutation_p.G677R	NM_001077494.2	NP_001070962.1	Q00653	NFKB2_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)	677			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)	CCTGGCAGCTGGACTGGGGTA	0.647			T	IGH@	B-NHL																																p.G677R		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.G2029A						PASS	.						33.0	41.0	39.0					10																	104160764		2063	4206	6269	SO:0001583	missense	4791	exon18			GCAGCTGGACTGG	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.2029G>A	10.37:g.104160764G>A	ENSP00000358983:p.Gly677Arg	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	112	54	0.482143	NM_001077494	A8K9D9|D3DR83|Q04860|Q9BU75|Q9H471|Q9H472	Missense_Mutation	SNP	ENST00000369966.3	37	CCDS41564.1	.	.	.	.	.	.	.	.	.	.	g	20.4	3.990200	0.74589	.	.	ENSG00000077150	ENST00000428099;ENST00000369966;ENST00000336486;ENST00000189444	T;T;T	0.61742	0.08;0.08;0.08	4.48	4.48	0.54585	Ankyrin repeat-containing domain (4);	0.109105	0.64402	D	0.000009	T	0.53562	0.1804	N	0.04724	-0.175	0.32550	N	0.532449	D;D	0.76494	0.999;0.999	D;D	0.75484	0.986;0.986	T	0.63377	-0.6651	10	0.52906	T	0.07	.	11.0484	0.47872	0.0869:0.0:0.9131:0.0	.	677;677	Q00653;A8K9D9	NFKB2_HUMAN;.	R	677	ENSP00000410256:G677R;ENSP00000358983:G677R;ENSP00000189444:G677R	ENSP00000189444:G677R	G	+	1	0	NFKB2	104150754	1.000000	0.71417	1.000000	0.80357	0.721000	0.41392	4.183000	0.58317	2.526000	0.85167	0.531000	0.56144	GGA	.	.	none		0.647	NFKB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050080.2		
PRB3	5544	hgsc.bcm.edu	37	12	11420563	11420563	+	Missense_Mutation	SNP	G	G	T	rs200902635		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	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	172	1	0.00581395		WXS	Illumina HiSeq	Phase_I	188	4	0.0212766	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	
TKTL2	84076	hgsc.bcm.edu	37	4	164394041	164394041	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr4:164394041T>C	ENST00000280605.3	-	1	1006	c.846A>G	c.(844-846)atA>atG	p.I282M		NM_032136.4	NP_115512.3	Q9H0I9	TKTL2_HUMAN	transketolase-like 2	282						cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|transketolase activity (GO:0004802)			breast(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(42)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	70	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				CATTGGTCTGTATCTGACTCT	0.408																																					p.I282M		Atlas-SNP	.											TKTL2,colon,carcinoma,-1,1	TKTL2	130	1	0			c.A846G						scavenged	.						162.0	164.0	163.0					4																	164394041		2203	4300	6503	SO:0001583	missense	84076	exon1			GGTCTGTATCTGA	BC028707	CCDS3805.1	4q32.2	2009-10-06			ENSG00000151005	ENSG00000151005			25313	protein-coding gene	gene with protein product	"""similar to transketolase"""					11230166	Standard	NM_032136		Approved	FLJ32975, DKFZP434L1717	uc003iqp.4	Q9H0I9	OTTHUMG00000161527	ENST00000280605.3:c.846A>G	4.37:g.164394041T>C	ENSP00000280605:p.Ile282Met	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	256	4	0.015625	NM_032136	A4FVB4|Q8NCT0|Q96M82	Missense_Mutation	SNP	ENST00000280605.3	37	CCDS3805.1	.	.	.	.	.	.	.	.	.	.	T	4.918	0.170509	0.09391	.	.	ENSG00000151005	ENST00000280605	T	0.23754	1.89	4.3	-5.0	0.03001	.	0.114059	0.56097	D	0.000027	T	0.24812	0.0602	M	0.73962	2.25	0.42611	D	0.993318	P	0.34684	0.463	B	0.38985	0.287	T	0.05115	-1.0905	10	0.46703	T	0.11	-0.848	7.4155	0.27042	0.0:0.2489:0.5194:0.2317	.	282	Q9H0I9	TKTL2_HUMAN	M	282	ENSP00000280605:I282M	ENSP00000280605:I282M	I	-	3	3	TKTL2	164613491	1.000000	0.71417	0.400000	0.26346	0.113000	0.19764	0.517000	0.22832	-0.854000	0.04131	-0.250000	0.11733	ATA	.	.	none		0.408	TKTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365207.1	NM_032136	
KMT2C	58508	hgsc.bcm.edu	37	7	151932990	151932990	+	Missense_Mutation	SNP	C	C	T	rs76844681		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	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	172	3	0.0174419		WXS	Illumina HiSeq	Phase_I	170	8	0.0470588	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		
HIST1H1C	3006	hgsc.bcm.edu	37	6	26056488	26056488	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr6:26056488C>T	ENST00000343677.2	-	1	211	c.169G>A	c.(169-171)Gtt>Att	p.V57I		NM_005319.3	NP_005310.1	P16403	H12_HUMAN	histone cluster 1, H1c	57	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(4)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	34						GCCAGAGAAACTCCGCTACGC	0.572																																					p.V57I		Atlas-SNP	.											.	HIST1H1C	80	.	0			c.G169A						PASS	.						74.0	83.0	80.0					6																	26056488		2203	4300	6503	SO:0001583	missense	3006	exon1			GAGAAACTCCGCT	X57129	CCDS4577.1	6p21.3	2012-10-02	2006-10-11	2003-02-21	ENSG00000187837	ENSG00000187837		"""Histones / Replication-dependent"""	4716	protein-coding gene	gene with protein product		142710	"""H1 histone family, member 2"", ""histone 1, H1c"""	H1F2		2759094, 12408966	Standard	NM_005319		Approved	H1.2, H1s-1, H1c	uc003nfw.3	P16403	OTTHUMG00000016140	ENST00000343677.2:c.169G>A	6.37:g.26056488C>T	ENSP00000339566:p.Val57Ile	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	144	61	0.423611	NM_005319	A8K4I2	Missense_Mutation	SNP	ENST00000343677.2	37	CCDS4577.1	.	.	.	.	.	.	.	.	.	.	C	14.93	2.681630	0.47991	.	.	ENSG00000187837	ENST00000343677	T	0.21932	1.98	5.73	5.73	0.89815	Histone H1/H5 (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.135447	0.48286	D	0.000194	T	0.25195	0.0612	M	0.87682	2.9	0.58432	D	0.999992	B	0.32968	0.392	B	0.37989	0.262	T	0.02477	-1.1153	10	0.42905	T	0.14	-28.79	15.5188	0.75846	0.0:0.8523:0.1477:0.0	.	57	P16403	H12_HUMAN	I	57	ENSP00000339566:V57I	ENSP00000339566:V57I	V	-	1	0	HIST1H1C	26164467	0.879000	0.30193	0.960000	0.40013	0.011000	0.07611	1.731000	0.38135	2.861000	0.98227	0.655000	0.94253	GTT	.	.	none		0.572	HIST1H1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043372.1	NM_005319	
RNF145	153830	hgsc.bcm.edu	37	5	158630641	158630641	+	5'UTR	SNP	C	C	T	rs74770414|rs74841177|rs368977591		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:158630641C>T	ENST00000424310.2	-	0	344				RNF145_ENST00000274542.2_Silent_p.K23K|RNF145_ENST00000518802.1_Silent_p.K25K|RNF145_ENST00000519865.1_5'UTR|RNF145_ENST00000521606.2_Silent_p.K12K|RNF145_ENST00000520638.1_Silent_p.K9K	NM_001199383.1	NP_001186312.1	Q96MT1	RN145_HUMAN	ring finger protein 145							integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ttttttttttctttttttttt	0.363																																					p.K25K		Atlas-SNP	.											RNF145,NS,carcinoma,-1,2	RNF145	110	2	0			c.G75A						scavenged	.						32.0	34.0	33.0					5																	158630641		2203	4300	6503	SO:0001623	5_prime_UTR_variant	153830	exon2			TTTTTTCTTTTTT	BC042684	CCDS4344.1, CCDS56390.1, CCDS56391.1, CCDS56392.1, CCDS56393.1	5q33.3	2013-01-09			ENSG00000145860	ENSG00000145860		"""RING-type (C3HC4) zinc fingers"""	20853	protein-coding gene	gene with protein product							Standard	NM_001199380		Approved	FLJ31951	uc003lxo.2	Q96MT1	OTTHUMG00000130306	ENST00000424310.2:c.-16G>A	5.37:g.158630641C>T		Somatic	23	1	0.0434783		WXS	Illumina HiSeq	Phase_I	37	4	0.108108	NM_001199380	B7Z903|B7Z949|E7EVI7|Q8IVP7	Silent	SNP	ENST00000424310.2	37	CCDS56390.1																																																																																			.	.	weak		0.363	RNF145-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374048.1	NM_144726	
SLC32A1	140679	hgsc.bcm.edu	37	20	37353459	37353459	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr20:37353459T>C	ENST00000217420.1	+	1	355	c.92T>C	c.(91-93)aTg>aCg	p.M31T		NM_080552.2	NP_542119.1	Q9H598	VIAAT_HUMAN	solute carrier family 32 (GABA vesicular transporter), member 1	31					aging (GO:0007568)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell tip (GO:0051286)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cone cell pedicle (GO:0044316)|dendrite (GO:0030425)|dendrite terminus (GO:0044292)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|neuron projection terminus (GO:0044306)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	gamma-aminobutyric acid:proton symporter activity (GO:0015495)|glycine transmembrane transporter activity (GO:0015187)			breast(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(16)|urinary_tract(1)	38		Myeloproliferative disorder(115;0.00878)			Glycine(DB00145)	TTCGCCAGGATGGGTTTTCAG	0.632																																					p.M31T		Atlas-SNP	.											SLC32A1,lower_third,carcinoma,0,1	SLC32A1	81	1	0			c.T92C						scavenged	.						48.0	32.0	38.0					20																	37353459		2203	4300	6503	SO:0001583	missense	140679	exon1			CCAGGATGGGTTT	AL133519	CCDS13307.1	20q11	2013-05-22			ENSG00000101438	ENSG00000101438		"""Solute carriers"""	11018	protein-coding gene	gene with protein product			"""vesicular inhibitory amino acid transporter"""	VIAAT		19843525	Standard	NM_080552		Approved	VGAT, bA122O1.1	uc002xjc.3	Q9H598	OTTHUMG00000032457	ENST00000217420.1:c.92T>C	20.37:g.37353459T>C	ENSP00000217420:p.Met31Thr	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	165	2	0.0121212	NM_080552	Q8N489	Missense_Mutation	SNP	ENST00000217420.1	37	CCDS13307.1	.	.	.	.	.	.	.	.	.	.	T	13.46	2.244930	0.39697	.	.	ENSG00000101438	ENST00000217420	T	0.08282	3.11	4.85	3.73	0.42828	.	0.044040	0.85682	D	0.000000	T	0.05273	0.0140	N	0.19112	0.55	0.44188	D	0.997007	B	0.19817	0.039	B	0.15484	0.013	T	0.39683	-0.9602	10	0.15952	T	0.53	-34.28	9.8857	0.41260	0.0:0.0:0.1724:0.8276	.	31	Q9H598	VIAAT_HUMAN	T	31	ENSP00000217420:M31T	ENSP00000217420:M31T	M	+	2	0	SLC32A1	36786873	1.000000	0.71417	1.000000	0.80357	0.800000	0.45204	5.932000	0.70121	0.674000	0.31244	-0.466000	0.05196	ATG	.	.	none		0.632	SLC32A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079206.1	NM_080552	
GLIS1	148979	hgsc.bcm.edu	37	1	53980302	53980302	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:53980302C>T	ENST00000312233.2	-	7	1920	c.1354G>A	c.(1354-1356)Gat>Aat	p.D452N		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						ACATACCCATCCCGGGTGCTC	0.647																																					p.D452N		Atlas-SNP	.											.	GLIS1	52	.	0			c.G1354A						PASS	.						76.0	78.0	77.0					1																	53980302		2203	4300	6503	SO:0001583	missense	148979	exon7			ACCCATCCCGGGT	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.1354G>A	1.37:g.53980302C>T	ENSP00000309653:p.Asp452Asn	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	161	29	0.180124	NM_147193		Missense_Mutation	SNP	ENST00000312233.2	37	CCDS582.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.237047	0.79800	.	.	ENSG00000174332	ENST00000312233	T	0.10573	2.86	4.97	4.97	0.65823	.	0.106321	0.41097	D	0.000949	T	0.13798	0.0334	L	0.29908	0.895	0.38952	D	0.958378	P	0.52842	0.956	P	0.50082	0.63	T	0.10132	-1.0643	10	0.23891	T	0.37	.	16.8949	0.86097	0.0:1.0:0.0:0.0	.	452	Q8NBF1	GLIS1_HUMAN	N	452	ENSP00000309653:D452N	ENSP00000309653:D452N	D	-	1	0	GLIS1	53752890	1.000000	0.71417	1.000000	0.80357	0.646000	0.38490	3.887000	0.56197	2.688000	0.91661	0.563000	0.77884	GAT	.	.	none		0.647	GLIS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022109.1	NM_147193	
FOXK1	221937	hgsc.bcm.edu	37	7	4794917	4794917	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr7:4794917T>C	ENST00000328914.4	+	4	953	c.953T>C	c.(952-954)aTc>aCc	p.I318T	FOXK1_ENST00000446823.1_Missense_Mutation_p.I155T	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)		GTGCAGGCCATCTCCTCCGCC	0.627																																					p.I318T		Atlas-SNP	.											KIAA0415_ENST00000450194,NS,carcinoma,-1,2	FOXK1	64	2	0			c.T953C						scavenged	.						69.0	60.0	63.0					7																	4794917		2203	4300	6503	SO:0001583	missense	221937	exon4			AGGCCATCTCCTC	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.953T>C	7.37:g.4794917T>C	ENSP00000328720:p.Ile318Thr	Somatic	95	1	0.0105263		WXS	Illumina HiSeq	Phase_I	84	3	0.0357143	NM_001037165		Missense_Mutation	SNP	ENST00000328914.4	37	CCDS34591.1	.	.	.	.	.	.	.	.	.	.	T	27.2	4.807145	0.90623	.	.	ENSG00000164916	ENST00000446823;ENST00000450194;ENST00000328914;ENST00000545598	D;D	0.97232	-4.3;-4.3	5.35	5.35	0.76521	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (4);Transcription factor, fork head, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.98979	0.9652	H	0.96805	3.885	0.80722	D	1	D;D	0.76494	0.999;0.985	D;D	0.91635	0.999;0.957	D	0.99429	1.0935	10	0.87932	D	0	.	14.5447	0.68020	0.0:0.0:0.0:1.0	.	318;155	P85037;P85037-2	FOXK1_HUMAN;.	T	155;82;318;201	ENSP00000394442:I155T;ENSP00000328720:I318T	ENSP00000328720:I318T	I	+	2	0	FOXK1	4761443	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.033000	0.88852	2.026000	0.59711	0.533000	0.62120	ATC	.	.	none		0.627	FOXK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323729.2		
ABCC2	1244	hgsc.bcm.edu	37	10	101558978	101558978	+	Silent	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr10:101558978G>A	ENST00000370449.4	+	8	995	c.882G>A	c.(880-882)aaG>aaA	p.K294K		NM_000392.3	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	294					cellular chloride ion homeostasis (GO:0030644)|drug transmembrane transport (GO:0006855)|prostaglandin transport (GO:0015732)|response to arsenic-containing substance (GO:0046685)|response to estrogen (GO:0043627)|response to heat (GO:0009408)|response to methotrexate (GO:0031427)|response to oxidative stress (GO:0006979)|thyroid hormone transport (GO:0070327)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)	p.K294N(1)		NS(1)|breast(5)|endometrium(9)|kidney(2)|large_intestine(20)|liver(1)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	67		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Aminohippurate(DB00345)|Arsenic trioxide(DB01169)|Atorvastatin(DB01076)|Canagliflozin(DB08907)|Carbamazepine(DB00564)|Carboplatin(DB00958)|Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Eprosartan(DB00876)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Ezetimibe(DB00973)|Furosemide(DB00695)|Fusidic Acid(DB02703)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Leucovorin(DB00650)|Levetiracetam(DB01202)|Lomefloxacin(DB00978)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nifedipine(DB01115)|Norgestimate(DB00957)|Ofloxacin(DB01165)|Olmesartan(DB00275)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Ritonavir(DB00503)|Saquinavir(DB01232)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Sulfasalazine(DB00795)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Tenofovir(DB00300)|Tetrahydrofolic acid(DB00116)|Ursodeoxycholic acid(DB01586)|Vasopressin(DB00067)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	ATGTTGAAAAGAAAAAAAAGA	0.443																																					p.K294K		Atlas-SNP	.											ABCC2,NS,carcinoma,0,1	ABCC2	160	1	1	Substitution - Missense(1)	breast(1)	c.G882A						scavenged	.						132.0	148.0	142.0					10																	101558978		2203	4300	6503	SO:0001819	synonymous_variant	1244	exon8			TGAAAAGAAAAAA	U63970	CCDS7484.1	10q24	2012-03-14			ENSG00000023839	ENSG00000023839		"""ATP binding cassette transporters / subfamily C"""	53	protein-coding gene	gene with protein product		601107	"""canalicular multispecific organic anion transporter 1"""	CMOAT		8797578, 9284939	Standard	XM_006717630		Approved	DJS, MRP2, cMRP	uc001kqf.2	Q92887	OTTHUMG00000018895	ENST00000370449.4:c.882G>A	10.37:g.101558978G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	57	2	0.0350877	NM_000392	B2RMT8|Q14022|Q5T2B1|Q92500|Q92798|Q99663|Q9UMS2	Silent	SNP	ENST00000370449.4	37	CCDS7484.1																																																																																			.	.	none		0.443	ABCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049825.1	NM_000392	
TRPM3	80036	hgsc.bcm.edu	37	9	73151520	73151520	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr9:73151520C>T	ENST00000377110.3	-	25	4716	c.4473G>A	c.(4471-4473)ccG>ccA	p.P1491P	TRPM3_ENST00000377106.1_Silent_p.P1363P|TRPM3_ENST00000408909.2_Silent_p.P1350P|TRPM3_ENST00000357533.2_Silent_p.P1495P|TRPM3_ENST00000396285.1_Silent_p.P1350P|TRPM3_ENST00000423814.3_Silent_p.P1518P|TRPM3_ENST00000360823.2_Silent_p.P1353P|TRPM3_ENST00000396292.4_Silent_p.P1363P|TRPM3_ENST00000377105.1_Silent_p.P1350P|TRPM3_ENST00000377111.2_Intron|TRPM3_ENST00000358082.3_Silent_p.P1353P|TRPM3_ENST00000396280.5_Silent_p.P1340P			Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	1516					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)	p.P1495P(1)|p.P1363P(1)|p.P1491P(1)		NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						TGTGGTACATCGGAGGCTCTG	0.483																																					p.P1491P		Atlas-SNP	.											TRPM3_ENST00000423814,NS,carcinoma,0,4	TRPM3	700	4	3	Substitution - coding silent(3)	lung(3)	c.G4473A						scavenged	.						104.0	109.0	107.0					9																	73151520		2203	4300	6503	SO:0001819	synonymous_variant	80036	exon25			GTACATCGGAGGC	AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17992	protein-coding gene	gene with protein product	"""melastatin 2"""	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000377110.3:c.4473G>A	9.37:g.73151520C>T		Somatic	354	0	0		WXS	Illumina HiSeq	Phase_I	395	5	0.0126582	NM_001007471	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Silent	SNP	ENST00000377110.3	37	CCDS43835.1	.	.	.	.	.	.	.	.	.	.	C	1.147	-0.647757	0.03506	.	.	ENSG00000083067	ENST00000396280	.	.	.	6.02	-6.87	0.01671	.	.	.	.	.	T	0.50803	0.1637	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56872	-0.7907	4	.	.	.	-14.4847	10.0628	0.42286	0.0737:0.134:0.6605:0.1318	.	.	.	.	N	1340	.	.	D	-	1	0	TRPM3	72341340	0.000000	0.05858	0.069000	0.20011	0.881000	0.50899	-2.538000	0.00938	-0.817000	0.04335	-1.267000	0.01435	GAT	.	.	none		0.483	TRPM3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214158.3	NM_206945	
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305785	39305785	+	Missense_Mutation	SNP	A	A	T	rs411367		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr17:39305785A>T	ENST00000343246.4	-	1	269	c.235T>A	c.(235-237)Tgc>Agc	p.C79S		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	79	26 X 5 AA repeats of C-C-[GRQVCHIEK]- [SPTR]-[VSTQYC].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(4)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			tggcagcagcaggggcggcag	0.657																																					p.C79S		Atlas-SNP	.											KRTAP4-5,colon,carcinoma,0,3	KRTAP4-5	34	3	0			c.T235A						PASS	.						12.0	18.0	16.0					17																	39305785		2089	4172	6261	SO:0001583	missense	85289	exon1			AGCAGCAGGGGCG	AJ406937	CCDS32650.1	17q21.2	2013-06-25			ENSG00000198271	ENSG00000198271		"""Keratin associated proteins"""	18899	protein-coding gene	gene with protein product						11279113	Standard	NM_033188		Approved	KAP4.5	uc002hwb.3	Q9BYR2	OTTHUMG00000133638	ENST00000343246.4:c.235T>A	17.37:g.39305785A>T	ENSP00000340546:p.Cys79Ser	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	56	7	0.125	NM_033188		Missense_Mutation	SNP	ENST00000343246.4	37	CCDS32650.1	773	0.35393772893772896	210	0.4268292682926829	126	0.34806629834254144	175	0.30594405594405594	262	0.34564643799472294	.	0.010	-1.763522	0.00651	.	.	ENSG00000198271	ENST00000343246	T	0.00534	6.74	2.78	-5.56	0.02529	.	0.768893	0.10092	N	0.717076	T	0.00012	0.0000	N	0.01431	-0.87	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.23297	-1.0192	9	0.02654	T	1	.	5.4481	0.16548	0.6146:0.0:0.1542:0.2312	rs411367;rs6503604	79	Q9BYR2	KRA45_HUMAN	S	79	ENSP00000340546:C79S	ENSP00000340546:C79S	C	-	1	0	KRTAP4-5	36559311	0.977000	0.34250	0.000000	0.03702	0.000000	0.00434	-0.260000	0.08708	-1.272000	0.02427	-2.057000	0.00402	TGC	A|0.646;T|0.354	0.354	strong		0.657	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1		
POTEE	445582	hgsc.bcm.edu	37	2	132021475	132021475	+	Missense_Mutation	SNP	G	G	A	rs11546936		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:132021475G>A	ENST00000356920.5	+	15	2541	c.2447G>A	c.(2446-2448)cGc>cAc	p.R816H	POTEE_ENST00000358087.5_3'UTR|PLEKHB2_ENST00000303908.3_Intron|PLEKHB2_ENST00000404460.1_Intron	NM_001083538.1	NP_001077007.1	Q6S8J3	POTEE_HUMAN	POTE ankyrin domain family, member E	816	Actin-like.				retina homeostasis (GO:0001895)|substantia nigra development (GO:0021762)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)											AAGGCCAACCGCGAGAAGATG	0.607																																					p.R816H		Atlas-SNP	.											ENSG00000188219,NS,carcinoma,+1,2	.	.	2	0			c.G2447A						scavenged	.						78.0	80.0	79.0					2																	132021475		2127	4190	6317	SO:0001583	missense	445582	exon15			CCAACCGCGAGAA	AY462868	CCDS46414.1	2q21.1	2014-04-10	2008-11-26	2008-11-26	ENSG00000188219	ENSG00000188219		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33895	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 2"""	608914	"""ANKRD26-like family C, member 1A"""	A26C1A			Standard	NM_001083538		Approved	POTE2, POTE-2, A26C1, POTE2gamma, CT104.2	uc002tsn.2	Q6S8J3	OTTHUMG00000186974	ENST00000356920.5:c.2447G>A	2.37:g.132021475G>A	ENSP00000439189:p.Arg816His	Somatic	214	12	0.0560748		WXS	Illumina HiSeq	Phase_I	262	23	0.0877863	NM_001083538	Q6S8J4|Q6S8J5|Q6S8J8	Missense_Mutation	SNP	ENST00000356920.5	37	CCDS46414.1	.	.	.	.	.	.	.	.	.	.	.	18.42	3.621132	0.66787	.	.	ENSG00000188219	ENST00000356920	D	0.97066	-4.23	.	.	.	Actin/actin-like conserved site (1);	.	.	.	.	D	0.98817	0.9601	H	0.99261	4.49	0.80722	D	1	D	0.89917	1.0	D	0.72625	0.978	D	0.96667	0.9493	8	0.87932	D	0	.	5.9051	0.18992	8.0E-4:0.0:0.9992:0.0	rs11546936	816	Q6S8J3	POTEE_HUMAN	H	816	ENSP00000439189:R816H	ENSP00000439189:R816H	R	+	2	0	AC131180.1	131737945	1.000000	0.71417	0.216000	0.23742	0.219000	0.24729	6.504000	0.73704	0.119000	0.18210	0.121000	0.15741	CGC	.	.	weak		0.607	POTEE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001083538	
PIGP	51227	hgsc.bcm.edu	37	21	38437947	38437947	+	Missense_Mutation	SNP	T	T	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr21:38437947T>A	ENST00000464265.1	-	4	635	c.412A>T	c.(412-414)Att>Ttt	p.I138F	PIGP_ENST00000399102.1_Missense_Mutation_p.I114F|PIGP_ENST00000399098.1_Missense_Mutation_p.I88F|PIGP_ENST00000360525.4_Missense_Mutation_p.I114F|PIGP_ENST00000329667.3_5'UTR|PIGP_ENST00000399103.1_Missense_Mutation_p.I114F	NM_153681.2	NP_710148.1	P57054	PIGP_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class P	138					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|integral component of membrane (GO:0016021)	phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)			kidney(1)|urinary_tract(1)	2		Myeloproliferative disorder(46;0.0412)				CTAATAGAAATATCTCTTAAG	0.358																																					p.I138F		Atlas-SNP	.											.	PIGP	9	.	0			c.A412T						PASS	.						143.0	139.0	140.0					21																	38437947		2203	4300	6503	SO:0001583	missense	51227	exon4			TAGAAATATCTCT	AB037162	CCDS13649.1, CCDS13650.1	21q22.2	2013-02-26	2006-06-28	2005-11-10	ENSG00000185808	ENSG00000185808	2.4.1.198	"""Phosphatidylinositol glycan anchor biosynthesis"""	3046	protein-coding gene	gene with protein product	"""phosphatidylinositol-n-acetylglucosaminyltranferase subunit"""	605938	"""Down syndrome critical region gene 5"", ""phosphatidylinositol glycan, class P"""	DSCR5		10814524, 15221505	Standard	NR_028352		Approved	DCRC, DSRC	uc002yvw.1	P57054	OTTHUMG00000086653	ENST00000464265.1:c.412A>T	21.37:g.38437947T>A	ENSP00000420037:p.Ile138Phe	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	191	45	0.235602	NM_153681	B2RB18|B2RE99|B5BU92|D3DSG7|J3KR75|Q53Y28|Q96KI1|Q9NZA6	Missense_Mutation	SNP	ENST00000464265.1	37	CCDS13649.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.000227	0.74818	.	.	ENSG00000185808	ENST00000464265;ENST00000360525;ENST00000399102;ENST00000399103;ENST00000399098	T;T;T;T;T	0.36340	1.26;1.26;1.26;1.26;1.26	5.52	3.01	0.34805	PIG-P (1);	0.107627	0.64402	D	0.000007	T	0.53578	0.1805	M	0.84683	2.71	0.39299	D	0.964862	P	0.49253	0.921	P	0.54210	0.745	T	0.59337	-0.7473	10	0.72032	D	0.01	-8.0575	10.1016	0.42509	0.0:0.1415:0.0:0.8585	.	138	P57054	PIGP_HUMAN	F	138;114;114;114;88	ENSP00000420037:I138F;ENSP00000353719:I114F;ENSP00000382053:I114F;ENSP00000382054:I114F;ENSP00000382049:I88F	ENSP00000353719:I114F	I	-	1	0	PIGP	37359817	0.997000	0.39634	0.999000	0.59377	0.996000	0.88848	1.091000	0.30915	0.323000	0.23307	0.533000	0.62120	ATT	.	.	none		0.358	PIGP-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000194769.2	NM_153681	
PRMT8	56341	hgsc.bcm.edu	37	12	3692249	3692249	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:3692249C>T	ENST00000382622.3	+	8	1244	c.854C>T	c.(853-855)aCg>aTg	p.T285M	PRMT8_ENST00000261252.4_Intron|PRMT8_ENST00000452611.2_Missense_Mutation_p.T276M	NM_019854.4	NP_062828.3	Q9NR22	ANM8_HUMAN	protein arginine methyltransferase 8	285	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				histone arginine methylation (GO:0034969)|histone H4-R3 methylation (GO:0043985)|histone methylation (GO:0016571)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|regulation of protein binding (GO:0043393)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	histone methyltransferase activity (H4-R3 specific) (GO:0044020)|histone-arginine N-methyltransferase activity (GO:0008469)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|protein-arginine omega-N monomethyltransferase activity (GO:0035241)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(9)|lung(14)|ovary(3)|skin(5)|upper_aerodigestive_tract(1)	37			OV - Ovarian serous cystadenocarcinoma(31;0.0109)|COAD - Colon adenocarcinoma(12;0.0264)			ACAGTGAAGACGGAAGAGCTA	0.517																																					p.T285M		Atlas-SNP	.											PRMT8,NS,carcinoma,-1,3	PRMT8	97	3	0			c.C854T						PASS	.						128.0	104.0	112.0					12																	3692249		2203	4300	6503	SO:0001583	missense	56341	exon8			TGAAGACGGAAGA	AF263539	CCDS8521.2, CCDS58200.1	12p13.3	2006-03-03	2006-02-16	2006-02-16	ENSG00000111218	ENSG00000111218		"""Protein arginine methyltransferases"""	5188	protein-coding gene	gene with protein product		610086	"""HMT1 hnRNP methyltransferase-like 3 (S. cerevisiae)"", ""HMT1 hnRNP methyltransferase-like 4 (S. cerevisiae)"""	HRMT1L3, HRMT1L4		16051612	Standard	NM_019854		Approved		uc001qmf.4	Q9NR22	OTTHUMG00000128493	ENST00000382622.3:c.854C>T	12.37:g.3692249C>T	ENSP00000372067:p.Thr285Met	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	102	22	0.215686	NM_019854	B2RDP0|Q8TBJ8	Missense_Mutation	SNP	ENST00000382622.3	37	CCDS8521.2	.	.	.	.	.	.	.	.	.	.	C	11.07	1.530304	0.27387	.	.	ENSG00000111218	ENST00000452611;ENST00000382622	T;T	0.78707	-1.2;-1.2	5.4	3.57	0.40892	.	0.202156	0.52532	D	0.000070	T	0.70193	0.3196	L	0.54323	1.7	0.37506	D	0.91696	P;P	0.42649	0.786;0.68	B;B	0.39027	0.288;0.15	T	0.73588	-0.3935	10	0.46703	T	0.11	.	9.2713	0.37673	0.0:0.8267:0.0:0.1733	.	276;285	Q9NR22-2;Q9NR22	.;ANM8_HUMAN	M	276;285	ENSP00000414507:T276M;ENSP00000372067:T285M	ENSP00000372067:T285M	T	+	2	0	PRMT8	3562510	0.988000	0.35896	1.000000	0.80357	0.093000	0.18481	2.678000	0.46900	1.298000	0.44778	-0.142000	0.14014	ACG	.	.	none		0.517	PRMT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250297.2	NM_019854	
SYT7	9066	hgsc.bcm.edu	37	11	61291310	61291310	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:61291310C>T	ENST00000263846.4	-	7	1223	c.896G>A	c.(895-897)gGg>gAg	p.G299E	SYT7_ENST00000540677.1_Missense_Mutation_p.G374E|SYT7_ENST00000535826.1_Missense_Mutation_p.G418E|SYT7_ENST00000542670.1_Missense_Mutation_p.G507E|SYT7_ENST00000542836.1_Missense_Mutation_p.G343E|SYT7_ENST00000540831.1_5'Flank|SYT7_ENST00000539008.1_Missense_Mutation_p.G582E	NM_004200.3	NP_004191.2	O43581	SYT7_HUMAN	synaptotagmin VII	299	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|plasma membrane repair (GO:0001778)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of insulin secretion (GO:0050796)	cell junction (GO:0030054)|dense core granule (GO:0031045)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			kidney(2)|large_intestine(3)|lung(4)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						TGATGTGCCCCCGATGTCCAT	0.597																																					p.G374E		Atlas-SNP	.											.	SYT7	39	.	0			c.G1121A						PASS	.						289.0	275.0	280.0					11																	61291310		2202	4299	6501	SO:0001583	missense	9066	exon8			GTGCCCCCGATGT	AF038535	CCDS31577.1, CCDS58139.1, CCDS73298.1	11q12-q13.1	2013-01-21			ENSG00000011347	ENSG00000011347		"""Synaptotagmins"""	11514	protein-coding gene	gene with protein product		604146	"""prostate cancer associated protein 7"""	PCANAP7		9615227	Standard	NM_001252065		Approved	IPCA-7, SYT-VII, MGC150517	uc009ynr.3	O43581	OTTHUMG00000168199	ENST00000263846.4:c.896G>A	11.37:g.61291310C>T	ENSP00000263846:p.Gly299Glu	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	192	41	0.213542	NM_001252065	F5GZU9|Q08AH6	Missense_Mutation	SNP	ENST00000263846.4	37	CCDS31577.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.233456	0.79688	.	.	ENSG00000011347	ENST00000263846;ENST00000540677;ENST00000539008;ENST00000542836;ENST00000542670;ENST00000535826	T;T;T;T;T;T	0.69040	-0.37;-0.37;-0.37;-0.37;-0.37;-0.37	4.48	4.48	0.54585	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	0.73892	0.3645	L	0.43701	1.375	0.80722	D	1	P;D	0.53151	0.948;0.958	P;P	0.59171	0.689;0.853	T	0.77702	-0.2489	10	0.72032	D	0.01	.	17.5306	0.87813	0.0:1.0:0.0:0.0	.	374;299	F5GZU9;O43581	.;SYT7_HUMAN	E	299;374;582;343;507;418	ENSP00000263846:G299E;ENSP00000444201:G374E;ENSP00000439694:G582E;ENSP00000444568:G343E;ENSP00000444019:G507E;ENSP00000437720:G418E	ENSP00000263846:G299E	G	-	2	0	SYT7	61047886	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.190000	0.50973	2.192000	0.70111	0.462000	0.41574	GGG	.	.	none		0.597	SYT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398733.1	NM_004200	
CUL4A	8451	hgsc.bcm.edu	37	13	113909104	113909104	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr13:113909104C>T	ENST00000375440.4	+	17	1934	c.1850C>T	c.(1849-1851)aCg>aTg	p.T617M	CUL4A_ENST00000451881.1_Missense_Mutation_p.T517M|CUL4A_ENST00000375441.3_Missense_Mutation_p.T517M|CUL4A_ENST00000326335.4_Missense_Mutation_p.T517M	NM_001008895.1	NP_001008895.1	Q13619	CUL4A_HUMAN	cullin 4A	617					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)			AAAATGGCCACGGGGATAGGT	0.453																																					p.T617M		Atlas-SNP	.											CUL4A,NS,carcinoma,0,1	CUL4A	50	1	0			c.C1850T						scavenged	.						98.0	95.0	96.0					13																	113909104		2203	4300	6503	SO:0001583	missense	8451	exon17			TGGCCACGGGGAT	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.1850C>T	13.37:g.113909104C>T	ENSP00000364589:p.Thr617Met	Somatic	91	1	0.010989		WXS	Illumina HiSeq	Phase_I	70	17	0.242857	NM_001008895	A2A2W2|O75834|Q589T6|Q5TC62|Q6UP08|Q9UP17	Missense_Mutation	SNP	ENST00000375440.4	37	CCDS41908.1	.	.	.	.	.	.	.	.	.	.	C	18.35	3.605273	0.66445	.	.	ENSG00000139842	ENST00000375441;ENST00000451881;ENST00000326335;ENST00000375440	T;T;T;T	0.77098	-1.07;-1.07;-1.07;-1.07	5.3	5.3	0.74995	Cullin, N-terminal (1);Winged helix-turn-helix transcription repressor DNA-binding (1);Cullin homology (2);	0.000000	0.85682	D	0.000000	D	0.91730	0.7385	H	0.95004	3.61	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.993	D	0.93689	0.7005	10	0.87932	D	0	-30.3978	19.3097	0.94182	0.0:1.0:0.0:0.0	.	617;617	Q13619;A8MSH7	CUL4A_HUMAN;.	M	517;517;517;617	ENSP00000364590:T517M;ENSP00000389118:T517M;ENSP00000322132:T517M;ENSP00000364589:T617M	ENSP00000322132:T517M	T	+	2	0	CUL4A	112957105	1.000000	0.71417	0.952000	0.39060	0.144000	0.21451	5.880000	0.69698	2.627000	0.88993	0.561000	0.74099	ACG	.	.	none		0.453	CUL4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045888.3	NM_003589	
PPP2R2B	5521	hgsc.bcm.edu	37	5	145969730	145969730	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:145969730C>T	ENST00000394413.3	-	9	1682	c.1112G>A	c.(1111-1113)cGt>cAt	p.R371H	PPP2R2B_ENST00000394411.4_Missense_Mutation_p.R371H|PPP2R2B_ENST00000394414.1_Missense_Mutation_p.R437H|CTB-99A3.1_ENST00000512730.1_RNA|PPP2R2B_ENST00000356826.3_Missense_Mutation_p.R371H|PPP2R2B_ENST00000504198.1_Missense_Mutation_p.R377H|PPP2R2B_ENST00000394409.3_Missense_Mutation_p.R429H|PPP2R2B_ENST00000453001.1_Missense_Mutation_p.R371H|PPP2R2B_ENST00000394410.2_Missense_Mutation_p.R360H|PPP2R2B_ENST00000508545.2_Missense_Mutation_p.R360H|PPP2R2B_ENST00000530902.1_5'UTR|PPP2R2B_ENST00000336640.6_Missense_Mutation_p.R374H			Q00005	2ABB_HUMAN	protein phosphatase 2, regulatory subunit B, beta	371					apoptotic process (GO:0006915)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	cytoskeleton (GO:0005856)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(9)|ovary(1)|prostate(4)|skin(3)	32			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GGTCACATCACGCTTGGTGTT	0.512																																					p.R477H		Atlas-SNP	.											PPP2R2B_ENST00000508545,NS,haematopoietic_neoplasm,-1,4	PPP2R2B	271	4	0			c.G1430A						PASS	.						85.0	79.0	81.0					5																	145969730		2203	4300	6503	SO:0001583	missense	5521	exon10			ACATCACGCTTGG	M64930	CCDS4283.1, CCDS4284.1, CCDS43380.1, CCDS4284.2, CCDS64282.1	5q32	2013-01-10	2010-04-14		ENSG00000156475	ENSG00000156475	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""WD repeat domain containing"""	9305	protein-coding gene	gene with protein product	"""PP2A subunit B isoform beta"""	604325	"""spinocerebellar ataxia 12"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), beta isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B, beta isoform"""	SCA12		1849734, 10581021	Standard	NM_181674		Approved	PR55-BETA, PR52B	uc003log.5	Q00005	OTTHUMG00000163381	ENST00000394413.3:c.1112G>A	5.37:g.145969730C>T	ENSP00000377935:p.Arg371His	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	142	47	0.330986	NM_181675	A6NEJ2|A8K102|B3KPD0|B7Z2F2|B7Z304|D3DQF7|D3DQF8|G3V149	Missense_Mutation	SNP	ENST00000394413.3	37	CCDS4284.1	.	.	.	.	.	.	.	.	.	.	C	18.36	3.607021	0.66558	.	.	ENSG00000156475	ENST00000394413;ENST00000508545;ENST00000394414;ENST00000394411;ENST00000356826;ENST00000453001;ENST00000394410;ENST00000336640;ENST00000504198;ENST00000394409	T;T;T;T;T;T;T;T;T;T	0.74315	-0.83;-0.83;1.47;-0.83;-0.83;-0.83;-0.83;-0.83;-0.83;1.47	5.29	5.29	0.74685	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.115539	0.64402	D	0.000011	T	0.73249	0.3563	L	0.58669	1.825	0.80722	D	1	B;B;B;B;B;B	0.19445	0.036;0.011;0.011;0.022;0.024;0.02	B;B;B;B;B;B	0.15870	0.008;0.005;0.005;0.014;0.005;0.009	T	0.69803	-0.5046	10	0.54805	T	0.06	-2.5928	19.1301	0.93402	0.0:1.0:0.0:0.0	.	429;377;360;437;374;371	Q00005-4;Q00005-3;G3V149;Q00005-5;Q00005-2;Q00005	.;.;.;.;.;2ABB_HUMAN	H	371;360;437;371;371;371;360;374;377;429	ENSP00000377935:R371H;ENSP00000431320:R360H;ENSP00000377936:R437H;ENSP00000377933:R371H;ENSP00000349283:R371H;ENSP00000398779:R371H;ENSP00000377932:R360H;ENSP00000336591:R374H;ENSP00000421396:R377H;ENSP00000377931:R429H	ENSP00000336591:R374H	R	-	2	0	AC011357.1	145949923	1.000000	0.71417	0.973000	0.42090	0.973000	0.67179	4.465000	0.60141	2.767000	0.95098	0.655000	0.94253	CGT	.	.	none		0.512	PPP2R2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251893.2	NM_181678	
SLC9A5	6553	hgsc.bcm.edu	37	16	67291451	67291451	+	Silent	SNP	G	G	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr16:67291451G>T	ENST00000299798.11	+	9	1508	c.1443G>T	c.(1441-1443)ctG>ctT	p.L481L		NM_004594.2	NP_004585.1	Q14940	SL9A5_HUMAN	solute carrier family 9, subfamily A (NHE5, cation proton antiporter 5), member 5	481					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)		ACCACATTCTGGCTGCAGTGG	0.622																																					p.L481L		Atlas-SNP	.											SLC9A5,NS,carcinoma,+2,1	SLC9A5	82	1	0			c.G1443T						scavenged	.						74.0	78.0	77.0					16																	67291451		1977	4137	6114	SO:0001819	synonymous_variant	6553	exon9			CATTCTGGCTGCA		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.1443G>T	16.37:g.67291451G>T		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	175	2	0.0114286	NM_004594	A5PKY7|Q9Y626	Silent	SNP	ENST00000299798.11	37	CCDS42178.1																																																																																			.	.	none		0.622	SLC9A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421386.1		
PTH2R	5746	hgsc.bcm.edu	37	2	209358138	209358138	+	Silent	SNP	A	A	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:209358138A>C	ENST00000272847.2	+	13	1620	c.1407A>C	c.(1405-1407)acA>acC	p.T469T	AC019185.4_ENST00000424628.1_RNA|PTH2R_ENST00000413482.1_3'UTR	NM_005048.2	NP_005039.1	P49190	PTH2R_HUMAN	parathyroid hormone 2 receptor	469					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	parathyroid hormone receptor activity (GO:0004991)			breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(21)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43				Epithelial(149;0.0684)|Lung(261;0.0785)|LUSC - Lung squamous cell carcinoma(261;0.0836)	Preotact(DB05829)	CGGCCAGCACACGCATGGTGC	0.592																																					p.T469T		Atlas-SNP	.											.	PTH2R	92	.	0			c.A1407C						PASS	.						44.0	36.0	39.0					2																	209358138		2203	4300	6503	SO:0001819	synonymous_variant	5746	exon13			CAGCACACGCATG	BC036811	CCDS2383.1	2q33	2012-08-10	2007-08-24	2007-08-24	ENSG00000144407	ENSG00000144407		"""GPCR / Class B : Parathyroid hormone receptors"""	9609	protein-coding gene	gene with protein product		601469	"""parathyroid hormone receptor 2"""	PTHR2			Standard	NM_005048		Approved		uc002vdb.4	P49190	OTTHUMG00000132960	ENST00000272847.2:c.1407A>C	2.37:g.209358138A>C		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	165	26	0.157576	NM_005048	Q8N429	Silent	SNP	ENST00000272847.2	37	CCDS2383.1																																																																																			.	.	none		0.592	PTH2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256519.2	NM_005048	
PAK2	5062	hgsc.bcm.edu	37	3	196509522	196509522	+	Missense_Mutation	SNP	C	C	G	rs67093638		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:196509522C>G	ENST00000327134.3	+	2	327	c.5C>G	c.(4-6)tCt>tGt	p.S2C	RNU6-42P_ENST00000384165.1_RNA	NM_002577.4	NP_002568.2	Q13177	PAK2_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 2	2					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis (GO:2001271)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-serine phosphorylation (GO:0018105)|phosphorylation (GO:0016310)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of defense response to virus by virus (GO:0050690)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activator activity (GO:0030296)	p.S2C(2)		breast(1)|cervix(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)	12	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.07e-23)|all cancers(36;6.38e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00405)		TGAATCATGTCTGATAACGGA	0.408																																					p.S2C		Atlas-SNP	.											PAK2_ENST00000327134,NS,carcinoma,0,4	PAK2	113	4	2	Substitution - Missense(2)	prostate(2)	c.C5G						scavenged	.						81.0	87.0	85.0					3																	196509522		2203	4300	6503	SO:0001583	missense	5062	exon2			TCATGTCTGATAA	U24153	CCDS3321.1	3q29	2008-06-17	2008-06-17			ENSG00000180370	2.7.11.1		8591	protein-coding gene	gene with protein product	"""S6/H4 kinase"""	605022	"""p21 (CDKN1A)-activated kinase 2"""			7744004, 7618083	Standard	NM_002577		Approved	PAK65, PAKgamma	uc003fwy.4	Q13177		ENST00000327134.3:c.5C>G	3.37:g.196509522C>G	ENSP00000314067:p.Ser2Cys	Somatic	141	1	0.0070922		WXS	Illumina HiSeq	Phase_I	147	2	0.0136054	NM_002577	Q13154|Q6ISC3	Missense_Mutation	SNP	ENST00000327134.3	37	CCDS3321.1	42	0.019230769230769232	6	0.012195121951219513	0	0.0	7	0.012237762237762238	29	0.03825857519788918	C	14.90	2.672409	0.47781	.	.	ENSG00000180370	ENST00000327134	T	0.70631	-0.5	5.21	5.21	0.72293	.	0.055816	0.64402	D	0.000001	T	0.30417	0.0764	N	0.25426	0.745	0.54753	D	0.999985	B	0.15141	0.012	B	0.20577	0.03	T	0.51284	-0.8725	10	0.62326	D	0.03	.	18.756	0.91833	0.0:1.0:0.0:0.0	.	2	Q13177	PAK2_HUMAN	C	2	ENSP00000314067:S2C	ENSP00000314067:S2C	S	+	2	0	PAK2	197993919	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.961000	0.49168	2.456000	0.83038	0.655000	0.94253	TCT	C|0.986;G|0.014	0.014	strong		0.408	PAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340548.1	NM_002577	
TUBA3C	7278	hgsc.bcm.edu	37	13	19751301	19751301	+	Silent	SNP	C	C	T	rs140548354		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	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	226	9	0.039823		WXS	Illumina HiSeq	Phase_I	241	11	0.0456432	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	
ABCA13	154664	hgsc.bcm.edu	37	7	48314897	48314897	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr7:48314897C>T	ENST00000435803.1	+	17	5658	c.5634C>T	c.(5632-5634)tcC>tcT	p.S1878S		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1878					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						ATGAAAGCTCCCGAATGGAAA	0.408																																					p.S1878S		Atlas-SNP	.											.	ABCA13	1192	.	0			c.C5634T						PASS	.						60.0	61.0	61.0					7																	48314897		1824	4073	5897	SO:0001819	synonymous_variant	154664	exon17			AAGCTCCCGAATG	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.5634C>T	7.37:g.48314897C>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	138	26	0.188406	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	37	CCDS47584.1																																																																																			.	.	none		0.408	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
PAX8	7849	hgsc.bcm.edu	37	2	114004442	114004442	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:114004442G>A	ENST00000429538.3	-	3	274	c.80C>T	c.(79-81)cCg>cTg	p.P27L	AC016683.6_ENST00000451179.1_RNA|AC016683.6_ENST00000556070.1_RNA|PAX8_ENST00000263334.5_Missense_Mutation_p.P27L|AC016683.6_ENST00000422956.2_RNA|PAX8_ENST00000397647.3_Missense_Mutation_p.P27L|PAX8_ENST00000263335.7_Missense_Mutation_p.P27L|PAX8_ENST00000348715.5_Missense_Mutation_p.P27L|AC016683.6_ENST00000436293.2_RNA|AC016683.6_ENST00000333145.5_RNA|AC016683.6_ENST00000553869.2_RNA|AC016683.6_ENST00000445745.1_RNA	NM_003466.3	NP_003457.1	Q06710	PAX8_HUMAN	paired box 8	27	Paired. {ECO:0000255|PROSITE- ProRule:PRU00381}.				anatomical structure morphogenesis (GO:0009653)|branching involved in ureteric bud morphogenesis (GO:0001658)|cellular response to gonadotropin stimulus (GO:0071371)|central nervous system development (GO:0007417)|inner ear morphogenesis (GO:0042472)|kidney development (GO:0001822)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|mesonephros development (GO:0001823)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric distal convoluted tubule development (GO:0072221)|metanephric epithelium development (GO:0072207)|metanephric nephron tubule formation (GO:0072289)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process involved in metanephric collecting duct development (GO:1900215)|negative regulation of apoptotic process involved in metanephric nephron tubule development (GO:1900218)|negative regulation of mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis (GO:0072305)|negative regulation of mesenchymal cell apoptotic process involved in metanephros development (GO:1900212)|otic vesicle development (GO:0071599)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0072108)|positive regulation of metanephric DCT cell differentiation (GO:2000594)|positive regulation of thyroid hormone generation (GO:2000611)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephric field specification (GO:0039003)|pronephros development (GO:0048793)|regulation of apoptotic process (GO:0042981)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of thyroid-stimulating hormone secretion (GO:2000612)|thyroid gland development (GO:0030878)|thyroid-stimulating hormone signaling pathway (GO:0038194)|transcription, DNA-templated (GO:0006351)|urogenital system development (GO:0001655)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|thyroid-stimulating hormone receptor activity (GO:0004996)|transcription regulatory region DNA binding (GO:0044212)		PAX8/PPARG(117)	breast(1)|endometrium(4)|kidney(2)|large_intestine(1)|liver(1)|lung(9)|ovary(1)|skin(1)	20						GACCACTTCCGGCAGAGGTCT	0.622			T	PPARG	follicular thyroid		Thyroid dysgenesis																														p.P27L	Ovarian(188;7 2067 9084 29802 29892)	Atlas-SNP	.		Dom	yes		2	2q12-q14	7849	paired box gene 8	yes	E	.	PAX8	42	.	0			c.C80T						PASS	.						33.0	38.0	37.0					2																	114004442		2100	4256	6356	SO:0001583	missense	7849	exon3			ACTTCCGGCAGAG	X69699	CCDS42735.1, CCDS42736.1, CCDS46398.1, CCDS46399.1	2q13	2011-06-20	2007-07-12		ENSG00000125618	ENSG00000125618		"""Paired boxes"", ""Homeoboxes / PRD class"""	8622	protein-coding gene	gene with protein product		167415	"""paired box gene 8"""			8431641, 7981748	Standard	NM_003466		Approved		uc010yxt.2	Q06710	OTTHUMG00000128529	ENST00000429538.3:c.80C>T	2.37:g.114004442G>A	ENSP00000395498:p.Pro27Leu	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	168	71	0.422619	NM_013952	Q09155|Q16337|Q16338|Q16339|Q4ZG35|Q96J49	Missense_Mutation	SNP	ENST00000429538.3	37	CCDS46398.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.504596	0.85176	.	.	ENSG00000125618	ENST00000263335;ENST00000397647;ENST00000348715;ENST00000429538;ENST00000263334	D;D;D;D;D	0.99709	-6.48;-6.48;-6.48;-6.48;-6.48	5.1	5.1	0.69264	Paired box protein, N-terminal (4);Winged helix-turn-helix transcription repressor DNA-binding (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.99792	0.9912	H	0.94698	3.57	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.998;0.994;1.0;0.998;0.995	D	0.96959	0.9700	10	0.87932	D	0	.	16.0313	0.80579	0.0:0.0:1.0:0.0	.	27;27;27;27;27	Q06710-2;Q06710-3;Q06710;Q06710-5;Q06710-4	.;.;PAX8_HUMAN;.;.	L	27	ENSP00000263335:P27L;ENSP00000380768:P27L;ENSP00000314750:P27L;ENSP00000395498:P27L;ENSP00000263334:P27L	ENSP00000263334:P27L	P	-	2	0	PAX8	113720912	1.000000	0.71417	0.940000	0.37924	0.600000	0.36913	9.796000	0.99103	2.382000	0.81193	0.655000	0.94253	CCG	.	.	none		0.622	PAX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250353.5		
IGFBP4	3487	hgsc.bcm.edu	37	17	38612729	38612729	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr17:38612729G>A	ENST00000269593.4	+	4	946	c.671G>A	c.(670-672)gGc>gAc	p.G224D	IGFBP4_ENST00000542955.1_Missense_Mutation_p.G124D	NM_001552.2	NP_001543.2	P22692	IBP4_HUMAN	insulin-like growth factor binding protein 4	224	Thyroglobulin type-1. {ECO:0000255|PROSITE-ProRule:PRU00500}.				cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|DNA metabolic process (GO:0006259)|inflammatory response (GO:0006954)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of MAPK cascade (GO:0043410)|regulation of cell growth (GO:0001558)|regulation of glucose metabolic process (GO:0010906)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|type B pancreatic cell proliferation (GO:0044342)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|endometrium(1)|kidney(1)|large_intestine(2)	5		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(5;5.91e-05)			GGGCAGCGTGGCAAGTGCTGG	0.627																																					p.G224D	GBM(160;940 3581 26177)	Atlas-SNP	.											.	IGFBP4	17	.	0			c.G671A						PASS	.						54.0	57.0	56.0					17																	38612729		2203	4300	6503	SO:0001583	missense	3487	exon4			AGCGTGGCAAGTG	M38177	CCDS11367.1	17q21.2	2014-09-16	2001-11-28		ENSG00000141753	ENSG00000141753			5473	protein-coding gene	gene with protein product	"""IGF-binding protein 4"""	146733	"""insulin-like growth factor-binding protein 4"""			1707125, 1704481	Standard	NM_001552		Approved	IBP4, BP-4, HT29-IGFBP, IGFBP-4	uc002hus.3	P22692	OTTHUMG00000133326	ENST00000269593.4:c.671G>A	17.37:g.38612729G>A	ENSP00000269593:p.Gly224Asp	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	193	24	0.124352	NM_001552	A0N9W2|B4E351|Q5U012|Q9UCL6	Missense_Mutation	SNP	ENST00000269593.4	37	CCDS11367.1	.	.	.	.	.	.	.	.	.	.	G	32	5.110443	0.94292	.	.	ENSG00000141753	ENST00000542955;ENST00000269593	T;T	0.70282	-0.47;-0.47	5.43	5.43	0.79202	Thyroglobulin type-1 (5);	0.000000	0.85682	D	0.000000	D	0.85017	0.5601	M	0.80332	2.49	0.58432	D	0.999992	D	0.89917	1.0	D	0.97110	1.0	D	0.86889	0.2047	10	0.87932	D	0	-2.4357	17.0572	0.86537	0.0:0.0:1.0:0.0	.	224	P22692	IBP4_HUMAN	D	124;224	ENSP00000437734:G124D;ENSP00000269593:G224D	ENSP00000269593:G224D	G	+	2	0	IGFBP4	35866255	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	8.449000	0.90337	2.546000	0.85860	0.655000	0.94253	GGC	.	.	none		0.627	IGFBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257134.1	NM_001552	
BMPR1A	657	hgsc.bcm.edu	37	10	88679129	88679129	+	Missense_Mutation	SNP	G	G	A	rs201509164		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr10:88679129G>A	ENST00000372037.3	+	10	1606	c.1069G>A	c.(1069-1071)Gca>Aca	p.A357T		NM_004329.2	NP_004320.2	P36894	BMR1A_HUMAN	bone morphogenetic protein receptor, type IA	357	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|developmental growth (GO:0048589)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic digit morphogenesis (GO:0042733)|embryonic organ development (GO:0048568)|endocardial cushion formation (GO:0003272)|heart formation (GO:0060914)|hindlimb morphogenesis (GO:0035137)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|lateral mesoderm development (GO:0048368)|lung development (GO:0030324)|mesendoderm development (GO:0048382)|mesoderm formation (GO:0001707)|Mullerian duct regression (GO:0001880)|negative regulation of neurogenesis (GO:0050768)|neural crest cell development (GO:0014032)|neural plate mediolateral regionalization (GO:0021998)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|paraxial mesoderm structural organization (GO:0048352)|pituitary gland development (GO:0021983)|positive regulation of bone mineralization (GO:0030501)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of lateral mesodermal cell fate specification (GO:0048378)|somitogenesis (GO:0001756)|stem cell maintenance (GO:0019827)|transforming growth factor beta receptor signaling pathway (GO:0007179)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|SMAD binding (GO:0046332)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)	p.A357T(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|skin(1)|stomach(1)	24						AGGAAAGCCCGCAATTGCTCA	0.483			"""Mis, N, F"""			gastrointestinal polyps			Juvenile Polyposis;Hereditary Mixed Polyposis syndrome type 2																												p.A357T	Ovarian(190;603 2086 22044 30335 47971)	Atlas-SNP	.	yes	Rec		Juvenile polyposis	10	10q22.3	657	"""bone morphogenetic protein receptor, type IA"""		E	BMPR1A,NS,carcinoma,0,1	BMPR1A	118	1	1	Substitution - Missense(1)	breast(1)	c.G1069A						scavenged	.						54.0	58.0	57.0					10																	88679129		2203	4297	6500	SO:0001583	missense	657	exon10	Familial Cancer Database	incl.: Juvenile Polyposis of the Stomach;HMPS2	AAGCCCGCAATTG	BC028383	CCDS7378.1	10q22.3	2014-09-17			ENSG00000107779	ENSG00000107779		"""CD molecules"""	1076	protein-coding gene	gene with protein product		601299		ACVRLK3		8397373, 9730621	Standard	NM_004329		Approved	ALK3, CD292	uc001kdy.3	P36894	OTTHUMG00000018657	ENST00000372037.3:c.1069G>A	10.37:g.88679129G>A	ENSP00000361107:p.Ala357Thr	Somatic	201	7	0.0348259		WXS	Illumina HiSeq	Phase_I	231	21	0.0909091	NM_004329	A8K6U9|Q8NEN8	Missense_Mutation	SNP	ENST00000372037.3	37	CCDS7378.1	.	.	.	.	.	.	.	.	.	.	G	34	5.338669	0.95783	.	.	ENSG00000107779	ENST00000224764;ENST00000372037	D	0.93307	-3.2	4.86	4.86	0.63082	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.95089	0.8409	L	0.39245	1.2	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	D	0.95846	0.8870	10	0.87932	D	0	.	18.3376	0.90294	0.0:0.0:1.0:0.0	.	357	P36894	BMR1A_HUMAN	T	357	ENSP00000361107:A357T	ENSP00000224764:A357T	A	+	1	0	BMPR1A	88669109	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.809000	0.99208	2.381000	0.81170	0.591000	0.81541	GCA	A|1.000;|0.000	1.000	weak		0.483	BMPR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049170.3	NM_004329	
C2CD4D	100191040	hgsc.bcm.edu	37	1	151810406	151810406	+	Nonstop_Mutation	SNP	A	A	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:151810406A>G	ENST00000454109.1	-	2	1645	c.1060T>C	c.(1060-1062)Tag>Cag	p.*354Q		NM_001136003.1	NP_001129475.1	B7Z1M9	C2D4D_HUMAN	C2 calcium-dependent domain containing 4D	0										skin(1)	1						GGCTCAGGCTACAGGCTGAGA	0.607																																					p.X354Q		Atlas-SNP	.											.	C2CD4D	3	.	0			c.T1060C						PASS	.						20.0	27.0	25.0					1																	151810406		691	1591	2282	SO:0001578	stop_lost	100191040	exon2			CAGGCTACAGGCT	BC171843	CCDS44224.1	1q21.3	2012-07-02			ENSG00000225556	ENSG00000225556			37210	protein-coding gene	gene with protein product	"""family with sequence similarity 148, member D"""						Standard	NM_001136003		Approved	FAM148D	uc010pdq.1	B7Z1M9	OTTHUMG00000167218	ENST00000454109.1:c.1060T>C	1.37:g.151810406A>G	ENSP00000389554:p.*354Gluext*?	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	95	4	0.0421053	NM_001136003	B2RXG8	Missense_Mutation	SNP	ENST00000454109.1	37	CCDS44224.1	.	.	.	.	.	.	.	.	.	.	A	5.152	0.213579	0.09757	.	.	ENSG00000225556	ENST00000454109	.	.	.	2.97	1.68	0.24146	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.7753	0.13176	0.7221:0.0:0.0:0.2779	.	.	.	.	Q	354	.	.	X	-	1	0	C2CD4D	150077030	0.989000	0.36119	0.867000	0.34043	0.305000	0.27757	2.091000	0.41691	1.348000	0.45733	0.379000	0.24179	TAG	.	.	none		0.607	C2CD4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393778.1	NM_001136003	
KIF21A	55605	hgsc.bcm.edu	37	12	39756911	39756911	+	Silent	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:39756911G>A	ENST00000361418.5	-	7	1023	c.1008C>T	c.(1006-1008)ctC>ctT	p.L336L	KIF21A_ENST00000361961.3_Silent_p.L336L|KIF21A_ENST00000395670.3_Silent_p.L336L|KIF21A_ENST00000544797.2_Silent_p.L336L|KIF21A_ENST00000541463.2_Silent_p.L336L			Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	336	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.L336L(1)		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)				TATTACCCCCGAGGGAATCCT	0.378																																					p.L336L		Atlas-SNP	.											KIF21A_ENST00000395670,NS,carcinoma,0,2	KIF21A	238	2	1	Substitution - coding silent(1)	endometrium(1)	c.C1008T						scavenged	.						151.0	148.0	149.0					12																	39756911		2203	4300	6503	SO:0001819	synonymous_variant	55605	exon7			ACCCCCGAGGGAA	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.1008C>T	12.37:g.39756911G>A		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	194	3	0.0154639	NM_001173463	A8MX28|B0I1R9|B9EGE4|F5H0C3|F5H219|Q2UVF1|Q6UKL9|Q7Z668|Q86WZ5|Q8IVZ8|Q9C0F5|Q9NXU4|Q9Y590	Silent	SNP	ENST00000361418.5	37	CCDS53776.1																																																																																			.	.	none		0.378	KIF21A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403581.1	NM_017641	
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39254124	39254124	+	Silent	SNP	C	C	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr17:39254124C>G	ENST00000333822.4	-	1	269	c.213G>C	c.(211-213)gtG>gtC	p.V71V		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	71	25 X 5 AA repeats of C-C-[IKRQVHEC]- [SPRT]-[STCVQPR].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						AGCAGCTGGACACACAGCAGC	0.667																																					p.V71V		Atlas-SNP	.											KRTAP4-8,colon,carcinoma,0,2	KRTAP4-8	57	2	0			c.G213C						scavenged	.						5.0	8.0	7.0					17																	39254124		620	1442	2062	SO:0001819	synonymous_variant	728224	exon1			GCTGGACACACAG	AJ406940	CCDS45674.1	17q21.2	2013-06-25			ENSG00000204880	ENSG00000204880		"""Keratin associated proteins"""	17230	protein-coding gene	gene with protein product						11279113	Standard	NM_031960		Approved	KAP4.8	uc010wfo.2	Q9BYQ9	OTTHUMG00000133580	ENST00000333822.4:c.213G>C	17.37:g.39254124C>G		Somatic	44	2	0.0454545		WXS	Illumina HiSeq	Phase_I	65	10	0.153846	NM_031960	A8MSH3	Silent	SNP	ENST00000333822.4	37	CCDS45674.1																																																																																			.	.	none		0.667	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
POMGNT2	84892	hgsc.bcm.edu	37	3	43122493	43122493	+	Missense_Mutation	SNP	G	G	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:43122493G>T	ENST00000344697.2	-	2	776	c.431C>A	c.(430-432)cCc>cAc	p.P144H	POMGNT2_ENST00000441964.1_Missense_Mutation_p.P144H	NM_032806.5	NP_116195.2	Q8NAT1	PMGT2_HUMAN	protein O-linked mannose N-acetylglucosaminyltransferase 2 (beta 1,4-)	144					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)										CACCGGCTTGGGCATGAAGCG	0.602																																					p.P144H		Atlas-SNP	.											C3orf39,NS,adenocarcinoma,0,2	.	.	2	0			c.C431A						scavenged	.						107.0	100.0	103.0					3																	43122493		2203	4300	6503	SO:0001583	missense	84892	exon2			GGCTTGGGCATGA	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.431C>A	3.37:g.43122493G>T	ENSP00000344125:p.Pro144His	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	128	3	0.0234375	NM_032806	B3KWC3|Q96SY3	Missense_Mutation	SNP	ENST00000344697.2	37	CCDS2709.1	.	.	.	.	.	.	.	.	.	.	G	17.99	3.523538	0.64747	.	.	ENSG00000144647	ENST00000441964;ENST00000344697	T;T	0.76839	-1.05;-1.05	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	D	0.85754	0.5770	L	0.50919	1.6	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.83919	0.0300	10	0.41790	T	0.15	-11.0049	19.2304	0.93836	0.0:0.0:1.0:0.0	.	144	Q8NAT1	AGO61_HUMAN	H	144	ENSP00000408992:P144H;ENSP00000344125:P144H	ENSP00000344125:P144H	P	-	2	0	C3orf39	43097497	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	9.869000	0.99810	2.782000	0.95742	0.655000	0.94253	CCC	.	.	none		0.602	POMGNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256643.1	NM_032806	
EMR2	30817	hgsc.bcm.edu	37	19	14865793	14865793	+	Silent	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:14865793G>A	ENST00000315576.3	-	14	2014	c.1563C>T	c.(1561-1563)gcC>gcT	p.A521A	EMR2_ENST00000346057.1_Silent_p.A472A|EMR2_ENST00000353005.1_Silent_p.A379A|EMR2_ENST00000595839.1_Silent_p.A379A|EMR2_ENST00000596991.2_Silent_p.A510A|EMR2_ENST00000601345.1_Silent_p.A510A|EMR2_ENST00000392964.3_Missense_Mutation_p.R186C|EMR2_ENST00000353876.1_Silent_p.A428A|EMR2_ENST00000392967.2_Silent_p.A510A|EMR2_ENST00000594294.1_Silent_p.A472A|EMR2_ENST00000392965.3_Intron|EMR2_ENST00000594076.1_Silent_p.A428A	NM_013447.3	NP_038475.2	Q9UHX3	EMR2_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 2	521	GPS. {ECO:0000255|PROSITE- ProRule:PRU00098}.				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						CCATGAGGACGGCAAAGCTGC	0.567																																					p.A521A		Atlas-SNP	.											EMR2,NS,carcinoma,-1,1	EMR2	99	1	0			c.C1563T						scavenged	.						159.0	120.0	133.0					19																	14865793		2203	4300	6503	SO:0001819	synonymous_variant	30817	exon14			GAGGACGGCAAAG	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.1563C>T	19.37:g.14865793G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	153	2	0.0130719	NM_013447	B4DQ96|E7ESD7|E9PBR1|E9PEL6|E9PFQ5|E9PG91|Q8NG96|Q9Y4B1	Silent	SNP	ENST00000315576.3	37	CCDS32935.1	.	.	.	.	.	.	.	.	.	.	G	3.603	-0.081254	0.07141	.	.	ENSG00000127507	ENST00000392964	T	0.40756	1.02	4.05	-3.2	0.05156	.	.	.	.	.	T	0.41719	0.1171	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49051	-0.8979	6	0.87932	D	0	.	4.1261	0.10128	0.4334:0.0:0.4102:0.1564	.	.	.	.	C	186	ENSP00000376691:R186C	ENSP00000376691:R186C	R	-	1	0	EMR2	14726793	0.000000	0.05858	0.782000	0.31804	0.009000	0.06853	-2.035000	0.01423	-0.579000	0.05952	-0.441000	0.05720	CGT	.	.	none		0.567	EMR2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466502.2		
GON4L	54856	hgsc.bcm.edu	37	1	155732033	155732033	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:155732033T>C	ENST00000368331.1	-	23	4907	c.4859A>G	c.(4858-4860)gAt>gGt	p.D1620G	GON4L_ENST00000471341.1_5'Flank|GON4L_ENST00000271883.5_Missense_Mutation_p.D1620G|GON4L_ENST00000437809.1_Missense_Mutation_p.D1620G	NM_001282858.1|NM_001282860.1	NP_001269787.1|NP_001269789.1	Q3T8J9	GON4L_HUMAN	gon-4-like (C. elegans)	1620					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)					CCTGAGTGGATCTCGCTCGAG	0.537																																					p.D1620G		Atlas-SNP	.											GON4L_ENST00000368331,NS,carcinoma,-1,2	GON4L	392	2	0			c.A4859G						scavenged	.						66.0	64.0	65.0					1																	155732033		2025	4177	6202	SO:0001583	missense	54856	exon23			AGTGGATCTCGCT	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.4859A>G	1.37:g.155732033T>C	ENSP00000357315:p.Asp1620Gly	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	162	3	0.0185185	NM_001037533	B7ZBL4|Q14C93|Q3T8J8|Q5VYZ5|Q5W0D5|Q6AWA6|Q6P1Q6|Q7Z3L3|Q8IY79|Q9BQI1|Q9HCG6	Missense_Mutation	SNP	ENST00000368331.1	37		.	.	.	.	.	.	.	.	.	.	T	21.4	4.145689	0.77888	.	.	ENSG00000116580	ENST00000437809;ENST00000368331;ENST00000271883	T;T;T	0.50548	0.74;0.74;0.74	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	T	0.48537	0.1505	L	0.29908	0.895	0.58432	D	0.999993	D;D;D	0.89917	0.997;1.0;1.0	D;D;D	0.87578	0.989;0.996;0.998	T	0.55854	-0.8075	10	0.72032	D	0.01	.	14.7661	0.69640	0.0:0.0:0.0:1.0	.	816;1620;1620	Q1ED43;Q3T8J9;Q3T8J9-3	.;GON4L_HUMAN;.	G	1620	ENSP00000396117:D1620G;ENSP00000357315:D1620G;ENSP00000271883:D1620G	ENSP00000271883:D1620G	D	-	2	0	GON4L	153998657	1.000000	0.71417	0.999000	0.59377	0.614000	0.37383	7.255000	0.78338	2.152000	0.67230	0.254000	0.18369	GAT	.	.	none		0.537	GON4L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_032292	
EMR1	2015	hgsc.bcm.edu	37	19	6919679	6919679	+	Missense_Mutation	SNP	G	G	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:6919679G>T	ENST00000312053.4	+	13	1578	c.1541G>T	c.(1540-1542)cGa>cTa	p.R514L	EMR1_ENST00000250572.8_Missense_Mutation_p.R514L|EMR1_ENST00000381404.4_Missense_Mutation_p.R462L|EMR1_ENST00000381407.5_Missense_Mutation_p.R373L|EMR1_ENST00000450315.3_Missense_Mutation_p.R337L	NM_001974.4	NP_001965.3	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 1	514	Ser/Thr-rich.				cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.R514Q(1)		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)					ATGAATTCTCGAGTCGTTGGG	0.473																																					p.R514L		Atlas-SNP	.											EMR1,NS,carcinoma,0,1	EMR1	153	1	1	Substitution - Missense(1)	lung(1)	c.G1541T						scavenged	.						125.0	114.0	118.0					19																	6919679		2203	4300	6503	SO:0001583	missense	2015	exon13			ATTCTCGAGTCGT	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.1541G>T	19.37:g.6919679G>T	ENSP00000311545:p.Arg514Leu	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	130	2	0.0153846	NM_001256253	A6NHV2|B7Z486|B7Z489|E7EPX9|E9PD45|H9KV79|Q2I7G5|Q6ZMN0|Q8NGA7	Missense_Mutation	SNP	ENST00000312053.4	37	CCDS12175.1	.	.	.	.	.	.	.	.	.	.	G	12.12	1.842936	0.32606	.	.	ENSG00000174837	ENST00000543519;ENST00000312053;ENST00000381404;ENST00000250572;ENST00000381407;ENST00000450315	T;T;T;T;T	0.79033	-1.16;-1.2;-1.23;-0.01;0.31	3.99	1.83	0.25207	.	.	.	.	.	T	0.81508	0.4837	M	0.74881	2.28	0.22066	N	0.999389	P;P;D;P;D	0.67145	0.949;0.896;0.996;0.935;0.992	P;B;P;B;P	0.56788	0.466;0.265;0.806;0.386;0.645	T	0.68074	-0.5505	9	0.35671	T	0.21	.	6.2419	0.20795	0.2343:0.0:0.7657:0.0	.	337;373;514;462;514	E7EPX9;B7Z486;Q14246-2;E9PD45;Q14246	.;.;.;.;EMR1_HUMAN	L	514;514;462;514;373;337	ENSP00000311545:R514L;ENSP00000370811:R462L;ENSP00000250572:R514L;ENSP00000370814:R373L;ENSP00000405974:R337L	ENSP00000250572:R514L	R	+	2	0	EMR1	6870679	0.884000	0.30299	0.271000	0.24616	0.474000	0.32979	1.300000	0.33436	0.454000	0.26884	0.491000	0.48974	CGA	.	.	none		0.473	EMR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458485.1		
TGM4	7047	hgsc.bcm.edu	37	3	44943132	44943132	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:44943132C>T	ENST00000296125.4	+	7	842	c.774C>T	c.(772-774)aaC>aaT	p.N258N	RP11-272D20.2_ENST00000427258.1_RNA	NM_003241.3	NP_003232.2	P49221	TGM4_HUMAN	transglutaminase 4	258					mating plug formation (GO:0042628)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			NS(1)|breast(1)|endometrium(2)|large_intestine(9)|lung(21)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	38				BRCA - Breast invasive adenocarcinoma(193;0.00963)|KIRC - Kidney renal clear cell carcinoma(197;0.0546)|Kidney(197;0.0686)	L-Glutamine(DB00130)	AGTACTACAACACGAAGCAGG	0.597																																					p.N258N		Atlas-SNP	.											TGM4,caecum,carcinoma,0,1	TGM4	82	1	0			c.C774T						scavenged	.						125.0	116.0	119.0					3																	44943132		2203	4300	6503	SO:0001819	synonymous_variant	7047	exon7			CTACAACACGAAG	BC007003	CCDS2723.1	3p22-p21.33	2013-05-02	2013-05-02		ENSG00000163810	ENSG00000163810	2.3.2.13	"""Transglutaminases"""	11780	protein-coding gene	gene with protein product		600585	"""transglutaminase 4 (prostate)"""			7665178, 7916568	Standard	NM_003241		Approved	TGP	uc003coc.4	P49221	OTTHUMG00000133096	ENST00000296125.4:c.774C>T	3.37:g.44943132C>T		Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	229	5	0.0218341	NM_003241	Q16707|Q96QN4	Silent	SNP	ENST00000296125.4	37	CCDS2723.1																																																																																			.	.	none		0.597	TGM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256755.2	NM_003241	
TRMT5	57570	hgsc.bcm.edu	37	14	61442460	61442460	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr14:61442460T>C	ENST00000261249.6	-	4	1561	c.1177A>G	c.(1177-1179)Ata>Gta	p.I393V	RP11-193F5.1_ENST00000553946.1_RNA|RNU6-398P_ENST00000384143.1_RNA	NM_020810.2	NP_065861.2			tRNA methyltransferase 5											NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(1)	11				OV - Ovarian serous cystadenocarcinoma(108;0.0873)		AGAAACTCTATAGCTTTTGCT	0.443																																					p.I393V		Atlas-SNP	.											TRMT5,colon,carcinoma,+1,1	TRMT5	44	1	0			c.A1177G						scavenged	.						89.0	89.0	89.0					14																	61442460		2203	4300	6503	SO:0001583	missense	57570	exon4			ACTCTATAGCTTT	AB037814	CCDS32092.1	14q23.1	2013-06-05	2013-06-05	2005-08-11		ENSG00000126814	2.1.1.228		23141	protein-coding gene	gene with protein product	"""tRNA (guanine(37)-N1)-methyltransferase"""	611023	"""KIAA1393"", ""tRNA methyltransferase 5 homolog (S. cerevisiae)"""	KIAA1393		15248782	Standard	XM_005267916		Approved	TRM5	uc001xff.4	Q32P41		ENST00000261249.6:c.1177A>G	14.37:g.61442460T>C	ENSP00000261249:p.Ile393Val	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	197	3	0.0152284	NM_020810		Missense_Mutation	SNP	ENST00000261249.6	37	CCDS32092.1	.	.	.	.	.	.	.	.	.	.	T	1.578	-0.532238	0.04112	.	.	ENSG00000126814	ENST00000261249	T	0.23147	1.92	6.17	1.44	0.22558	.	0.226262	0.46758	N	0.000262	T	0.09512	0.0234	N	0.04090	-0.28	0.31756	N	0.633947	B	0.02656	0.0	B	0.13407	0.009	T	0.33445	-0.9868	10	0.07030	T	0.85	-15.4336	10.4839	0.44711	0.0:0.3409:0.0:0.6591	.	393	Q32P41	TRM5_HUMAN	V	393	ENSP00000261249:I393V	ENSP00000261249:I393V	I	-	1	0	TRMT5	60512213	0.049000	0.20398	0.722000	0.30670	0.991000	0.79684	0.175000	0.16762	0.580000	0.29522	0.533000	0.62120	ATA	.	.	none		0.443	TRMT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412831.1	NM_02081	
EML2	24139	hgsc.bcm.edu	37	19	46116911	46116911	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:46116911G>A	ENST00000245925.3	-	18	1762	c.1712C>T	c.(1711-1713)gCg>gTg	p.A571V	EML2_ENST00000589876.1_Missense_Mutation_p.A571V|EML2_ENST00000536630.1_Missense_Mutation_p.A718V|EML2_ENST00000587152.1_Missense_Mutation_p.A772V	NM_012155.2	NP_036287.1	O95834	EMAL2_HUMAN	echinoderm microtubule associated protein like 2	571	Tandem atypical propeller in EMLs. {ECO:0000250}.				negative regulation of microtubule polymerization (GO:0031115)|regulation of microtubule nucleation (GO:0010968)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	microtubule binding (GO:0008017)|tubulin binding (GO:0015631)	p.A571V(1)		NS(1)|breast(2)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(13)|ovary(1)|urinary_tract(1)	31		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00553)|GBM - Glioblastoma multiforme(486;0.131)|Epithelial(262;0.197)		AGTGCCGTCCGCCCCCTCAGA	0.572																																					p.A772V		Atlas-SNP	.											EML2,caecum,carcinoma,0,1	EML2	64	1	1	Substitution - Missense(1)	large_intestine(1)	c.C2315T						PASS	.						113.0	94.0	100.0					19																	46116911		2203	4300	6503	SO:0001583	missense	24139	exon21			CCGTCCGCCCCCT	AF103939	CCDS12670.1, CCDS54280.1, CCDS59399.1	19q13.32	2013-01-10				ENSG00000125746		"""WD repeat domain containing"""	18035	protein-coding gene	gene with protein product	"""echinoderm MT-associated protein (EMAP)-like protein 70"", ""microtubule-associated protein like echinoderm EMAP"""					11694528, 10521658	Standard	NM_012155		Approved	EMAP2, ELP70, EMAP-2	uc010xxm.2	O95834		ENST00000245925.3:c.1712C>T	19.37:g.46116911G>A	ENSP00000245925:p.Ala571Val	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	113	18	0.159292	NM_001193268	B7Z3I2|B7Z3Q9|K7ERL7|Q59EN8|Q8N5A2|Q9UG50	Missense_Mutation	SNP	ENST00000245925.3	37	CCDS12670.1	.	.	.	.	.	.	.	.	.	.	G	10.25	1.299646	0.23650	.	.	ENSG00000125746	ENST00000536630;ENST00000245925;ENST00000448055	T;T	0.29397	1.57;2.74	4.75	2.65	0.31530	WD40/YVTN repeat-like-containing domain (1);Soluble quinoprotein glucose/sorbosone dehydrogenase (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.26231	0.0640	M	0.66439	2.03	0.52501	D	0.999954	B;B;B	0.34255	0.206;0.445;0.03	B;B;B	0.24155	0.051;0.03;0.022	T	0.15694	-1.0428	10	0.54805	T	0.06	-19.9707	8.8426	0.35151	0.1883:0.0:0.8117:0.0	.	737;718;571	B7Z3Q9;B7Z3I2;O95834	.;.;EMAL2_HUMAN	V	718;571;729	ENSP00000442365:A718V;ENSP00000245925:A571V	ENSP00000245925:A571V	A	-	2	0	EML2	50808751	0.860000	0.29831	0.756000	0.31282	0.028000	0.11728	4.029000	0.57253	1.385000	0.46445	0.563000	0.77884	GCG	.	.	none		0.572	EML2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459608.1	NM_012155	
PABPC1	26986	hgsc.bcm.edu	37	8	101721960	101721960	+	Splice_Site	SNP	C	C	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr8:101721960C>A	ENST00000318607.5	-	8	2101		c.e8-1		PABPC1_ENST00000519004.1_Splice_Site|PABPC1_ENST00000522387.1_Splice_Site|AP001205.1_ENST00000579868.1_RNA|PABPC1_ENST00000519596.1_Splice_Site	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1						cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494)			breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	40	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			CCATCATAACCTATTAAAAAA	0.348																																					.		Atlas-SNP	.											.	PABPC1	76	.	0			c.973-1G>T						PASS	.						35.0	34.0	35.0					8																	101721960		2203	4300	6503	SO:0001630	splice_region_variant	26986	exon9			CATAACCTATTAA	Y00345	CCDS6289.1	8q22.2-q23	2013-02-12	2004-04-20		ENSG00000070756	ENSG00000070756		"""RNA binding motif (RRM) containing"""	8554	protein-coding gene	gene with protein product		604679	"""poly(A)-binding protein, cytoplasmic 2"""	PAB1, PABPC2		2885805	Standard	XM_005250861		Approved	PABP1, PABPL1	uc003yjs.1	P11940	OTTHUMG00000164779	ENST00000318607.5:c.973-1G>T	8.37:g.101721960C>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	126	42	0.333333	NM_002568	Q15097|Q93004	Splice_Site	SNP	ENST00000318607.5	37	CCDS6289.1	.	.	.	.	.	.	.	.	.	.	C	14.47	2.545658	0.45280	.	.	ENSG00000070756	ENST00000318607;ENST00000347137;ENST00000519004;ENST00000522387;ENST00000519596;ENST00000519100	.	.	.	5.06	4.17	0.49024	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.6976	0.57014	0.0:0.9191:0.0:0.0809	.	.	.	.	.	-1	.	.	.	-	.	.	PABPC1	101791136	1.000000	0.71417	0.998000	0.56505	0.877000	0.50540	7.706000	0.84615	2.514000	0.84764	0.655000	0.94253	.	.	.	none		0.348	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568	Intron
MAGEE1	57692	hgsc.bcm.edu	37	X	75648638	75648638	+	Silent	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:75648638G>A	ENST00000361470.2	+	1	593	c.315G>A	c.(313-315)ctG>ctA	p.L105L		NM_020932.2	NP_065983.1	Q9HCI5	MAGE1_HUMAN	melanoma antigen family E, 1	105						dendrite (GO:0030425)|dystrophin-associated glycoprotein complex (GO:0016010)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(12)|lung(20)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	51						CCTCCGTGCTGCCCACCCCCA	0.677																																					p.L105L		Atlas-SNP	.											.	MAGEE1	236	.	0			c.G315A						PASS	.						21.0	22.0	22.0					X																	75648638		2203	4299	6502	SO:0001819	synonymous_variant	57692	exon1			CGTGCTGCCCACC	AF490507	CCDS14433.1	Xq13	2008-02-05			ENSG00000198934	ENSG00000198934			24934	protein-coding gene	gene with protein product		300759				14623885	Standard	NM_020932		Approved	KIAA1587, DAMAGE	uc004ecm.2	Q9HCI5	OTTHUMG00000021879	ENST00000361470.2:c.315G>A	X.37:g.75648638G>A		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	152	21	0.138158	NM_020932	Q5JXC7|Q86TG0|Q8TD92|Q9H216	Silent	SNP	ENST00000361470.2	37	CCDS14433.1																																																																																			.	.	none		0.677	MAGEE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057298.1	NM_020932	
HYAL3	8372	hgsc.bcm.edu	37	3	50332345	50332345	+	Missense_Mutation	SNP	T	T	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:50332345T>G	ENST00000336307.1	-	2	961	c.689A>C	c.(688-690)cAa>cCa	p.Q230P	IFRD2_ENST00000436390.1_5'Flank|IFRD2_ENST00000417626.2_5'Flank|HYAL3_ENST00000513170.1_Intron|IFRD2_ENST00000484043.1_5'Flank|HYAL3_ENST00000450982.1_Missense_Mutation_p.Q230P|HYAL3_ENST00000359051.3_Missense_Mutation_p.Q230P|HYAL3_ENST00000415204.1_Intron|IFRD2_ENST00000336089.4_5'Flank|IFRD2_ENST00000429673.2_5'Flank	NM_001200029.1|NM_003549.3	NP_001186958.1|NP_003540.2	O43820	HYAL3_HUMAN	hyaluronoglucosaminidase 3	230					carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to UV-B (GO:0071493)|hyaluronan catabolic process (GO:0030214)|inflammatory response (GO:0006954)|response to antibiotic (GO:0046677)|response to virus (GO:0009615)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|lysosome (GO:0005764)	hyaluronoglucuronidase activity (GO:0033906)|hyalurononglucosaminidase activity (GO:0004415)			central_nervous_system(1)|endometrium(2)|kidney(1)|lung(5)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	19				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		CCAATGCAGTTGAGTGTTGCG	0.622																																					p.Q230P		Atlas-SNP	.											.	HYAL3	34	.	0			c.A689C						PASS	.						64.0	64.0	64.0					3																	50332345		2203	4300	6503	SO:0001583	missense	8372	exon2			TGCAGTTGAGTGT	AF040710	CCDS2815.1, CCDS56259.1, CCDS56260.1, CCDS56257.1	3p21.3	2004-03-12			ENSG00000186792	ENSG00000186792			5322	protein-coding gene	gene with protein product		604038				10493834	Standard	NM_003549		Approved	LUCA-3, LUCA14, Minna14	uc021wyn.1	O43820	OTTHUMG00000156936	ENST00000336307.1:c.689A>C	3.37:g.50332345T>G	ENSP00000337425:p.Gln230Pro	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	211	88	0.417062	NM_001200030	O60540|Q8NFK2|Q8NFK3|Q8NFK4|Q96E56|Q9BRW9	Missense_Mutation	SNP	ENST00000336307.1	37	CCDS2815.1	.	.	.	.	.	.	.	.	.	.	T	16.70	3.196026	0.58126	.	.	ENSG00000186792	ENST00000359051;ENST00000336307;ENST00000450982	T;T;T	0.24908	1.83;1.83;1.83	5.26	1.71	0.24356	Aldolase-type TIM barrel (1);Glycoside hydrolase, superfamily (1);	0.428784	0.22758	U	0.055998	T	0.42675	0.1213	M	0.88979	2.995	0.27105	N	0.962515	P;D	0.53151	0.939;0.958	P;P	0.52386	0.697;0.571	T	0.35992	-0.9766	10	0.72032	D	0.01	-2.7947	7.8275	0.29324	0.0:0.2392:0.0:0.7608	.	230;230	O43820;O43820-2	HYAL3_HUMAN;.	P	230	ENSP00000351946:Q230P;ENSP00000337425:Q230P;ENSP00000391922:Q230P	ENSP00000337425:Q230P	Q	-	2	0	HYAL3	50307349	0.000000	0.05858	0.992000	0.48379	0.932000	0.56968	-0.339000	0.07832	0.850000	0.35239	0.460000	0.39030	CAA	.	.	none		0.622	HYAL3-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000346664.1	NM_003549	
LONRF3	79836	hgsc.bcm.edu	37	X	118109491	118109491	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:118109491G>A	ENST00000371628.3	+	1	779	c.748G>A	c.(748-750)Ggc>Agc	p.G250S	LONRF3_ENST00000304778.7_Missense_Mutation_p.G250S|LONRF3_ENST00000422289.2_5'Flank	NM_001031855.1	NP_001027026.1	Q496Y0	LONF3_HUMAN	LON peptidase N-terminal domain and ring finger 3	250							ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	36						CCGGCACGAGGGCAACCGACT	0.687																																					p.G250S		Atlas-SNP	.											.	LONRF3	138	.	0			c.G748A						PASS	.						16.0	11.0	13.0					X																	118109491		2177	4244	6421	SO:0001583	missense	79836	exon1			CACGAGGGCAACC	AK026265	CCDS14575.1, CCDS35374.1, CCDS76014.1	Xq24	2013-01-09	2005-08-19	2005-08-19	ENSG00000175556	ENSG00000175556		"""RING-type (C3HC4) zinc fingers"""	21152	protein-coding gene	gene with protein product			"""ring finger protein 127"""	RNF127			Standard	XM_005262476		Approved	FLJ22612	uc004eqw.3	Q496Y0	OTTHUMG00000022262	ENST00000371628.3:c.748G>A	X.37:g.118109491G>A	ENSP00000360690:p.Gly250Ser	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	147	24	0.163265	NM_001031855	Q5JPN6|Q8NB00|Q9H647	Missense_Mutation	SNP	ENST00000371628.3	37	CCDS35374.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.78|17.78	3.473780|3.473780	0.63737|0.63737	.|.	.|.	ENSG00000175556|ENSG00000175556	ENST00000439603|ENST00000365713;ENST00000304778;ENST00000371628	.|T;T;T	.|0.80566	.|-1.39;-1.39;-1.39	4.26|4.26	4.26|4.26	0.50523|0.50523	.|Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	D|D	0.87245|0.87245	0.6129|0.6129	M|M	0.86343|0.86343	2.81|2.81	0.80722|0.80722	D|D	1|1	.|P;P	.|0.47762	.|0.9;0.866	.|B;P	.|0.51701	.|0.397;0.677	D|D	0.88596|0.88596	0.3146|0.3146	6|10	.|0.44086	.|T	.|0.13	-0.604|-0.604	15.2074|15.2074	0.73190|0.73190	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|250;250	.|Q496Y0-2;Q496Y0	.|.;LONF3_HUMAN	E|S	56|250	.|ENSP00000360691:G250S;ENSP00000307732:G250S;ENSP00000360690:G250S	.|ENSP00000307732:G250S	G|G	+|+	2|1	0|0	LONRF3|LONRF3	117993519|117993519	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	5.909000|5.909000	0.69923|0.69923	2.122000|2.122000	0.65172|0.65172	0.529000|0.529000	0.55759|0.55759	GGG|GGC	.	.	none		0.687	LONRF3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355124.2	NM_024778	
OR2W3	343171	hgsc.bcm.edu	37	1	248059470	248059470	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:248059470C>T	ENST00000360358.3	+	1	582	c.582C>T	c.(580-582)gcC>gcT	p.A194A	OR2W3_ENST00000537741.1_Silent_p.A194A	NM_001001957.2	NP_001001957.2	Q7Z3T1	OR2W3_HUMAN	olfactory receptor, family 2, subfamily W, member 3	194						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(2)|large_intestine(2)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)	49	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0319)			GCACTGTGGCCATCGAAGGCA	0.597																																					p.A194A		Atlas-SNP	.											OR2W3,right_lower_lobe,carcinoma,+2,1	OR2W3	113	1	0			c.C582T						PASS	.						143.0	122.0	130.0					1																	248059470		2203	4300	6503	SO:0001819	synonymous_variant	343171	exon1			TGTGGCCATCGAA	N75737	CCDS31099.1	1q44	2012-08-09		2004-03-10	ENSG00000238243	ENSG00000238243		"""GPCR / Class A : Olfactory receptors"""	15021	protein-coding gene	gene with protein product				OR2W8P, OR2W3P		14983052	Standard	NM_001001957		Approved	OST718	uc010pzb.2	Q7Z3T1	OTTHUMG00000040204	ENST00000360358.3:c.582C>T	1.37:g.248059470C>T		Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	298	64	0.214765	NM_001001957	Q6IF06|Q8NG86	Silent	SNP	ENST00000360358.3	37	CCDS31099.1																																																																																			.	.	none		0.597	OR2W3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096861.1	NM_001001957	
USP11	8237	hgsc.bcm.edu	37	X	47092477	47092477	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:47092477C>T	ENST00000218348.3	+	1	164	c.164C>T	c.(163-165)gCg>gTg	p.A55V	USP11_ENST00000377107.2_Missense_Mutation_p.A12V	NM_004651.3	NP_004642.2	P51784	UBP11_HUMAN	ubiquitin specific peptidase 11	55					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(14)|ovary(3)|pancreas(1)|stomach(1)	40						gctgctgctgcggcggctgtg	0.647																																					p.A55V		Atlas-SNP	.											.	USP11	93	.	0			c.C164T						PASS	.						11.0	11.0	11.0					X																	47092477		2170	4226	6396	SO:0001583	missense	8237	exon1			CTGCTGCGGCGGC	U44839	CCDS14277.1	Xp11.23	2008-02-05	2005-08-08		ENSG00000102226	ENSG00000102226		"""Ubiquitin-specific peptidases"""	12609	protein-coding gene	gene with protein product		300050	"""ubiquitin specific protease 11"""			12838346	Standard	XM_005272674		Approved	UHX1	uc004dhp.3	P51784	OTTHUMG00000021437	ENST00000218348.3:c.164C>T	X.37:g.47092477C>T	ENSP00000218348:p.Ala55Val	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	83	24	0.289157	NM_004651	B2RTX1|Q8IUG6|Q9BWE1	Missense_Mutation	SNP	ENST00000218348.3	37	CCDS14277.1	.	.	.	.	.	.	.	.	.	.	C	16.54	3.151779	0.57151	.	.	ENSG00000102226	ENST00000377107;ENST00000218348	T;T	0.22134	1.97;1.99	1.61	1.61	0.23674	.	0.542706	0.13946	N	0.351850	T	0.19406	0.0466	N	0.19112	0.55	0.09310	N	1	D	0.67145	0.996	P	0.54372	0.75	T	0.06679	-1.0813	10	0.66056	D	0.02	.	6.0062	0.19547	0.0:1.0:0.0:0.0	.	55	P51784	UBP11_HUMAN	V	12;55	ENSP00000366311:A12V;ENSP00000218348:A55V	ENSP00000218348:A55V	A	+	2	0	USP11	46977421	0.069000	0.21087	0.003000	0.11579	0.006000	0.05464	0.406000	0.21032	1.066000	0.40716	0.513000	0.50165	GCG	.	.	none		0.647	USP11-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_004651	
MAATS1	89876	hgsc.bcm.edu	37	3	119466110	119466110	+	Splice_Site	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:119466110G>A	ENST00000273390.5	+	15	2128	c.2051G>A	c.(2050-2052)cGc>cAc	p.R684H	RP11-169N13.4_ENST00000489428.2_RNA	NM_033364.3	NP_203528	Q7Z4T9	MAAT1_HUMAN	MYCBP-associated, testis expressed 1	520						mitochondrion (GO:0005739)											ATGGAAAGCCGGTGTGTATCA	0.388																																					p.R684H		Atlas-SNP	.											C3orf15,NS,carcinoma,+1,2	.	.	2	0			c.G2051A						scavenged	.						76.0	68.0	71.0					3																	119466110		2203	4300	6503	SO:0001630	splice_region_variant	89876	exon15			AAAGCCGGTGTGT	AB063296	CCDS2994.1	3q12-q13.3	2014-07-31	2012-12-07	2012-09-26	ENSG00000183833	ENSG00000183833			24010	protein-coding gene	gene with protein product	"""AMY-1-associating protein expressed in testis 1"", ""MYCBP-binding protein"", ""spermatogenesis associated 26"""	609910	"""chromosome 3 open reading frame 15"", ""MYCBP/AMY-1-associated, testis expressed 1"""	C3orf15		12223483, 14551891, 17967944	Standard	NM_033364		Approved	AAT1, AAT1alpha, SPATA26, CaM-IP2	uc003ede.4	Q7Z4T9	OTTHUMG00000159422	ENST00000273390.5:c.2051+1G>A	3.37:g.119466110G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	56	3	0.0535714	NM_033364	A0AVK2|A8K1J9|B3KP23|B4DG52|B4DZ14|C9JUG4|Q68DX2|Q8TD41|Q96A45|Q96JE8	Missense_Mutation	SNP	ENST00000273390.5	37	CCDS2994.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.389491	0.82902	.	.	ENSG00000183833	ENST00000273390	T	0.24350	1.86	5.68	4.8	0.61643	.	0.241129	0.40222	N	0.001147	T	0.50171	0.1600	M	0.77103	2.36	0.80722	D	1	B;D;P	0.76494	0.391;0.999;0.647	B;D;B	0.65874	0.067;0.939;0.111	T	0.54589	-0.8271	10	0.54805	T	0.06	-13.3469	14.3754	0.66869	0.0707:0.0:0.9293:0.0	.	520;622;684	Q7Z4T9;Q7Z4T9-3;Q7Z4T9-7	AAT1_HUMAN;.;.	H	684	ENSP00000273390:R684H	ENSP00000273390:R684H	R	+	2	0	C3orf15	120948800	1.000000	0.71417	0.994000	0.49952	0.918000	0.54935	4.272000	0.58908	1.403000	0.46800	0.591000	0.81541	CGC	.	.	none		0.388	MAATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355222.1	NM_033364	Missense_Mutation
DGAT2L6	347516	hgsc.bcm.edu	37	X	69424867	69424867	+	Missense_Mutation	SNP	G	G	A	rs35142503		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:69424867G>A	ENST00000333026.3	+	7	1025	c.925G>A	c.(925-927)Gca>Aca	p.A309T		NM_198512.1	NP_940914.1	Q6ZPD8	DG2L6_HUMAN	diacylglycerol O-acyltransferase 2-like 6	309					lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	transferase activity, transferring acyl groups other than amino-acyl groups (GO:0016747)			breast(1)|endometrium(2)|large_intestine(3)|lung(5)|ovary(1)	12						CAAGTATCACGCACTCTACAT	0.458																																					p.A309T		Atlas-SNP	.											.	DGAT2L6	40	.	0			c.G925A						PASS	.	G	THR/ALA	4,3831		0,4,1628,571	95.0	75.0	82.0		925	1.6	0.2	X	dbSNP_126	82	0,6728		0,0,2428,1872	yes	missense	DGAT2L6	NM_198512.1	58	0,4,4056,2443	AA,AG,GG,G		0.0,0.1043,0.0379	benign	309/338	69424867	4,10559	2203	4300	6503	SO:0001583	missense	347516	exon7			TATCACGCACTCT	AK129500	CCDS14397.1	Xq13.1	2008-02-05			ENSG00000184210	ENSG00000184210			23250	protein-coding gene	gene with protein product		300926				15671038	Standard	NM_198512		Approved	DC3, FLJ25989	uc004dxx.1	Q6ZPD8	OTTHUMG00000021774	ENST00000333026.3:c.925G>A	X.37:g.69424867G>A	ENSP00000328036:p.Ala309Thr	Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	297	49	0.164983	NM_198512	Q6IEE2	Missense_Mutation	SNP	ENST00000333026.3	37	CCDS14397.1	.	.	.	.	.	.	.	.	.	.	G	8.546	0.874318	0.17395	0.001043	0.0	ENSG00000184210	ENST00000333026	D	0.93547	-3.24	4.74	1.62	0.23740	.	0.774326	0.12002	N	0.508712	D	0.88640	0.6491	L	0.49455	1.56	0.21822	N	0.999526	B	0.16603	0.018	B	0.16289	0.015	T	0.73404	-0.3993	10	0.19147	T	0.46	-22.9304	7.1522	0.25616	0.3674:0.0:0.6325:0.0	rs35142503	309	Q6ZPD8	DG2L6_HUMAN	T	309	ENSP00000328036:A309T	ENSP00000328036:A309T	A	+	1	0	DGAT2L6	69341592	0.000000	0.05858	0.172000	0.22920	0.534000	0.34807	0.658000	0.24979	0.002000	0.14630	-0.192000	0.12808	GCA	G|0.987;A|0.013	0.013	weak		0.458	DGAT2L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057067.1	NM_198512	
SLITRK2	84631	hgsc.bcm.edu	37	X	144904787	144904787	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:144904787G>A	ENST00000370490.1	+	1	5099	c.844G>A	c.(844-846)Gtc>Atc	p.V282I	SLITRK2_ENST00000447897.2_Missense_Mutation_p.V282I|SLITRK2_ENST00000428560.2_Missense_Mutation_p.V282I|SLITRK2_ENST00000434188.2_Missense_Mutation_p.V282I|SLITRK2_ENST00000413937.2_Missense_Mutation_p.V282I			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	282					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)					TGACACCCACGTCCAAAGGCT	0.562																																					p.V282I		Atlas-SNP	.											.	SLITRK2	221	.	0			c.G844A						PASS	.						79.0	72.0	74.0					X																	144904787		2203	4300	6503	SO:0001583	missense	84631	exon5			ACCCACGTCCAAA	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.844G>A	X.37:g.144904787G>A	ENSP00000359521:p.Val282Ile	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	78	13	0.166667	NM_001144005	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Missense_Mutation	SNP	ENST00000370490.1	37	CCDS14680.1	.	.	.	.	.	.	.	.	.	.	G	4.111	0.018746	0.07959	.	.	ENSG00000185985	ENST00000335565;ENST00000447897;ENST00000370490;ENST00000434188;ENST00000413937;ENST00000428560	T;T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98;0.98	5.67	-4.09	0.03951	.	0.813170	0.11203	N	0.588607	T	0.22322	0.0538	N	0.12182	0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.21143	-1.0254	10	0.18710	T	0.47	-1.0238	14.6093	0.68504	0.7205:0.0:0.2795:0.0	.	282	Q9H156	SLIK2_HUMAN	I	282	ENSP00000334374:V282I;ENSP00000411681:V282I;ENSP00000359521:V282I;ENSP00000397015:V282I;ENSP00000407347:V282I;ENSP00000412010:V282I	ENSP00000334374:V282I	V	+	1	0	SLITRK2	144712479	0.000000	0.05858	0.001000	0.08648	0.837000	0.47467	-0.586000	0.05787	-1.074000	0.03132	-0.914000	0.02751	GTC	.	.	none		0.562	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539	
PCDHB16	57717	hgsc.bcm.edu	37	5	140564228	140564228	+	Silent	SNP	G	G	A	rs540563709		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:140564228G>A	ENST00000361016.2	+	1	3249	c.2094G>A	c.(2092-2094)tcG>tcA	p.S698S		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	698					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)			CCTCGGTGTCGTCGCTCTTCC	0.697																																					p.S698S		Atlas-SNP	.											PCDHB16,colon,carcinoma,0,2	PCDHB16	159	2	0			c.G2094A						PASS	.						71.0	75.0	74.0					5																	140564228		2201	4297	6498	SO:0001819	synonymous_variant	57717	exon1			GGTGTCGTCGCTC	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.2094G>A	5.37:g.140564228G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	55	19	0.345455	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Silent	SNP	ENST00000361016.2	37	CCDS4251.1																																																																																			.	.	none		0.697	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957	
CXCR4	7852	hgsc.bcm.edu	37	2	136872552	136872552	+	Missense_Mutation	SNP	C	C	T	rs145335491		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:136872552C>T	ENST00000241393.3	-	2	1050	c.946G>A	c.(946-948)Gca>Aca	p.A316T	CXCR4_ENST00000466288.1_5'UTR|CXCR4_ENST00000409817.1_Missense_Mutation_p.A320T	NM_003467.2	NP_003458.1	P61073	CXCR4_HUMAN	chemokine (C-X-C motif) receptor 4	316					activation of MAPK activity (GO:0000187)|ameboidal cell migration (GO:0001667)|apoptotic process (GO:0006915)|brain development (GO:0007420)|calcium-mediated signaling (GO:0019722)|cellular response to cytokine stimulus (GO:0071345)|chemokine-mediated signaling pathway (GO:0070098)|dendritic cell chemotaxis (GO:0002407)|entry into host cell (GO:0030260)|G-protein coupled receptor signaling pathway (GO:0007186)|germ cell development (GO:0007281)|germ cell migration (GO:0008354)|inflammatory response (GO:0006954)|motor neuron axon guidance (GO:0008045)|myelin maintenance (GO:0043217)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|neutrophil activation (GO:0042119)|patterning of blood vessels (GO:0001569)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of oligodendrocyte differentiation (GO:0048714)|regulation of cell migration (GO:0030334)|regulation of chemotaxis (GO:0050920)|response to hypoxia (GO:0001666)|response to virus (GO:0009615)|T cell proliferation (GO:0042098)|viral process (GO:0016032)	cell leading edge (GO:0031252)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|C-X-C chemokine receptor activity (GO:0016494)|coreceptor activity (GO:0015026)|G-protein coupled receptor activity (GO:0004930)|myosin light chain binding (GO:0032027)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|virus receptor activity (GO:0001618)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(14)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25				BRCA - Breast invasive adenocarcinoma(221;0.155)	Framycetin(DB00452)|Plerixafor(DB06809)	GAGGTGAGTGCGTGCTGGGCA	0.502																																					p.A320T		Atlas-SNP	.											CXCR4,NS,carcinoma,0,1	CXCR4	51	1	0			c.G958A						scavenged	.	C	THR/ALA,THR/ALA	2,4404	4.2+/-10.8	0,2,2201	383.0	362.0	369.0		958,946	5.3	1.0	2	dbSNP_134	369	0,8600		0,0,4300	no	missense,missense	CXCR4	NM_001008540.1,NM_003467.2	58,58	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging,probably-damaging	320/357,316/353	136872552	2,13004	2203	4300	6503	SO:0001583	missense	7852	exon1			TGAGTGCGTGCTG	AF005058	CCDS33295.1, CCDS46420.1	2q21	2014-09-17	2002-08-22		ENSG00000121966	ENSG00000121966		"""CD molecules"", ""GPCR / Class A : Chemokine receptors : C-X-C motif"""	2561	protein-coding gene	gene with protein product		162643	"""chemokine (C-X-C motif), receptor 4 (fusin)"""			9599023, 9379028	Standard	NM_001008540		Approved	LESTR, NPY3R, HM89, NPYY3R, D2S201E, fusin, HSY3RR, NPYR, CD184	uc002tuz.3	P61073	OTTHUMG00000153583	ENST00000241393.3:c.946G>A	2.37:g.136872552C>T	ENSP00000241393:p.Ala316Thr	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	229	4	0.0174672	NM_001008540	B2R5N0|O60835|P30991|P56438|Q53S69|Q9BXA0|Q9UKN2	Missense_Mutation	SNP	ENST00000241393.3	37	CCDS46420.1	.	.	.	.	.	.	.	.	.	.	C	15.42	2.827050	0.50739	4.54E-4	0.0	ENSG00000121966	ENST00000409817;ENST00000241393;ENST00000537957	T;T	0.36699	1.24;1.24	6.16	5.26	0.73747	.	0.159423	0.56097	N	0.000031	T	0.41190	0.1148	N	0.14661	0.345	0.80722	D	1	D;D	0.89917	0.986;1.0	B;D	0.68765	0.417;0.96	T	0.34502	-0.9826	10	0.32370	T	0.25	.	14.7183	0.69286	0.0:0.9286:0.0:0.0714	.	316;320	P61073;P61073-2	CXCR4_HUMAN;.	T	320;316;186	ENSP00000386884:A320T;ENSP00000241393:A316T	ENSP00000241393:A316T	A	-	1	0	CXCR4	136589022	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	3.555000	0.53727	1.557000	0.49525	0.650000	0.86243	GCA	C|1.000;T|0.000	0.000	weak		0.502	CXCR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331732.1		
IQCA1	79781	hgsc.bcm.edu	37	2	237327861	237327861	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:237327861C>T	ENST00000409907.3	-	8	1339	c.1065G>A	c.(1063-1065)aaG>aaA	p.K355K	IQCA1_ENST00000465621.1_5'UTR|IQCA1_ENST00000309507.5_Silent_p.K351K|IQCA1_ENST00000431676.2_Intron	NM_024726.4	NP_079002.3	Q86XH1	IQCA1_HUMAN	IQ motif containing with AAA domain 1	355	Lys-rich.						ATP binding (GO:0005524)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)	26						ttttcttcttcttctttttgt	0.279																																					p.K362K		Atlas-SNP	.											IQCA1_ENST00000409907,NS,carcinoma,0,2	IQCA1	170	2	0			c.G1086A						scavenged	.						18.0	17.0	18.0					2																	237327861		1352	2959	4311	SO:0001819	synonymous_variant	79781	exon8			CTTCTTCTTCTTT	AK026180	CCDS46549.1, CCDS59441.1, CCDS74677.1	2q37.3	2014-07-18	2008-07-02	2008-07-02	ENSG00000132321	ENSG00000132321		"""ATPases / AAA-type"""	26195	protein-coding gene	gene with protein product	"""dynein regulatory complex subunit 11"""		"""IQ motif containing with AAA domain"""	IQCA		23427265	Standard	NM_024726		Approved	FLJ22527, DRC11	uc002vwb.3	Q86XH1	OTTHUMG00000153058	ENST00000409907.3:c.1065G>A	2.37:g.237327861C>T		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	210	3	0.0142857	NM_001270585	B4DFH9|E7EWQ0|Q4G164|Q53R37|Q53RV3|Q96NS7|Q9H680	Silent	SNP	ENST00000409907.3	37	CCDS46549.1	.	.	.	.	.	.	.	.	.	.	C	0.014	-1.586357	0.00872	.	.	ENSG00000132321	ENST00000418802	.	.	.	2.87	-0.837	0.10766	.	.	.	.	.	T	0.41696	0.1170	.	.	.	0.39502	D	0.968216	.	.	.	.	.	.	T	0.28004	-1.0057	4	.	.	.	.	2.334	0.04242	0.2747:0.3362:0.0:0.3891	.	.	.	.	K	374	.	.	E	-	1	0	IQCA1	236992600	0.001000	0.12720	0.343000	0.25615	0.040000	0.13550	-3.676000	0.00396	-0.184000	0.10567	-0.345000	0.07892	GAA	.	.	none		0.279	IQCA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000329266.1	NM_024726	
ELF1	1997	hgsc.bcm.edu	37	13	41507882	41507882	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr13:41507882C>T	ENST00000239882.3	-	9	1853	c.1539G>A	c.(1537-1539)caG>caA	p.Q513Q	ELF1_ENST00000498824.1_5'UTR|ELF1_ENST00000442101.1_Silent_p.Q489Q	NM_172373.3	NP_758961.1	P32519	ELF1_HUMAN	E74-like factor 1 (ets domain transcription factor)	513					cell differentiation (GO:0030154)|negative regulation of T cell receptor signaling pathway (GO:0050860)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine production (GO:0001817)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37		Lung NSC(96;8.3e-05)|Prostate(109;0.0233)|Breast(139;0.0296)|Lung SC(185;0.0367)		all cancers(112;1.87e-08)|Epithelial(112;8.45e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000202)|GBM - Glioblastoma multiforme(144;0.00266)|BRCA - Breast invasive adenocarcinoma(63;0.072)		TGCAAATGGTCTGAACATTGC	0.517																																					p.Q513Q		Atlas-SNP	.											ELF1,NS,carcinoma,-2,1	ELF1	65	1	0			c.G1539A						PASS	.						108.0	104.0	106.0					13																	41507882		2203	4300	6503	SO:0001819	synonymous_variant	1997	exon9			AATGGTCTGAACA	M82882	CCDS9374.1	13q13	2008-07-18			ENSG00000120690	ENSG00000120690			3316	protein-coding gene	gene with protein product		189973				1545787	Standard	NM_001145353		Approved		uc001uxs.3	P32519	OTTHUMG00000016783	ENST00000239882.3:c.1539G>A	13.37:g.41507882C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	137	62	0.452555	NM_172373	B4E2I5|E9PDQ9|Q8N6F6|Q9UDE1	Silent	SNP	ENST00000239882.3	37	CCDS9374.1																																																																																			.	.	none		0.517	ELF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044654.3	NM_172373	
ANKRD53	79998	hgsc.bcm.edu	37	2	71212171	71212171	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:71212171C>T	ENST00000360589.3	+	6	1368	c.1334C>T	c.(1333-1335)gCg>gTg	p.A445V	ANKRD53_ENST00000441349.1_3'UTR|ANKRD53_ENST00000457410.1_Missense_Mutation_p.A411V|AC007040.11_ENST00000606025.1_Intron|ANKRD53_ENST00000272421.6_3'UTR	NM_001115116.1	NP_001108588.1	Q8N9V6	ANR53_HUMAN	ankyrin repeat domain 53	445										endometrium(2)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	11						CACTGGGTGGCGCCCGTGCCG	0.652											OREG0014687	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A445V		Atlas-SNP	.											.	ANKRD53	55	.	0			c.C1334T						PASS	.						7.0	10.0	9.0					2																	71212171		683	1580	2263	SO:0001583	missense	79998	exon6			GGGTGGCGCCCGT	BC035234	CCDS1913.1, CCDS46321.1	2p13.3	2013-01-10			ENSG00000144031	ENSG00000144031		"""Ankyrin repeat domain containing"""	25691	protein-coding gene	gene with protein product							Standard	NM_024933		Approved	FLJ12056, FLJ36160	uc002shl.4	Q8N9V6	OTTHUMG00000129712	ENST00000360589.3:c.1334C>T	2.37:g.71212171C>T	ENSP00000353796:p.Ala445Val	Somatic	39	0	0	1128	WXS	Illumina HiSeq	Phase_I	22	5	0.227273	NM_001115116	Q8IYP8	Missense_Mutation	SNP	ENST00000360589.3	37	CCDS46321.1	.	.	.	.	.	.	.	.	.	.	C	14.89	2.669230	0.47677	.	.	ENSG00000144031	ENST00000457410;ENST00000360589	T;T	0.64085	0.01;-0.08	5.16	-0.376	0.12505	.	1.236970	0.05473	N	0.553515	T	0.40791	0.1131	L	0.29908	0.895	0.09310	N	1	P	0.49961	0.93	B	0.34873	0.191	T	0.38090	-0.9677	10	0.40728	T	0.16	-1.5817	2.8344	0.05509	0.2989:0.3228:0.2918:0.0865	.	445	Q8N9V6	ANR53_HUMAN	V	411;445	ENSP00000407004:A411V;ENSP00000353796:A445V	ENSP00000353796:A445V	A	+	2	0	ANKRD53	71065679	0.000000	0.05858	0.006000	0.13384	0.054000	0.15201	-0.783000	0.04638	0.076000	0.16826	0.561000	0.74099	GCG	.	.	none		0.652	ANKRD53-004	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330275.2	NM_024933	
ENGASE	64772	hgsc.bcm.edu	37	17	77079972	77079972	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr17:77079972G>A	ENST00000579016.1	+	10	1381	c.1381G>A	c.(1381-1383)Gga>Aga	p.G461R	ENGASE_ENST00000584568.1_3'UTR	NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	461						cytoplasm (GO:0005737)	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity (GO:0033925)			breast(2)|endometrium(4)|large_intestine(1)|lung(15)|prostate(2)|skin(1)	25						TGCCTGGCACGGAGGCAGCTC	0.662																																					p.G461R		Atlas-SNP	.											ENGASE,lower_third,carcinoma,0,1	ENGASE	55	1	0			c.G1381A						scavenged	.						30.0	38.0	36.0					17																	77079972		2173	4249	6422	SO:0001583	missense	64772	exon10			TGGCACGGAGGCA	AF512564	CCDS42394.1	17q25.3	2009-03-03			ENSG00000167280	ENSG00000167280	3.2.1.96		24622	protein-coding gene	gene with protein product	"""Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase"", ""Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase"""	611898				12114544, 18586680	Standard	NM_001042573		Approved	FLJ21865	uc002jwv.4	Q8NFI3	OTTHUMG00000167714	ENST00000579016.1:c.1381G>A	17.37:g.77079972G>A	ENSP00000462333:p.Gly461Arg	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	79	2	0.0253165	NM_001042573	Q659F0|Q8TB86|Q9H6U4	Missense_Mutation	SNP	ENST00000579016.1	37	CCDS42394.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.962406	0.92791	.	.	ENSG00000167280	ENST00000545583	.	.	.	4.82	4.82	0.62117	.	0.000000	0.85682	D	0.000000	T	0.76793	0.4037	M	0.72894	2.215	0.80722	D	1	D	0.76494	0.999	P	0.61328	0.887	T	0.80261	-0.1456	9	0.72032	D	0.01	-6.1571	18.2613	0.90037	0.0:0.0:1.0:0.0	.	461	Q8NFI3	ENASE_HUMAN	R	461	.	ENSP00000438577:G461R	G	+	1	0	ENGASE	74591567	1.000000	0.71417	1.000000	0.80357	0.722000	0.41435	7.354000	0.79424	2.377000	0.81083	0.561000	0.74099	GGA	.	.	none		0.662	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759	
GABRQ	55879	hgsc.bcm.edu	37	X	151820139	151820139	+	Missense_Mutation	SNP	A	A	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:151820139A>C	ENST00000370306.2	+	8	1072	c.1052A>C	c.(1051-1053)tAt>tCt	p.Y351S		NM_018558.2	NP_061028.3	Q9UN88	GBRT_HUMAN	gamma-aminobutyric acid (GABA) A receptor, theta	351					neurotransmitter transport (GO:0006836)|signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|neurotransmitter transporter activity (GO:0005326)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(9)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	52	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|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)	TACATCAACTATCTTTTCTAC	0.507																																					p.Y351S		Atlas-SNP	.											.	GABRQ	131	.	0			c.A1052C						PASS	.						282.0	225.0	244.0					X																	151820139		2203	4300	6503	SO:0001583	missense	55879	exon8			TCAACTATCTTTT	U47334	CCDS14707.1	Xq28	2012-06-22	2012-02-03		ENSG00000147402	ENSG00000268089		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	14454	protein-coding gene	gene with protein product	"""GABA(A) receptor, theta"""	300349	"""gamma-aminobutyric acid (GABA) receptor, theta"""			10804200, 10449790	Standard	NM_018558		Approved	THETA	uc004ffp.1	Q9UN88	OTTHUMG00000022649	ENST00000370306.2:c.1052A>C	X.37:g.151820139A>C	ENSP00000359329:p.Tyr351Ser	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	289	47	0.16263	NM_018558	A6NFN1|Q32MB4|Q9NZK8	Missense_Mutation	SNP	ENST00000370306.2	37	CCDS14707.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.256619	0.80246	.	.	ENSG00000147402	ENST00000370306	D	0.87809	-2.3	5.88	4.68	0.58851	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.156200	0.30565	N	0.009347	D	0.91253	0.7243	M	0.62723	1.935	0.44337	D	0.997227	D	0.89917	1.0	D	0.83275	0.996	D	0.90553	0.4510	10	0.87932	D	0	.	9.5	0.39011	0.8398:0.0:0.0:0.1602	.	351	Q9UN88	GBRT_HUMAN	S	351	ENSP00000359329:Y351S	ENSP00000359329:Y351S	Y	+	2	0	GABRQ	151570795	1.000000	0.71417	0.740000	0.30986	0.936000	0.57629	7.438000	0.80431	0.786000	0.33708	0.486000	0.48141	TAT	.	.	none		0.507	GABRQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058763.2	NM_018558	
BMP5	653	hgsc.bcm.edu	37	6	55659189	55659189	+	Silent	SNP	G	G	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr6:55659189G>T	ENST00000370830.3	-	3	1418	c.720C>A	c.(718-720)gcC>gcA	p.A240A	BMP5_ENST00000446683.2_Silent_p.A240A	NM_021073.2	NP_066551.1	P22003	BMP5_HUMAN	bone morphogenetic protein 5	240					cartilage development (GO:0051216)|growth (GO:0040007)|male genitalia development (GO:0030539)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of steroid biosynthetic process (GO:0010894)|ossification (GO:0001503)|pattern specification process (GO:0007389)|positive regulation of dendrite development (GO:1900006)|positive regulation of DNA-dependent DNA replication (GO:2000105)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system development (GO:0001501)|type B pancreatic cell development (GO:0003323)	extracellular space (GO:0005615)|membrane-bounded vesicle (GO:0031988)	BMP receptor binding (GO:0070700)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	45	Lung NSC(77;0.0462)		LUSC - Lung squamous cell carcinoma(124;0.181)			CTAAAGCTTGGGCCTTTCTTG	0.383																																					p.A240A		Atlas-SNP	.											.	BMP5	94	.	0			c.C720A						PASS	.						100.0	101.0	101.0					6																	55659189		2203	4300	6503	SO:0001819	synonymous_variant	653	exon3			AGCTTGGGCCTTT		CCDS4958.1	6p12.1	2014-01-30			ENSG00000112175	ENSG00000112175		"""Bone morphogenetic proteins"", ""Endogenous ligands"""	1072	protein-coding gene	gene with protein product		112265				1427904, 11580864	Standard	NM_021073		Approved		uc003pcq.3	P22003	OTTHUMG00000014903	ENST00000370830.3:c.720C>A	6.37:g.55659189G>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	52	9	0.173077	NM_021073	B4E0Y4|Q9H547|Q9NTM5	Silent	SNP	ENST00000370830.3	37	CCDS4958.1																																																																																			.	.	none		0.383	BMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041000.1		
RIF1	55183	hgsc.bcm.edu	37	2	152300225	152300225	+	Splice_Site	SNP	T	T	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:152300225T>G	ENST00000243326.5	+	17	2469		c.e17+2		RIF1_ENST00000453091.2_Splice_Site|RIF1_ENST00000444746.2_Splice_Site|RIF1_ENST00000430328.2_Splice_Site|RIF1_ENST00000428287.2_Splice_Site			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1						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)		ATTAATCAGGTATGAAATAAA	0.313																																					.		Atlas-SNP	.											.	RIF1	244	.	0			c.1986+2T>G						PASS	.						63.0	67.0	65.0					2																	152300225		2202	4300	6502	SO:0001630	splice_region_variant	55183	exon18			ATCAGGTATGAAA	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.1986+2T>G	2.37:g.152300225T>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	74	28	0.378378	NM_018151	A0AVS0|Q9NS16	Splice_Site	SNP	ENST00000243326.5	37	CCDS2194.1	.	.	.	.	.	.	.	.	.	.	T	19.10	3.762703	0.69763	.	.	ENSG00000080345	ENST00000444746;ENST00000453091;ENST00000428287;ENST00000243326;ENST00000414861;ENST00000430328	.	.	.	5.34	5.34	0.76211	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.5395	0.61666	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	RIF1	152008471	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	6.811000	0.75221	2.027000	0.59764	0.377000	0.23210	.	.	.	none		0.313	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254836.3		Intron
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240549	39240549	+	Missense_Mutation	SNP	C	C	G	rs200397258	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr17:39240549C>G	ENST00000391417.4	+	1	91	c.91C>G	c.(91-93)Cag>Gag	p.Q31E		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	31	31 X 5 AA repeats of C-C-[GIKRQVHEML]- [SPTRV]-[STVQRCP].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				NS(1)|endometrium(3)|kidney(1)|lung(1)|prostate(2)|urinary_tract(1)	9						CAGCTGCTGTCAGACCACCTG	0.632													c|||	90	0.0179712	0.0416	0.013	5008	,	,		15484	0.0198		0.004	False		,,,				2504	0.002				p.Q31E		Atlas-SNP	.											KRTAP4-9_ENST00000377734,right_lower_lobe,carcinoma,0,2	KRTAP4-7	49	2	0			c.C91G						scavenged	.						16.0	23.0	21.0					17																	39240549		692	1591	2283	SO:0001583	missense	100132476	exon1			TGCTGTCAGACCA	AJ406939	CCDS45673.1	17q21.2	2013-06-25			ENSG00000240871	ENSG00000240871		"""Keratin associated proteins"""	18898	protein-coding gene	gene with protein product						11279113	Standard	NM_033061		Approved	KAP4.7	uc010wfn.2	Q9BYR0	OTTHUMG00000133582	ENST00000391417.4:c.91C>G	17.37:g.39240549C>G	ENSP00000375236:p.Gln31Glu	Somatic	88	4	0.0454545		WXS	Illumina HiSeq	Phase_I	98	13	0.132653	NM_033061	A0AVM6|A8MQ08|A8MTL4	Missense_Mutation	SNP	ENST00000391417.4	37	CCDS45673.1	.	.	.	.	.	.	.	.	.	.	.	1.541	-0.541861	0.04053	.	.	ENSG00000240871;ENSG00000212722	ENST00000391417;ENST00000377734	T	0.00597	6.31	3.51	-5.02	0.02982	.	0.616411	0.13532	U	0.380865	T	0.00384	0.0012	.	.	.	0.09310	N	1	B	0.25105	0.118	B	0.16289	0.015	T	0.39722	-0.9600	9	0.27785	T	0.31	.	7.7095	0.28669	0.3855:0.2289:0.3856:0.0	.	31	Q9BYR0	KRA47_HUMAN	E	31	ENSP00000375236:Q31E	ENSP00000375236:Q31E	Q	+	1	0	KRTAP4-9;KRTAP4-7	36494075	0.065000	0.20965	0.000000	0.03702	0.181000	0.23173	-0.407000	0.07178	-1.274000	0.02421	-0.505000	0.04504	CAG	.	.	weak		0.632	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1		
ZNF814	730051	hgsc.bcm.edu	37	19	58385714	58385714	+	Missense_Mutation	SNP	T	T	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:58385714T>G	ENST00000435989.2	-	3	1278	c.1044A>C	c.(1042-1044)gaA>gaC	p.E348D	ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000600634.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	348					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						AATGTTTTTTTTCAGTGTGAA	0.368																																					p.E348D		Atlas-SNP	.											ZNF814,NS,carcinoma,0,2	ZNF814	93	2	0			c.A1044C						scavenged	.						192.0	147.0	160.0					19																	58385714		692	1591	2283	SO:0001583	missense	730051	exon3			TTTTTTTTCAGTG		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"""Zinc fingers, C2H2-type"", ""-"""	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.1044A>C	19.37:g.58385714T>G	ENSP00000410545:p.Glu348Asp	Somatic	252	1	0.00396825		WXS	Illumina HiSeq	Phase_I	335	6	0.0179104	NM_001144989	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	37	CCDS46212.1	.	.	.	.	.	.	.	.	.	.	.	13.49	2.252737	0.39797	.	.	ENSG00000204514	ENST00000435989	T	0.18502	2.21	2.01	0.932	0.19466	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09468	0.0233	N	0.13371	0.34	0.19775	N	0.999954	B	0.15473	0.013	B	0.13407	0.009	T	0.30650	-0.9971	9	0.66056	D	0.02	.	5.8021	0.18420	0.0:0.152:0.0:0.848	.	348	B7Z6K7	ZN814_HUMAN	D	348	ENSP00000410545:E348D	ENSP00000410545:E348D	E	-	3	2	ZNF814	63077526	0.000000	0.05858	0.013000	0.15412	0.381000	0.30169	-0.928000	0.03980	0.089000	0.17243	0.113000	0.15668	GAA	.	.	none		0.368	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708	
ALDH3B2	222	hgsc.bcm.edu	37	11	67432799	67432799	+	Silent	SNP	G	G	A	rs80147122		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	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	275	2	0.00727273		WXS	Illumina HiSeq	Phase_I	273	8	0.029304	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	
KIAA1549	57670	hgsc.bcm.edu	37	7	138602479	138602479	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr7:138602479C>T	ENST00000422774.1	-	2	1941	c.1893G>A	c.(1891-1893)ccG>ccA	p.P631P	KIAA1549_ENST00000242365.4_Silent_p.P581P|KIAA1549_ENST00000440172.1_Silent_p.P631P			Q9HCM3	K1549_HUMAN	KIAA1549	631	Ser-rich.					integral component of membrane (GO:0016021)			KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						TGAGTTCCAGCGGGGGTGTTG	0.502			O	BRAF	pilocytic astrocytoma																																p.P631P	NSCLC(119;1534 1718 44213 46230 50068)	Atlas-SNP	.		Dom	yes		7	7q34	57670	KIAA1549		O	.	KIAA1549	314	.	0			c.G1893A						PASS	.						29.0	33.0	32.0					7																	138602479		1899	4122	6021	SO:0001819	synonymous_variant	57670	exon2			TTCCAGCGGGGGT		CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.1893G>A	7.37:g.138602479C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	71	11	0.15493	NM_020910	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Silent	SNP	ENST00000422774.1	37	CCDS56513.1																																																																																			.	.	none		0.502	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1		
UBE3B	89910	hgsc.bcm.edu	37	12	109940887	109940887	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:109940887G>A	ENST00000342494.3	+	14	1937	c.1342G>A	c.(1342-1344)Ggg>Agg	p.G448R	UBE3B_ENST00000280774.5_Missense_Mutation_p.G448R|UBE3B_ENST00000434735.2_Missense_Mutation_p.G448R|UBE3B_ENST00000535900.1_3'UTR	NM_130466.3	NP_569733.2	Q7Z3V4	UBE3B_HUMAN	ubiquitin protein ligase E3B	448					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.G448R(1)		NS(1)|breast(3)|endometrium(6)|kidney(4)|large_intestine(7)|lung(20)|ovary(2)|urinary_tract(2)	45						CAGGCCTGTCGGGGGTAAACG	0.522																																					p.G448R		Atlas-SNP	.											UBE3B,rectum,carcinoma,0,1	UBE3B	116	1	1	Substitution - Missense(1)	large_intestine(1)	c.G1342A						scavenged	.						121.0	115.0	117.0					12																	109940887		2203	4300	6503	SO:0001583	missense	89910	exon14			CCTGTCGGGGGTA	BC032301	CCDS9129.1, CCDS58277.1	12q24.12	2004-03-02			ENSG00000151148	ENSG00000151148			13478	protein-coding gene	gene with protein product		608047					Standard	NM_130466		Approved		uc001toq.4	Q7Z3V4	OTTHUMG00000169254	ENST00000342494.3:c.1342G>A	12.37:g.109940887G>A	ENSP00000340596:p.Gly448Arg	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	113	2	0.0176991	NM_130466	A5D8Z3|Q05BX9|Q659F7|Q7Z7Q1|Q9BXZ4	Missense_Mutation	SNP	ENST00000342494.3	37	CCDS9129.1	.	.	.	.	.	.	.	.	.	.	G	32	5.161550	0.94727	.	.	ENSG00000151148	ENST00000434735;ENST00000280774;ENST00000539599;ENST00000342494	T;T;T;T	0.45668	1.24;0.89;1.49;1.24	5.81	5.81	0.92471	.	0.044702	0.85682	N	0.000000	T	0.48370	0.1496	M	0.63428	1.95	0.80722	D	1	D	0.60575	0.988	P	0.44696	0.458	T	0.53358	-0.8450	10	0.66056	D	0.02	-7.5618	18.6619	0.91474	0.0:0.0:1.0:0.0	.	448	Q7Z3V4	UBE3B_HUMAN	R	448	ENSP00000391529:G448R;ENSP00000280774:G448R;ENSP00000443131:G448R;ENSP00000340596:G448R	ENSP00000280774:G448R	G	+	1	0	UBE3B	108425270	1.000000	0.71417	0.956000	0.39512	0.932000	0.56968	8.952000	0.93031	2.741000	0.93983	0.655000	0.94253	GGG	.	.	none		0.522	UBE3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403119.1	NM_183415	
SOCS1	8651	hgsc.bcm.edu	37	16	11348808	11348808	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr16:11348808C>T	ENST00000332029.2	-	2	678	c.528G>A	c.(526-528)gaG>gaA	p.E176E	RMI2_ENST00000572173.1_Intron	NM_003745.1	NP_003736.1	O15524	SOCS1_HUMAN	suppressor of cytokine signaling 1	176	Interaction with Elongin BC complex. {ECO:0000250}.|SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				cellular response to amino acid stimulus (GO:0071230)|cytokine-mediated signaling pathway (GO:0019221)|fat cell differentiation (GO:0045444)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of protein phosphorylation (GO:0001932)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)	insulin-like growth factor receptor binding (GO:0005159)|kinase inhibitor activity (GO:0019210)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)	p.E176fs*35(3)|p.0?(1)|p.Y64fs*1(1)|p.V171_R179del(1)|p.E176E(1)|p.R127_*212del(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(66)|lung(3)	71						GGCGGCACAGCTCCTGCAGCG	0.731			"""F, O"""		"""Hodgkin Lymphoma, PMBL"""																																p.E176E	Colon(177;456 3548 27231)	Atlas-SNP	.		Rec	yes		16	16p13.13	8651	suppressor of cytokine signaling 1		L	SOCS1,lymph_node,lymphoid_neoplasm,0,1	SOCS1	84	1	8	Deletion - Frameshift(4)|Deletion - In frame(2)|Whole gene deletion(1)|Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(8)	c.G528A						PASS	.						7.0	7.0	7.0					16																	11348808		2131	4193	6324	SO:0001819	synonymous_variant	8651	exon2			GCACAGCTCCTGC	U88326	CCDS10546.1	16p13.13	2013-02-14			ENSG00000185338	ENSG00000185338		"""Suppressors of cytokine signaling"", ""SH2 domain containing"""	19383	protein-coding gene	gene with protein product		603597				7796808, 9266833	Standard	NM_003745		Approved	SOCS-1, SSI-1, JAB, TIP3, Cish1	uc002dar.1	O15524	OTTHUMG00000129792	ENST00000332029.2:c.528G>A	16.37:g.11348808C>T		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	11	6	0.545455	NM_003745	O15097|Q9NSA7	Silent	SNP	ENST00000332029.2	37	CCDS10546.1																																																																																			.	.	none		0.731	SOCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252018.1		
POM121L12	285877	hgsc.bcm.edu	37	7	53103673	53103673	+	Silent	SNP	C	C	A	rs1184320	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr7:53103673C>A	ENST00000408890.4	+	1	325	c.309C>A	c.(307-309)ccC>ccA	p.P103P		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	103										endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						CTGCCCTTCCCGGGGAGACCG	0.726													C|||	2433	0.485823	0.4682	0.3444	5008	,	,		13024	0.5992		0.3688	False		,,,				2504	0.6135				p.P103P		Atlas-SNP	.											.	POM121L12	146	.	0			c.C309A						PASS	.	C		1694,2198		379,936,631	20.0	24.0	22.0		309	-1.2	0.0	7	dbSNP_87	22	2863,5365		484,1895,1735	no	coding-synonymous	POM121L12	NM_182595.3		863,2831,2366	AA,AC,CC		34.7958,43.5252,37.599		103/297	53103673	4557,7563	1946	4114	6060	SO:0001819	synonymous_variant	285877	exon1			CCTTCCCGGGGAG		CCDS43584.1	7p12.1	2012-03-13	2012-03-13		ENSG00000221900	ENSG00000221900			25369	protein-coding gene	gene with protein product			"""POM121 membrane glycoprotein-like 12"""				Standard	NM_182595		Approved	DKFZp564N2472	uc003tpz.3	Q8N7R1	OTTHUMG00000155995	ENST00000408890.4:c.309C>A	7.37:g.53103673C>A		Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	15	8	0.533333	NM_182595	Q8NDI9	Silent	SNP	ENST00000408890.4	37	CCDS43584.1																																																																																			C|0.563;A|0.437	0.437	strong		0.726	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595	
LCMT1	51451	hgsc.bcm.edu	37	16	25186263	25186263	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr16:25186263A>G	ENST00000399069.3	+	10	1045	c.890A>G	c.(889-891)gAa>gGa	p.E297G	LCMT1_ENST00000380966.4_Missense_Mutation_p.E242G|LCMT1_ENST00000572869.1_3'UTR	NM_016309.2	NP_057393.2	Q9UIC8	LCMT1_HUMAN	leucine carboxyl methyltransferase 1	297					C-terminal protein methylation (GO:0006481)|cellular protein modification process (GO:0006464)|negative regulation of protein complex assembly (GO:0031333)|protein methylation (GO:0006479)|regulation of apoptotic process (GO:0042981)|regulation of glucose metabolic process (GO:0010906)|regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090266)	cytosol (GO:0005829)	protein C-terminal carboxyl O-methyltransferase activity (GO:0003880)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)								GBM - Glioblastoma multiforme(48;0.0336)	L-Leucine(DB00149)	CACAGGATAGAATCACTTGAA	0.428																																					p.E297G	Colon(200;565 2072 24396 47922 50898)	Atlas-SNP	.											.	LCMT1	22	.	0			c.A890G						PASS	.						57.0	55.0	56.0					16																	25186263		1850	4091	5941	SO:0001583	missense	51451	exon10			GGATAGAATCACT	AF037601	CCDS45445.1, CCDS45446.1	16p12.1	2014-08-01			ENSG00000205629	ENSG00000205629			17557	protein-coding gene	gene with protein product	"""protein phosphatase methyltransferase 1"""	610286				10810093	Standard	XM_005255354		Approved	CGI-68, PPMT1	uc002dnx.1	Q9UIC8	OTTHUMG00000177182	ENST00000399069.3:c.890A>G	16.37:g.25186263A>G	ENSP00000382021:p.Glu297Gly	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	85	18	0.211765	NM_016309	A6NL89|A8K770|Q53FC5|Q96CI5|Q9H6I9|Q9NTG4|Q9Y378	Missense_Mutation	SNP	ENST00000399069.3	37	CCDS45445.1	.	.	.	.	.	.	.	.	.	.	A	16.74	3.207519	0.58343	.	.	ENSG00000205629	ENST00000399069;ENST00000380966;ENST00000380962	T;T	0.24350	1.86;1.86	5.15	4.04	0.47022	.	0.000000	0.85682	D	0.000000	T	0.50803	0.1637	M	0.84156	2.68	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.99	T	0.53337	-0.8453	10	0.87932	D	0	-25.0191	9.3407	0.38079	0.8194:0.1806:0.0:0.0	.	242;297	Q9UIC8-3;Q9UIC8	.;LCMT1_HUMAN	G	297;242;314	ENSP00000382021:E297G;ENSP00000370353:E242G	ENSP00000370349:E314G	E	+	2	0	LCMT1	25093764	1.000000	0.71417	0.875000	0.34327	0.525000	0.34531	7.428000	0.80296	0.900000	0.36469	0.533000	0.62120	GAA	.	.	none		0.428	LCMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435747.4	NM_016309	
TNFRSF8	943	hgsc.bcm.edu	37	1	12164562	12164562	+	Missense_Mutation	SNP	C	C	T	rs370304432		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:12164562C>T	ENST00000263932.2	+	4	617	c.395C>T	c.(394-396)cCg>cTg	p.P132L	TNFRSF8_ENST00000417814.2_Missense_Mutation_p.P21L	NM_001243.3|NM_001281430.1	NP_001234.2|NP_001268359.1	P28908	TNR8_HUMAN	tumor necrosis factor receptor superfamily, member 8	132					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)	p.P132L(1)		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)	TCTGTCTGTCCGGCAGGGATG	0.577																																					p.P132L		Atlas-SNP	.											TNFRSF8,bladder,carcinoma,0,2	TNFRSF8	70	2	1	Substitution - Missense(1)	urinary_tract(1)	c.C395T						scavenged	.	C	LEU/PRO	0,4406		0,0,2203	132.0	101.0	112.0		395	2.9	0.0	1		112	1,8599		0,1,4299	no	missense	TNFRSF8	NM_001243.3	98	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	132/596	12164562	1,13005	2203	4300	6503	SO:0001583	missense	943	exon4			TCTGTCCGGCAGG	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.395C>T	1.37:g.12164562C>T	ENSP00000263932:p.Pro132Leu	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	160	2	0.0125	NM_001243	B1AN79|B9EGD9|D3YTD8|Q6P4D9	Missense_Mutation	SNP	ENST00000263932.2	37	CCDS144.1	.	.	.	.	.	.	.	.	.	.	.	13.79	2.340993	0.41498	0.0	1.16E-4	ENSG00000120949	ENST00000263932;ENST00000417814	T;D	0.95001	3.35;-3.58	4.89	2.86	0.33363	TNFR/CD27/30/40/95 cysteine-rich region (2);	1.555060	0.03424	N	0.206769	D	0.91620	0.7352	L	0.58101	1.795	0.09310	N	1	B;B	0.30033	0.266;0.266	B;B	0.20577	0.03;0.03	T	0.79862	-0.1624	10	0.30078	T	0.28	-3.1656	5.4053	0.16318	0.1985:0.7003:0.0:0.1013	.	21;132	D3YTD8;P28908	.;TNR8_HUMAN	L	132;21	ENSP00000263932:P132L;ENSP00000390650:P21L	ENSP00000263932:P132L	P	+	2	0	TNFRSF8	12087149	0.001000	0.12720	0.025000	0.17156	0.064000	0.16182	1.202000	0.32271	1.397000	0.46682	0.650000	0.86243	CCG	.	.	none		0.577	TNFRSF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005130.1		
ADCY2	108	hgsc.bcm.edu	37	5	7766919	7766919	+	Splice_Site	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:7766919G>A	ENST00000338316.4	+	17	2303	c.2214G>A	c.(2212-2214)ccG>ccA	p.P738P	ADCY2_ENST00000537121.1_Splice_Site_p.P558P	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	738					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						TTTTCCTCCCGGTAAGAACAT	0.423																																					p.P738P		Atlas-SNP	.											ADCY2,right_upper_lobe,carcinoma,0,1	ADCY2	337	1	0			c.G2214A						scavenged	.						190.0	197.0	194.0					5																	7766919		2203	4300	6503	SO:0001630	splice_region_variant	108	exon17			CCTCCCGGTAAGA	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.2214+1G>A	5.37:g.7766919G>A		Somatic	166	1	0.0060241		WXS	Illumina HiSeq	Phase_I	199	5	0.0251256	NM_020546	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Silent	SNP	ENST00000338316.4	37	CCDS3872.2																																																																																			.	.	none		0.423	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546	Silent
SARM1	23098	hgsc.bcm.edu	37	17	26708753	26708753	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr17:26708753C>T	ENST00000457710.3	+	2	1371	c.900C>T	c.(898-900)ctC>ctT	p.L300L	SARM1_ENST00000379061.4_3'UTR|CTB-96E2.3_ENST00000591482.1_RNA	NM_015077.2	NP_055892.2	Q6SZW1	SARM1_HUMAN	sterile alpha and TIR motif containing 1	334					innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|regulation of apoptotic process (GO:0042981)|regulation of dendrite morphogenesis (GO:0048814)|regulation of neuron death (GO:1901214)|response to glucose (GO:0009749)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of mitochondrial outer membrane (GO:0031315)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|synapse (GO:0045202)				cervix(1)|endometrium(1)|large_intestine(3)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	12	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.154)		TGCCGTTGCTCGACTCTAACC	0.677																																					p.L333L		Atlas-SNP	.											.	SARM1	40	.	0			c.C999T						PASS	.						11.0	13.0	12.0					17																	26708753		2134	4199	6333	SO:0001819	synonymous_variant	23098	exon3			GTTGCTCGACTCT	AB011096		17q11	2013-01-10			ENSG00000004139	ENSG00000004139		"""Sterile alpha motif (SAM) domain containing"""	17074	protein-coding gene	gene with protein product		607732				9628581	Standard	NM_015077		Approved	SARM, SAMD2, KIAA0524	uc010crl.1	Q6SZW1	OTTHUMG00000132499	ENST00000457710.3:c.900C>T	17.37:g.26708753C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	38	4	0.105263	NM_015077	O60277|Q7LGG3|Q9NXY5	Silent	SNP	ENST00000457710.3	37																																																																																				.	.	none		0.677	SARM1-001	NOVEL	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000255679.3	NM_015077	
GABRQ	55879	hgsc.bcm.edu	37	X	151820129	151820129	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:151820129T>C	ENST00000370306.2	+	8	1062	c.1042T>C	c.(1042-1044)Tac>Cac	p.Y348H		NM_018558.2	NP_061028.3	Q9UN88	GBRT_HUMAN	gamma-aminobutyric acid (GABA) A receptor, theta	348					neurotransmitter transport (GO:0006836)|signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|neurotransmitter transporter activity (GO:0005326)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(9)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	52	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|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)	GGAGTATGTCTACATCAACTA	0.512																																					p.Y348H		Atlas-SNP	.											.	GABRQ	131	.	0			c.T1042C						PASS	.						320.0	251.0	274.0					X																	151820129		2203	4300	6503	SO:0001583	missense	55879	exon8			TATGTCTACATCA	U47334	CCDS14707.1	Xq28	2012-06-22	2012-02-03		ENSG00000147402	ENSG00000268089		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	14454	protein-coding gene	gene with protein product	"""GABA(A) receptor, theta"""	300349	"""gamma-aminobutyric acid (GABA) receptor, theta"""			10804200, 10449790	Standard	NM_018558		Approved	THETA	uc004ffp.1	Q9UN88	OTTHUMG00000022649	ENST00000370306.2:c.1042T>C	X.37:g.151820129T>C	ENSP00000359329:p.Tyr348His	Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	305	47	0.154098	NM_018558	A6NFN1|Q32MB4|Q9NZK8	Missense_Mutation	SNP	ENST00000370306.2	37	CCDS14707.1	.	.	.	.	.	.	.	.	.	.	T	15.54	2.862737	0.51482	.	.	ENSG00000147402	ENST00000370306	D	0.85411	-1.98	5.88	4.72	0.59763	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.153676	0.30969	N	0.008512	T	0.78685	0.4322	L	0.45137	1.4	0.36846	D	0.887645	B	0.28208	0.203	B	0.32583	0.148	T	0.72174	-0.4370	10	0.16420	T	0.52	.	9.1238	0.36803	0.0:0.0866:0.0:0.9133	.	348	Q9UN88	GBRT_HUMAN	H	348	ENSP00000359329:Y348H	ENSP00000359329:Y348H	Y	+	1	0	GABRQ	151570785	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.032000	0.64140	0.837000	0.34925	0.486000	0.48141	TAC	.	.	none		0.512	GABRQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058763.2	NM_018558	
CARD11	84433	hgsc.bcm.edu	37	7	2976756	2976756	+	Missense_Mutation	SNP	A	A	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr7:2976756A>C	ENST00000396946.4	-	9	1659	c.1256T>G	c.(1255-1257)aTc>aGc	p.I419S		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	419					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)		CACCATCTCGATCCTCATCTC	0.592			Mis		DLBCL																																p.I419S		Atlas-SNP	.		Dom	yes		7	7p22	84433	"""caspase recruitment domain family, member 11"""		L	.	CARD11	339	.	0			c.T1256G						PASS	.						165.0	133.0	144.0					7																	2976756		2203	4300	6503	SO:0001583	missense	84433	exon9			ATCTCGATCCTCA	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.1256T>G	7.37:g.2976756A>C	ENSP00000380150:p.Ile419Ser	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	148	63	0.425676	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	37	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	A	9.722	1.159872	0.21454	.	.	ENSG00000198286	ENST00000396946	T	0.31510	1.49	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.22244	0.0536	N	0.19112	0.55	0.80722	D	1	B	0.19331	0.035	B	0.20384	0.029	T	0.03608	-1.1020	10	0.38643	T	0.18	-22.9658	14.2746	0.66173	1.0:0.0:0.0:0.0	.	419	Q9BXL7	CAR11_HUMAN	S	419	ENSP00000380150:I419S	ENSP00000380150:I419S	I	-	2	0	CARD11	2943282	1.000000	0.71417	0.252000	0.24328	0.976000	0.68499	7.318000	0.79029	1.981000	0.57761	0.459000	0.35465	ATC	.	.	none		0.592	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415	
CAMKV	79012	hgsc.bcm.edu	37	3	49897116	49897116	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:49897116G>A	ENST00000477224.1	-	11	1619	c.1141C>T	c.(1141-1143)Ccc>Tcc	p.P381S	CAMKV_ENST00000466940.1_Intron|CAMKV_ENST00000498324.1_5'Flank|CAMKV_ENST00000296471.7_Missense_Mutation_p.P353S|CAMKV_ENST00000488336.1_Intron|CAMKV_ENST00000463537.1_Intron|CAMKV_ENST00000467248.1_Missense_Mutation_p.P306S			Q8NCB2	CAMKV_HUMAN	CaM kinase-like vesicle-associated	381	Ala-rich.					cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			central_nervous_system(1)|large_intestine(2)|lung(2)|ovary(2)	7				BRCA - Breast invasive adenocarcinoma(193;4.62e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		CGGTCTGCGGGGGCCACATTA	0.647																																					p.P381S		Atlas-SNP	.											CAMKV_ENST00000477224,colon,carcinoma,+2,1	CAMKV	84	1	0			c.C1141T						scavenged	.						75.0	76.0	76.0					3																	49897116		2203	4300	6503	SO:0001583	missense	79012	exon11			CTGCGGGGGCCAC	BC017363	CCDS33762.1	3p21.31	2005-03-04			ENSG00000164076	ENSG00000164076			28788	protein-coding gene	gene with protein product		614993				12477932	Standard	XM_005265478		Approved	MGC8407, VACAMKL	uc003cxt.1	Q8NCB2	OTTHUMG00000158288	ENST00000477224.1:c.1141C>T	3.37:g.49897116G>A	ENSP00000419195:p.Pro381Ser	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	126	2	0.015873	NM_024046	A6NFD4|Q6FIB8|Q8NBS8|Q8NC85|Q8NDU4|Q8WTT8|Q9BQC9|Q9H0Q5	Missense_Mutation	SNP	ENST00000477224.1	37	CCDS33762.1	.	.	.	.	.	.	.	.	.	.	G	5.582	0.292246	0.10567	.	.	ENSG00000164076	ENST00000296471;ENST00000477224;ENST00000467248	T;T;T	0.69685	0.58;-0.22;-0.42	5.64	-0.471	0.12119	.	0.597721	0.13999	N	0.348290	T	0.42040	0.1185	N	0.14661	0.345	0.09310	N	0.999994	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	0.19549	-1.0302	10	0.31617	T	0.26	.	5.7413	0.18096	0.2866:0.2905:0.4228:0.0	.	381;306;353;381	B2RDF9;B4DM24;Q8NCB2-2;Q8NCB2	.;.;.;CAMKV_HUMAN	S	353;381;306	ENSP00000296471:P353S;ENSP00000419195:P381S;ENSP00000420053:P306S	ENSP00000296471:P353S	P	-	1	0	CAMKV	49872120	0.010000	0.17322	0.120000	0.21714	0.916000	0.54674	0.046000	0.14035	0.233000	0.21120	-0.302000	0.09304	CCC	.	.	none		0.647	CAMKV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350584.4	NM_024046	
GPR133	283383	hgsc.bcm.edu	37	12	131439191	131439191	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:131439191C>T	ENST00000261654.5	+	2	648	c.89C>T	c.(88-90)tCg>tTg	p.S30L	GPR133_ENST00000535015.1_Missense_Mutation_p.S30L	NM_198827.3	NP_942122.2	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133	30					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.S30*(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)		TACTCCAGATCGCAGGACCAT	0.567																																					p.S30L		Atlas-SNP	.											GPR133,colon,carcinoma,0,2	GPR133	136	2	1	Substitution - Nonsense(1)	large_intestine(1)	c.C89T						scavenged	.						114.0	97.0	103.0					12																	131439191		2203	4300	6503	SO:0001583	missense	283383	exon2			CCAGATCGCAGGA	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.89C>T	12.37:g.131439191C>T	ENSP00000261654:p.Ser30Leu	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	275	3	0.0109091	NM_198827	B2CKK9|B7ZLF7|Q2M1L3|Q6ZMQ1|Q7Z7M2|Q86SM4	Missense_Mutation	SNP	ENST00000261654.5	37	CCDS9272.1	.	.	.	.	.	.	.	.	.	.	C	9.475	1.096582	0.20552	.	.	ENSG00000111452	ENST00000261654;ENST00000543826;ENST00000542091;ENST00000535015	T;T	0.40476	1.03;1.03	4.42	1.41	0.22369	.	2.349640	0.01850	N	0.035877	T	0.35828	0.0945	L	0.46157	1.445	0.09310	N	1	B;B	0.10296	0.003;0.003	B;B	0.04013	0.001;0.001	T	0.09250	-1.0683	10	0.17832	T	0.49	.	5.7384	0.18079	0.0:0.521:0.0:0.479	.	30;30	B7ZLF7;Q6QNK2	.;GP133_HUMAN	L	30	ENSP00000261654:S30L;ENSP00000444425:S30L	ENSP00000261654:S30L	S	+	2	0	GPR133	130005144	0.000000	0.05858	0.000000	0.03702	0.076000	0.17211	0.366000	0.20365	0.276000	0.22118	-0.258000	0.10820	TCG	.	.	none		0.567	GPR133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399356.1	NM_198827	
TTN	7273	hgsc.bcm.edu	37	2	179438134	179438134	+	Missense_Mutation	SNP	C	C	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:179438134C>A	ENST00000591111.1	-	276	68026	c.67802G>T	c.(67801-67803)tGc>tTc	p.C22601F	TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.C15177F|TTN_ENST00000589042.1_Missense_Mutation_p.C24242F|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.C15302F|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.C21674F|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.C15369F			Q8WZ42	TITIN_HUMAN	titin	22601	Fibronectin type-III 64. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.C15177F(1)|p.C21672F(1)|p.C15369F(1)|p.C15302F(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATGTCCCCAGCAGACAACCAT	0.448																																					p.C24242F		Atlas-SNP	.											TTN_ENST00000359218,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,4	TTN	18412	4	4	Substitution - Missense(4)	central_nervous_system(4)	c.G72725T						scavenged	.						77.0	76.0	76.0					2																	179438134		1922	4126	6048	SO:0001583	missense	7273	exon326			CCCCAGCAGACAA	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.67802G>T	2.37:g.179438134C>A	ENSP00000465570:p.Cys22601Phe	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	187	2	0.0106952	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	11.79	1.744868	0.30865	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.56776	0.44;0.44;0.44;0.44	6.08	5.2	0.72013	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.71459	0.3342	M	0.73962	2.25	0.80722	D	1	D;D;D;D	0.58970	0.984;0.984;0.984;0.97	P;P;P;P	0.62184	0.899;0.899;0.899;0.857	T	0.76228	-0.3036	9	0.87932	D	0	.	17.6637	0.88198	0.0:0.8773:0.1227:0.0	.	15177;15302;15369;22601	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	F	21674;15177;15369;15302;15175	ENSP00000343764:C21674F;ENSP00000434586:C15177F;ENSP00000340554:C15369F;ENSP00000352154:C15302F	ENSP00000340554:C15369F	C	-	2	0	TTN	179146380	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.942000	0.56614	1.561000	0.49584	0.655000	0.94253	TGC	.	.	none		0.448	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
DEPDC1B	55789	hgsc.bcm.edu	37	5	59941337	59941337	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:59941337T>C	ENST00000265036.5	-	4	627	c.560A>G	c.(559-561)aAg>aGg	p.K187R	DEPDC1B_ENST00000545085.1_Missense_Mutation_p.K160R|DEPDC1B_ENST00000453022.2_Missense_Mutation_p.K187R	NM_018369.2	NP_060839.2	Q8WUY9	DEP1B_HUMAN	DEP domain containing 1B	187					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(2)|skin(2)	17		Lung NSC(810;0.000214)|Prostate(74;0.0147)|Breast(144;0.0991)|Ovarian(174;0.17)				TGTCATAGACTTCCATATCTC	0.383																																					p.K187R		Atlas-SNP	.											DEPDC1B,NS,carcinoma,-1,1	DEPDC1B	56	1	0			c.A560G						scavenged	.						69.0	70.0	70.0					5																	59941337		2203	4300	6503	SO:0001583	missense	55789	exon4			ATAGACTTCCATA	AF303178	CCDS3977.1, CCDS47214.1	5q12	2008-02-05			ENSG00000035499	ENSG00000035499			24902	protein-coding gene	gene with protein product	"""breast cancer cell 3"""					12477932	Standard	NM_001145208		Approved	XTP1, BRCC3	uc003jsh.3	Q8WUY9	OTTHUMG00000097083	ENST00000265036.5:c.560A>G	5.37:g.59941337T>C	ENSP00000265036:p.Lys187Arg	Somatic	200	1	0.005		WXS	Illumina HiSeq	Phase_I	297	3	0.010101	NM_001145208	A8K3R9|B4DUT4|Q86WJ3|Q8IZY6|Q9NUN3|Q9NW57	Missense_Mutation	SNP	ENST00000265036.5	37	CCDS3977.1	.	.	.	.	.	.	.	.	.	.	T	13.90	2.373660	0.42105	.	.	ENSG00000035499	ENST00000265036;ENST00000453022;ENST00000545085	T;T;T	0.31769	2.16;1.87;1.48	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	T	0.25606	0.0623	L	0.33137	0.985	0.49299	D	0.999773	B;P	0.39391	0.209;0.671	B;B	0.36464	0.162;0.225	T	0.02491	-1.1151	9	.	.	.	-27.8066	16.5602	0.84551	0.0:0.0:0.0:1.0	.	187;187	B4DUT4;Q8WUY9	.;DEP1B_HUMAN	R	187;187;160	ENSP00000265036:K187R;ENSP00000389101:K187R;ENSP00000438320:K160R	.	K	-	2	0	DEPDC1B	59977094	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.124000	0.57924	2.367000	0.80283	0.528000	0.53228	AAG	.	.	none		0.383	DEPDC1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214207.1	NM_018369	
C3	718	hgsc.bcm.edu	37	19	6694547	6694547	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:6694547C>T	ENST00000245907.6	-	24	3141	c.3049G>A	c.(3049-3051)Ggc>Agc	p.G1017S		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	1017					complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|fatty acid metabolic process (GO:0006631)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of activation of membrane attack complex (GO:0001970)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of glucose transport (GO:0010828)|positive regulation of lipid storage (GO:0010884)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|regulation of immune response (GO:0050776)|regulation of triglyceride biosynthetic process (GO:0010866)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	C5L2 anaphylatoxin chemotactic receptor binding (GO:0031715)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(5)|endometrium(7)|kidney(6)|large_intestine(18)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)	72				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Intravenous Immunoglobulin(DB00028)	GGCGTCATGCCGATCATGTTC	0.612																																					p.G1017S		Atlas-SNP	.											C3,NS,carcinoma,+1,1	C3	192	1	0			c.G3049A						scavenged	.						121.0	94.0	103.0					19																	6694547		2203	4300	6503	SO:0001583	missense	718	exon24			TCATGCCGATCAT	J04763	CCDS32883.1	19p13.3-p13.2	2014-09-17			ENSG00000125730	ENSG00000125730	3.4.21.43	"""Complement system"", ""Endogenous ligands"""	1318	protein-coding gene	gene with protein product	"""C3a anaphylatoxin"", ""complement component C3a"", ""complement component C3b"", ""prepro-C3"""	120700					Standard	NM_000064		Approved	CPAMD1, ARMD9, C3a, C3b	uc002mfm.3	P01024	OTTHUMG00000150335	ENST00000245907.6:c.3049G>A	19.37:g.6694547C>T	ENSP00000245907:p.Gly1017Ser	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	167	3	0.0179641	NM_000064	A7E236	Missense_Mutation	SNP	ENST00000245907.6	37	CCDS32883.1	.	.	.	.	.	.	.	.	.	.	c	3.443	-0.113656	0.06881	.	.	ENSG00000125730	ENST00000245907	T	0.37752	1.18	5.76	-7.64	0.01286	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);Alpha-2-macroglobulin, thiol-ester bond-forming (1);	1.059860	0.07133	N	0.845901	T	0.11537	0.0281	N	0.04355	-0.22	0.09310	N	1	P	0.38551	0.636	B	0.32677	0.15	T	0.23476	-1.0187	10	0.21540	T	0.41	.	6.9634	0.24610	0.1843:0.3314:0.0:0.4843	.	1017	P01024	CO3_HUMAN	S	1017	ENSP00000245907:G1017S	ENSP00000245907:G1017S	G	-	1	0	C3	6645547	0.000000	0.05858	0.000000	0.03702	0.088000	0.18126	-4.085000	0.00298	-1.580000	0.01644	-2.299000	0.00261	GGC	.	.	none		0.612	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064	
CR1	1378	hgsc.bcm.edu	37	1	207787831	207787831	+	Nonsense_Mutation	SNP	G	G	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:207787831G>T	ENST00000367049.4	+	40	6658	c.6658G>T	c.(6658-6660)Gaa>Taa	p.E2220*	CR1_ENST00000367053.1_Nonsense_Mutation_p.E1770*|CR1_ENST00000367052.1_Nonsense_Mutation_p.E1770*|CR1_ENST00000367051.1_Nonsense_Mutation_p.E1770*|CR1_ENST00000400960.2_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	282	0	0		WXS	Illumina HiSeq	Phase_I	237	3	0.0126582	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	
STAT6	6778	hgsc.bcm.edu	37	12	57493818	57493818	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:57493818T>C	ENST00000300134.3	-	14	1893	c.1568A>G	c.(1567-1569)gAc>gGc	p.D523G	STAT6_ENST00000454075.3_Missense_Mutation_p.D523G|STAT6_ENST00000543873.2_Missense_Mutation_p.D523G|STAT6_ENST00000556155.1_Missense_Mutation_p.D523G|STAT6_ENST00000538913.2_Missense_Mutation_p.D413G|STAT6_ENST00000537215.2_Missense_Mutation_p.D413G	NM_001178078.1|NM_003153.4	NP_001171549.1|NP_003144.3	P42226	STAT6_HUMAN	signal transducer and activator of transcription 6, interleukin-4 induced	523	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cellular response to hydrogen peroxide (GO:0070301)|cellular response to reactive nitrogen species (GO:1902170)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|mammary gland epithelial cell proliferation (GO:0033598)|mammary gland morphogenesis (GO:0060443)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of isotype switching to IgE isotypes (GO:0048295)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|T-helper 1 cell lineage commitment (GO:0002296)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane raft (GO:0045121)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein phosphatase binding (GO:0019903)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(2)|lung(8)|ovary(4)|skin(1)	28						TTTGGTGAGGTCCAGGACACC	0.612																																					p.D523G		Atlas-SNP	.											.	STAT6	69	.	0			c.A1568G						PASS	.						93.0	73.0	80.0					12																	57493818		2203	4300	6503	SO:0001583	missense	6778	exon14			GTGAGGTCCAGGA	BC005823, BQ028928	CCDS8931.1, CCDS53804.1	12q13	2013-02-14				ENSG00000166888		"""SH2 domain containing"""	11368	protein-coding gene	gene with protein product		601512				9605853, 8085155	Standard	NM_003153		Approved	D12S1644, IL-4-STAT	uc001sna.3	P42226		ENST00000300134.3:c.1568A>G	12.37:g.57493818T>C	ENSP00000300134:p.Asp523Gly	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	152	56	0.368421	NM_001178079	A8K316|B7ZA27|F5GXI9|Q5FBW5|Q71UP4	Missense_Mutation	SNP	ENST00000300134.3	37	CCDS8931.1	.	.	.	.	.	.	.	.	.	.	T	24.4	4.527568	0.85706	.	.	ENSG00000166888	ENST00000300134;ENST00000535201;ENST00000538913;ENST00000543873;ENST00000556155;ENST00000537215;ENST00000454075;ENST00000542721;ENST00000542516;ENST00000555375	D;D;D;D;D;D;D	0.89875	-2.58;-2.58;-2.58;-2.58;-2.58;-2.58;-2.58	4.92	4.92	0.64577	STAT transcription factor, DNA-binding (1);p53-like transcription factor, DNA-binding (1);SH2 motif (1);EF-hand-like domain (1);	0.055888	0.64402	D	0.000001	D	0.92766	0.7700	M	0.64997	1.995	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.79784	0.984;0.993	D	0.93346	0.6714	10	0.87932	D	0	-25.2637	12.5465	0.56203	0.0:0.0:0.0:1.0	.	523;523	A8K4S9;P42226	.;STAT6_HUMAN	G	523;413;413;523;523;413;523;413;523;89	ENSP00000300134:D523G;ENSP00000445409:D413G;ENSP00000438451:D523G;ENSP00000451742:D523G;ENSP00000444530:D413G;ENSP00000401486:D523G;ENSP00000450921:D89G	ENSP00000300134:D523G	D	-	2	0	STAT6	55780085	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.810000	0.86072	2.062000	0.61559	0.533000	0.62120	GAC	.	.	none		0.612	STAT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412248.3	NM_003153	
SCRN1	9805	hgsc.bcm.edu	37	7	30008595	30008595	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr7:30008595C>T	ENST00000426154.1	-	2	265	c.89G>A	c.(88-90)cGg>cAg	p.R30Q	SCRN1_ENST00000425819.2_Intron|SCRN1_ENST00000409570.1_Missense_Mutation_p.R30Q|SCRN1_ENST00000409497.1_Missense_Mutation_p.R30Q|SCRN1_ENST00000242059.5_Missense_Mutation_p.R30Q|SCRN1_ENST00000434476.2_Missense_Mutation_p.R50Q|SCRN1_ENST00000494620.1_5'UTR	NM_001145513.1	NP_001138985.1	Q12765	SCRN1_HUMAN	secernin 1	30					exocytosis (GO:0006887)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	dipeptidase activity (GO:0016805)			breast(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(12)|ovary(2)|prostate(2)|skin(2)	25						ATCTCTGGGCCGGGCTGAATT	0.517																																					p.R50Q		Atlas-SNP	.											SCRN1,colon,carcinoma,+1,1	SCRN1	85	1	0			c.G149A						scavenged	.						122.0	99.0	107.0					7																	30008595		2203	4300	6503	SO:0001583	missense	9805	exon2			CTGGGCCGGGCTG	D83777	CCDS5422.1, CCDS47567.1, CCDS47568.1	7p14.3-p14.1	2006-09-06			ENSG00000136193	ENSG00000136193			22192	protein-coding gene	gene with protein product		614965				12221138	Standard	NM_014766		Approved	KIAA0193	uc011kaa.2	Q12765	OTTHUMG00000097093	ENST00000426154.1:c.89G>A	7.37:g.30008595C>T	ENSP00000409068:p.Arg30Gln	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	142	5	0.0352113	NM_001145514	A8K0E9|B4DHM0|B4DIP5|C9JPG0|Q25QX7|Q8IWD1	Missense_Mutation	SNP	ENST00000426154.1	37	CCDS5422.1	.	.	.	.	.	.	.	.	.	.	C	35	5.527702	0.96446	.	.	ENSG00000136193	ENST00000242059;ENST00000426154;ENST00000409497;ENST00000434476;ENST00000421434;ENST00000438497;ENST00000409570	T;T;T;T;T;T;T	0.38560	2.77;2.77;2.77;2.86;1.95;1.19;1.13	5.63	5.63	0.86233	.	0.000000	0.64402	D	0.000003	T	0.76104	0.3941	H	0.95504	3.68	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.83439	0.0042	9	.	.	.	-16.8326	18.2365	0.89951	0.0:1.0:0.0:0.0	.	50;30	C9JPG0;Q12765	.;SCRN1_HUMAN	Q	30;30;30;50;30;30;30	ENSP00000242059:R30Q;ENSP00000409068:R30Q;ENSP00000386872:R30Q;ENSP00000388942:R50Q;ENSP00000413184:R30Q;ENSP00000406289:R30Q;ENSP00000387052:R30Q	.	R	-	2	0	SCRN1	29975120	1.000000	0.71417	0.987000	0.45799	0.985000	0.73830	7.056000	0.76662	2.647000	0.89833	0.555000	0.69702	CGG	.	.	none		0.517	SCRN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214231.2	NM_014766	
MUC6	4588	hgsc.bcm.edu	37	11	1017974	1017974	+	Missense_Mutation	SNP	C	C	G	rs200353019		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	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	537	11	0.0204842		WXS	Illumina HiSeq	Phase_I	545	17	0.0311927	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	
ITPKB	3707	hgsc.bcm.edu	37	1	226925148	226925148	+	Silent	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:226925148G>A	ENST00000272117.3	-	1	11	c.12C>T	c.(10-12)taC>taT	p.Y4Y	ITPKB_ENST00000366784.1_Silent_p.Y4Y|ITPKB_ENST00000429204.1_Silent_p.Y4Y			P27987	IP3KB_HUMAN	inositol-trisphosphate 3-kinase B	4					cell surface receptor signaling pathway (GO:0007166)|inositol phosphate metabolic process (GO:0043647)|MAPK cascade (GO:0000165)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of Ras protein signal transduction (GO:0046579)|positive thymic T cell selection (GO:0045059)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(1)	30		Prostate(94;0.0773)				GCGCATAGCAGTACACAGCCA	0.726																																					p.Y4Y	Colon(84;110 1851 5306 33547)	Atlas-SNP	.											.	ITPKB	158	.	0			c.C12T						PASS	.						17.0	20.0	19.0					1																	226925148		2139	4199	6338	SO:0001819	synonymous_variant	3707	exon2			ATAGCAGTACACA	AJ242780	CCDS1555.1	1q42.12	2011-04-28	2011-04-28		ENSG00000143772	ENSG00000143772	2.7.1.127		6179	protein-coding gene	gene with protein product		147522	"""inositol 1,4,5-trisphosphate 3-kinase B"""			1654894, 1330886	Standard	NM_002221		Approved	IP3KB, IP3-3KB	uc010pvo.2	P27987	OTTHUMG00000037582	ENST00000272117.3:c.12C>T	1.37:g.226925148G>A		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	33	7	0.212121	NM_002221	Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47	Silent	SNP	ENST00000272117.3	37	CCDS1555.1																																																																																			.	.	none		0.726	ITPKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091632.1	NM_002221	
KRTAP4-9	100132386	hgsc.bcm.edu	37	17	39262103	39262103	+	Missense_Mutation	SNP	A	A	T	rs374629799	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr17:39262103A>T	ENST00000391415.1	+	1	520	c.463A>T	c.(463-465)Agc>Tgc	p.S155C		NM_001146041.1	NP_001139513.1	Q9BYQ8	KRA49_HUMAN	keratin associated protein 4-9	155	29 X 5 AA repeats of C-C-[RQVHIEK]- [SPTR]-[VSTQCRNP].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|urinary_tract(3)	14						ccccagctgcagcatctccag	0.672													a|||	152	0.0303514	0.0893	0.0216	5008	,	,		18051	0.001		0.0139	False		,,,				2504	0.0041				p.S155C		Atlas-SNP	.											KRTAP4-9_ENST00000377734,NS,carcinoma,0,2	KRTAP4-9	110	2	0			c.A463T						scavenged	.						6.0	9.0	8.0					17																	39262103		679	1572	2251	SO:0001583	missense	100132386	exon1			AGCTGCAGCATCT	AJ406941	CCDS54124.1	17q21.2	2013-06-25			ENSG00000212722	ENSG00000212722		"""Keratin associated proteins"""	18910	protein-coding gene	gene with protein product							Standard	NM_001146041		Approved	KAP4.9	uc010wfp.2	Q9BYQ8	OTTHUMG00000133584	ENST00000391415.1:c.463A>T	17.37:g.39262103A>T	ENSP00000375234:p.Ser155Cys	Somatic	90	1	0.0111111		WXS	Illumina HiSeq	Phase_I	80	2	0.025	NM_001146041		Missense_Mutation	SNP	ENST00000391415.1	37	CCDS54124.1	.	.	.	.	.	.	.	.	.	.	.	0.091	-1.167638	0.01660	.	.	ENSG00000212722	ENST00000377734;ENST00000391415;ENST00000333994	T	0.00584	6.4	3.1	-1.38	0.09027	.	.	.	.	.	T	0.00109	0.0003	N	0.00041	-2.485	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48186	-0.9057	9	0.02654	T	1	.	0.2915	0.00259	0.1968:0.2502:0.1975:0.3554	.	155	Q9BYQ8	KRA49_HUMAN	C	143;155;146	ENSP00000375234:S155C	ENSP00000334461:S146C	S	+	1	0	KRTAP4-9	36515629	0.946000	0.32159	0.002000	0.10522	0.205000	0.24178	1.056000	0.30480	-0.110000	0.12022	-1.044000	0.02363	AGC	.	.	weak		0.672	KRTAP4-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257688.1	NM_001146041	
GPATCH3	63906	hgsc.bcm.edu	37	1	27219894	27219894	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:27219894A>G	ENST00000361720.5	-	4	1120	c.1097T>C	c.(1096-1098)gTg>gCg	p.V366A		NM_022078.2	NP_071361.2	Q96I76	GPTC3_HUMAN	G patch domain containing 3	366							nucleic acid binding (GO:0003676)			endometrium(2)|large_intestine(1)|lung(11)|skin(1)	15		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;3.97e-51)|OV - Ovarian serous cystadenocarcinoma(117;9.55e-30)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000513)|STAD - Stomach adenocarcinoma(196;0.000595)|KIRC - Kidney renal clear cell carcinoma(1967;0.00072)|READ - Rectum adenocarcinoma(331;0.0419)		GTCATAGTACACACTCATGTC	0.478																																					p.V366A		Atlas-SNP	.											GPATCH3,NS,carcinoma,-1,1	GPATCH3	30	1	0			c.T1097C						scavenged	.						405.0	383.0	391.0					1																	27219894		2203	4300	6503	SO:0001583	missense	63906	exon4			TAGTACACACTCA	BC007767	CCDS290.1	1p35.3-p35.1	2013-01-28		2006-12-13	ENSG00000198746	ENSG00000198746		"""G patch domain containing"""	25720	protein-coding gene	gene with protein product				GPATC3			Standard	NM_022078		Approved	FLJ12455	uc001bne.3	Q96I76	OTTHUMG00000004229	ENST00000361720.5:c.1097T>C	1.37:g.27219894A>G	ENSP00000354645:p.Val366Ala	Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	216	3	0.0138889	NM_022078	Q5JYH2|Q8NDJ2|Q9H9Z3	Missense_Mutation	SNP	ENST00000361720.5	37	CCDS290.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.53|14.53	2.563590|2.563590	0.45694|0.45694	.|.	.|.	ENSG00000198746|ENSG00000198746	ENST00000445019|ENST00000361720;ENST00000536641;ENST00000374122	.|T	.|0.42900	.|0.96	5.27|5.27	5.27|5.27	0.74061|0.74061	.|.	.|0.284832	.|0.34156	.|N	.|0.004205	T|T	0.30008|0.30008	0.0751|0.0751	L|L	0.27053|0.27053	0.805|0.805	0.41124|0.41124	D|D	0.985837|0.985837	.|B	.|0.22080	.|0.064	.|B	.|0.22753	.|0.041	T|T	0.09907|0.09907	-1.0653|-1.0653	5|10	.|0.30078	.|T	.|0.28	-11.5986|-11.5986	11.3831|11.3831	0.49770|0.49770	0.8488:0.1512:0.0:0.0|0.8488:0.1512:0.0:0.0	.|.	.|366	.|Q96I76	.|GPTC3_HUMAN	R|A	16|366;348;177	.|ENSP00000354645:V366A	.|ENSP00000354645:V366A	C|V	-|-	1|2	0|0	GPATCH3|GPATCH3	27092481|27092481	1.000000|1.000000	0.71417|0.71417	0.927000|0.927000	0.36925|0.36925	0.973000|0.973000	0.67179|0.67179	6.598000|6.598000	0.74122|0.74122	2.209000|2.209000	0.71365|0.71365	0.533000|0.533000	0.62120|0.62120	TGT|GTG	.	.	none		0.478	GPATCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012181.1	NM_022078	
LPPR4	9890	hgsc.bcm.edu	37	1	99771406	99771406	+	Nonsense_Mutation	SNP	C	C	T	rs567805874		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:99771406C>T	ENST00000370185.3	+	7	1629	c.1132C>T	c.(1132-1134)Cga>Tga	p.R378*	LPPR4_ENST00000457765.1_Nonsense_Mutation_p.R320*|LPPR4_ENST00000370184.1_Nonsense_Mutation_p.R220*	NM_014839.4	NP_055654.2	Q7Z2D5	LPPR4_HUMAN		378					axonogenesis (GO:0007409)|inner ear development (GO:0048839)|phospholipid dephosphorylation (GO:0046839)	integral component of plasma membrane (GO:0005887)	lipid phosphatase activity (GO:0042577)|phosphatidate phosphatase activity (GO:0008195)	p.R378G(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(39)|ovary(3)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	72		all_epithelial(167;3.54e-06)|all_lung(203;0.00139)|Lung NSC(277;0.00202)		Epithelial(280;0.0736)|all cancers(265;0.0975)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)|Colorectal(170;0.22)		CATCCTCAACCGAAACCACAG	0.463																																					p.R378X		Atlas-SNP	.											LPPR4,colon,carcinoma,-1,2	LPPR4	143	2	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.C1132T						scavenged	.						96.0	93.0	94.0					1																	99771406		2203	4300	6503	SO:0001587	stop_gained	0	exon7			CTCAACCGAAACC																												ENST00000370185.3:c.1132C>T	1.37:g.99771406C>T	ENSP00000359204:p.Arg378*	Somatic	286	0	0		WXS	Illumina HiSeq	Phase_I	278	3	0.0107914	NM_014839	E7EPS1|O75043|Q5T9R9|Q86XQ5|Q8N3F1|Q96MP0	Nonsense_Mutation	SNP	ENST00000370185.3	37	CCDS757.1	.	.	.	.	.	.	.	.	.	.	C	39	7.823181	0.98510	.	.	ENSG00000117600	ENST00000370185;ENST00000457765;ENST00000263178;ENST00000370184	.	.	.	5.71	4.78	0.61160	.	0.255371	0.34338	N	0.004059	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-15.1208	13.8899	0.63733	0.3329:0.6671:0.0:0.0	.	.	.	.	X	378;320;378;220	.	.	R	+	1	2	RP4-788L13.1	99543994	1.000000	0.71417	0.999000	0.59377	0.562000	0.35680	2.860000	0.48372	1.367000	0.46095	0.650000	0.86243	CGA	.	.	none		0.463	LPPR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029670.2		
AMBRA1	55626	hgsc.bcm.edu	37	11	46564251	46564251	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:46564251C>T	ENST00000458649.2	-	7	1734	c.1316G>A	c.(1315-1317)aGa>aAa	p.R439K	AMBRA1_ENST00000533727.1_Missense_Mutation_p.R349K|AMBRA1_ENST00000426438.1_Missense_Mutation_p.R439K|AMBRA1_ENST00000314845.3_Missense_Mutation_p.R349K|AMBRA1_ENST00000534300.1_Missense_Mutation_p.R439K|AMBRA1_ENST00000528950.1_Missense_Mutation_p.R439K|AMBRA1_ENST00000298834.3_Missense_Mutation_p.R439K			Q9C0C7	AMRA1_HUMAN	autophagy/beclin-1 regulator 1	439					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)		GGCACTGGTTCTGGGCGGGGG	0.562																																					p.R349K		Atlas-SNP	.											.	AMBRA1	201	.	0			c.G1046A						PASS	.						67.0	67.0	67.0					11																	46564251		2201	4299	6500	SO:0001583	missense	55626	exon8			CTGGTTCTGGGCG	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.1316G>A	11.37:g.46564251C>T	ENSP00000415327:p.Arg439Lys	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	172	38	0.22093	NM_001267783	A6XN33|D3DQP8|G3V193|Q86XD6|Q9H8Z0|Q9NXE7	Missense_Mutation	SNP	ENST00000458649.2	37		.	.	.	.	.	.	.	.	.	.	C	18.52	3.642548	0.67244	.	.	ENSG00000110497	ENST00000314845;ENST00000533727;ENST00000534300;ENST00000426438;ENST00000298834;ENST00000314823;ENST00000458649;ENST00000528950	T;D;T;T;T;T;T	0.84146	-1.24;-1.81;-1.08;-1.21;-1.08;-1.05;-1.21	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	D	0.89339	0.6687	L	0.32530	0.975	0.58432	D	0.999992	D;D;D;D;D;D	0.64830	0.994;0.99;0.99;0.974;0.99;0.974	D;D;D;D;D;D	0.72982	0.97;0.979;0.979;0.969;0.979;0.969	D	0.89784	0.3963	10	0.72032	D	0.01	.	20.1542	0.98100	0.0:1.0:0.0:0.0	.	439;439;439;349;349;349	Q9C0C7;Q9C0C7-3;Q9C0C7-2;G3V193;Q9C0C7-5;Q9C0C7-4	AMRA1_HUMAN;.;.;.;.;.	K	349;349;439;439;439;349;439;439	ENSP00000318313:R349K;ENSP00000433372:R349K;ENSP00000431926:R439K;ENSP00000410899:R439K;ENSP00000298834:R439K;ENSP00000415327:R439K;ENSP00000433945:R439K	ENSP00000298834:R439K	R	-	2	0	AMBRA1	46520827	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.172000	0.77604	2.767000	0.95098	0.563000	0.77884	AGA	.	.	none		0.562	AMBRA1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000390103.1	NM_017749	
CNTRL	11064	hgsc.bcm.edu	37	9	123931934	123931934	+	Missense_Mutation	SNP	G	G	T	rs376768102		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr9:123931934G>T	ENST00000373855.1	+	39	6376	c.6116G>T	c.(6115-6117)gGt>gTt	p.G2039V	CNTRL_ENST00000373850.1_Missense_Mutation_p.G1487V|CNTRL_ENST00000373845.2_3'UTR|CNTRL_ENST00000238341.5_Missense_Mutation_p.G2039V			Q7Z7A1	CNTRL_HUMAN	centriolin	2039	Required for centrosome localization.|Sufficient for interaction with HOOK2.				cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)				haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(2)|ovary(4)|skin(3)	20						GAGAAATCAGGTGAGCTGTTG	0.502																																					p.G2039V		Atlas-SNP	.											.	CNTRL	161	.	0			c.G6116T						PASS	.						94.0	96.0	95.0					9																	123931934		2203	4300	6503	SO:0001583	missense	11064	exon37			AATCAGGTGAGCT	AF513978	CCDS35118.1	9q33.2	2014-02-20	2011-05-23	2011-05-23	ENSG00000119397	ENSG00000119397			1858	protein-coding gene	gene with protein product		605496	"""centrosomal protein 1"", ""centrosomal protein 110kDa"""	CEP1, CEP110		10688839	Standard	XM_005251679		Approved		uc004bkx.1	Q7Z7A1	OTTHUMG00000020581	ENST00000373855.1:c.6116G>T	9.37:g.123931934G>T	ENSP00000362962:p.Gly2039Val	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	96	41	0.427083	NM_007018	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Missense_Mutation	SNP	ENST00000373855.1	37	CCDS35118.1	.	.	.	.	.	.	.	.	.	.	G	2.693	-0.272727	0.05716	.	.	ENSG00000119397	ENST00000373855;ENST00000238341;ENST00000454238;ENST00000439778;ENST00000394368;ENST00000373850;ENST00000373845	T;T;T	0.30182	1.84;1.84;1.54	6.02	-1.54	0.08584	.	.	.	.	.	T	0.17916	0.0430	L	0.29908	0.895	0.19300	N	0.99998	B	0.24823	0.112	B	0.16722	0.016	T	0.19516	-1.0303	9	0.33141	T	0.24	.	5.9625	0.19307	0.4083:0.223:0.3687:0.0	.	2039	Q7Z7A1	CNTRL_HUMAN	V	2039;2039;2039;795;196;1487;721	ENSP00000362962:G2039V;ENSP00000238341:G2039V;ENSP00000362956:G1487V	ENSP00000238341:G2039V	G	+	2	0	CNTRL	122971755	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.236000	0.09003	-0.605000	0.05753	-0.150000	0.13652	GGT	.	.	alt		0.502	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1	NM_007018	
FUT10	84750	hgsc.bcm.edu	37	8	33246864	33246864	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr8:33246864T>C	ENST00000327671.5	-	4	1460	c.829A>G	c.(829-831)Atc>Gtc	p.I277V	FUT10_ENST00000518672.1_Missense_Mutation_p.I249V|FUT10_ENST00000524021.1_Missense_Mutation_p.I249V|FUT10_ENST00000518076.1_5'UTR|FUT10_ENST00000335589.3_Missense_Mutation_p.I215V	NM_032664.3	NP_116053.3	Q6P4F1	FUT10_HUMAN	fucosyltransferase 10 (alpha (1,3) fucosyltransferase)	277					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)		AAAGCTAGGATAAACTTATAC	0.448																																					p.I277V		Atlas-SNP	.											FUT10,brain,glioma,+2,1	FUT10	62	1	0			c.A829G						scavenged	.						100.0	93.0	95.0					8																	33246864		2203	4300	6503	SO:0001583	missense	84750	exon4			CTAGGATAAACTT	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.829A>G	8.37:g.33246864T>C	ENSP00000332757:p.Ile277Val	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	154	2	0.012987	NM_032664	A8KAC8|Q70GG3|Q8IVI6|Q8IVI7|Q8IVJ3|Q8TE43|Q9BSR3	Missense_Mutation	SNP	ENST00000327671.5	37	CCDS6088.1	.	.	.	.	.	.	.	.	.	.	t	2.360	-0.346870	0.05208	.	.	ENSG00000172728	ENST00000327671;ENST00000380081;ENST00000518672;ENST00000524021;ENST00000335589	T;T;T;T	0.23950	1.88;1.88;1.88;1.88	5.22	4.06	0.47325	.	0.056930	0.64402	D	0.000002	T	0.19685	0.0473	L	0.28400	0.85	0.43857	D	0.996456	B;B;B;B;B;B	0.20261	0.043;0.002;0.008;0.003;0.016;0.009	B;B;B;B;B;B	0.25987	0.065;0.006;0.012;0.01;0.026;0.017	T	0.04017	-1.0984	10	0.52906	T	0.07	-1.3923	9.3853	0.38338	0.0:0.086:0.0:0.914	.	327;277;249;215;277;319	B4E056;Q6P4F1-5;Q6P4F1-4;Q6P4F1-3;Q6P4F1;E7EU36	.;.;.;.;FUT10_HUMAN;.	V	277;319;249;249;215	ENSP00000332757:I277V;ENSP00000430428:I249V;ENSP00000429870:I249V;ENSP00000334997:I215V	ENSP00000332757:I277V	I	-	1	0	FUT10	33366406	1.000000	0.71417	0.997000	0.53966	0.831000	0.47069	2.928000	0.48908	0.931000	0.37242	0.451000	0.29950	ATC	.	.	none		0.448	FUT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376540.1	NM_032664	
SYMPK	8189	hgsc.bcm.edu	37	19	46352062	46352062	+	Silent	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:46352062G>A	ENST00000245934.7	-	6	616	c.372C>T	c.(370-372)aaC>aaT	p.N124N		NM_004819.2	NP_004810.2	Q92797	SYMPK_HUMAN	symplekin	124	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)		TCTTCACCACGTTCACATTCT	0.552																																					p.N124N		Atlas-SNP	.											.	SYMPK	104	.	0			c.C372T						PASS	.						190.0	147.0	161.0					19																	46352062		2203	4300	6503	SO:0001819	synonymous_variant	8189	exon6			CACCACGTTCACA	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.372C>T	19.37:g.46352062G>A		Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	260	135	0.519231	NM_004819	O00521|O00689|O00733|Q59GT5|Q8N2U5	Silent	SNP	ENST00000245934.7	37	CCDS12676.2																																																																																			.	.	none		0.552	SYMPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316581.1	NM_004819	
KRT12	3859	hgsc.bcm.edu	37	17	39021152	39021152	+	Missense_Mutation	SNP	A	A	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr17:39021152A>T	ENST00000251643.4	-	3	736	c.713T>A	c.(712-714)gTg>gAg	p.V238E	RP5-1110E20.1_ENST00000579136.1_RNA	NM_000223.3	NP_000214.1	Q99456	K1C12_HUMAN	keratin 12	238	Coil 1B.|Rod.				visual perception (GO:0007601)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(2)	15		Breast(137;0.000301)			Griseofulvin(DB00400)	CTCGTCCAGCACCCGGCGCAG	0.572																																					p.V238E		Atlas-SNP	.											.	KRT12	53	.	0			c.T713A						PASS	.						102.0	98.0	100.0					17																	39021152		2203	4300	6503	SO:0001583	missense	3859	exon3			TCCAGCACCCGGC		CCDS11378.1	17q21.2	2013-06-20	2008-08-01		ENSG00000187242	ENSG00000187242		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6414	protein-coding gene	gene with protein product	"""Meesmann corneal dystrophy"""	601687				9171831, 16831889	Standard	NM_000223		Approved	K12	uc002hvk.2	Q99456	OTTHUMG00000133369	ENST00000251643.4:c.713T>A	17.37:g.39021152A>T	ENSP00000251643:p.Val238Glu	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	148	26	0.175676	NM_000223	B2R9E0	Missense_Mutation	SNP	ENST00000251643.4	37	CCDS11378.1	.	.	.	.	.	.	.	.	.	.	A	34	5.341017	0.95783	.	.	ENSG00000187242	ENST00000251643	D	0.88431	-2.38	5.96	5.96	0.96718	Filament (1);	0.000000	0.44688	D	0.000422	D	0.94961	0.8370	M	0.84585	2.705	0.58432	D	0.999999	D	0.89917	1.0	D	0.79784	0.993	D	0.95526	0.8599	10	0.87932	D	0	.	16.4484	0.83959	1.0:0.0:0.0:0.0	.	238	Q99456	K1C12_HUMAN	E	238	ENSP00000251643:V238E	ENSP00000251643:V238E	V	-	2	0	KRT12	36274678	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.193000	0.94954	2.285000	0.76669	0.533000	0.62120	GTG	.	.	none		0.572	KRT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257214.2	NM_000223	
CASQ2	845	hgsc.bcm.edu	37	1	116243937	116243937	+	Silent	SNP	A	A	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:116243937A>G	ENST00000261448.5	-	11	1364	c.1125T>C	c.(1123-1125)gaT>gaC	p.D375D	CASQ2_ENST00000456138.2_Silent_p.D304D	NM_001232.3	NP_001223.2	O14958	CASQ2_HUMAN	calsequestrin 2 (cardiac muscle)	375	Asp/Glu-rich (acidic).				cardiac muscle contraction (GO:0060048)|cellular response to caffeine (GO:0071313)|detection of calcium ion (GO:0005513)|ion transmembrane transport (GO:0034220)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|protein polymerization (GO:0051258)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of heart rate (GO:0002027)|regulation of membrane repolarization (GO:0060306)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|sequestering of calcium ion (GO:0051208)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|junctional sarcoplasmic reticulum membrane (GO:0014701)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|protein homodimerization activity (GO:0042803)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|skin(1)	18	Lung SC(450;0.211)	all_cancers(81;1.25e-06)|all_epithelial(167;1.02e-06)|all_lung(203;8.03e-06)|Lung NSC(69;5.01e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		catcttcatcatcatcttcaG	0.408																																					p.D375D		Atlas-SNP	.											CASQ2,NS,carcinoma,-2,1	CASQ2	54	1	0			c.T1125C						scavenged	.						171.0	143.0	153.0					1																	116243937		2203	4300	6503	SO:0001819	synonymous_variant	845	exon11			TTCATCATCATCT	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.1125T>C	1.37:g.116243937A>G		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	255	3	0.0117647	NM_001232	B2R7M6|B4DIB0|Q5T1D2|Q8TBW8	Silent	SNP	ENST00000261448.5	37	CCDS884.1																																																																																			.	.	none		0.408	CASQ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033091.1	NM_001232	
NRAP	4892	hgsc.bcm.edu	37	10	115381651	115381651	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr10:115381651T>C	ENST00000359988.3	-	24	2990	c.2746A>G	c.(2746-2748)Aag>Gag	p.K916E	NRAP_ENST00000369360.3_Missense_Mutation_p.K889E|NRAP_ENST00000369358.4_Missense_Mutation_p.K924E|NRAP_ENST00000360478.3_Missense_Mutation_p.K881E	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)		CCATAAGCCTTCTTGGCCCAT	0.493																																					p.K916E		Atlas-SNP	.											NRAP,NS,carcinoma,+1,1	NRAP	208	1	0			c.A2746G						scavenged	.						247.0	185.0	206.0					10																	115381651		2203	4300	6503	SO:0001583	missense	4892	exon24			AAGCCTTCTTGGC		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.2746A>G	10.37:g.115381651T>C	ENSP00000353078:p.Lys916Glu	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	191	2	0.0104712	NM_001261463		Missense_Mutation	SNP	ENST00000359988.3	37	CCDS7579.1	.	.	.	.	.	.	.	.	.	.	T	24.4	4.525566	0.85600	.	.	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478	T;T;T;T	0.38401	1.14;1.14;1.14;1.14	5.99	5.99	0.97316	.	0.097482	0.64402	D	0.000001	T	0.50701	0.1631	M	0.83774	2.66	0.42217	D	0.991836	P;P;P	0.45672	0.749;0.734;0.864	B;P;P	0.50314	0.434;0.637;0.515	T	0.52495	-0.8568	10	0.27082	T	0.32	.	11.3194	0.49412	0.1675:0.0:0.0:0.8325	.	916;881;916	A0AVL2;Q86VF7-4;Q86VF7	.;.;NRAP_HUMAN	E	924;889;916;881	ENSP00000358365:K924E;ENSP00000358367:K889E;ENSP00000353078:K916E;ENSP00000353666:K881E	ENSP00000353078:K916E	K	-	1	0	NRAP	115371641	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.329000	0.52060	2.291000	0.77112	0.533000	0.62120	AAG	.	.	none		0.493	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175	
PCM1	5108	hgsc.bcm.edu	37	8	17843569	17843569	+	Silent	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr8:17843569T>C	ENST00000519253.1	+	26	4634	c.4383T>C	c.(4381-4383)ccT>ccC	p.P1461P	PCM1_ENST00000524226.1_Silent_p.P1407P|PCM1_ENST00000327578.8_Silent_p.P160P|PCM1_ENST00000325083.8_Silent_p.P1461P			Q15154	PCM1_HUMAN	pericentriolar material 1	1461	Interaction with HAP1.				centrosome organization (GO:0051297)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|interkinetic nuclear migration (GO:0022027)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|microtubule anchoring (GO:0034453)|microtubule anchoring at centrosome (GO:0034454)|mitotic cell cycle (GO:0000278)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|positive regulation of intracellular protein transport (GO:0090316)|protein localization to centrosome (GO:0071539)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|pericentriolar material (GO:0000242)|protein complex (GO:0043234)	identical protein binding (GO:0042802)		PCM1/JAK2(30)	breast(4)|endometrium(8)|kidney(5)|large_intestine(16)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	48				Colorectal(111;0.0789)		AACTTACTCCTAGTGAGAGCC	0.323			T	"""RET, JAK2"""	"""papillary thyroid, CML, MPD"""																																p.P1461P		Atlas-SNP	.		Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"""E, L"""	.	PCM1	120	.	0			c.T4383C						PASS	.						85.0	82.0	83.0					8																	17843569		1842	4078	5920	SO:0001819	synonymous_variant	5108	exon26			TACTCCTAGTGAG		CCDS47812.1	8p22-p21.3	2008-08-08			ENSG00000078674	ENSG00000078674			8727	protein-coding gene	gene with protein product		600299				8120099, 15659651	Standard	NM_006197		Approved	PTC4	uc003wyi.4	Q15154	OTTHUMG00000163699	ENST00000519253.1:c.4383T>C	8.37:g.17843569T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	97	4	0.0412371	NM_006197	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Silent	SNP	ENST00000519253.1	37		.	.	.	.	.	.	.	.	.	.	T	9.433	1.086118	0.20390	.	.	ENSG00000078674	ENST00000522275	.	.	.	5.05	0.866	0.19079	.	.	.	.	.	T	0.42921	0.1224	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.20773	-1.0265	4	.	.	.	-5.5681	2.3121	0.04189	0.2364:0.3965:0.2305:0.1365	.	.	.	.	P	201	.	.	L	+	2	0	PCM1	17887849	0.921000	0.31238	0.999000	0.59377	0.981000	0.71138	0.014000	0.13333	0.071000	0.16664	-0.182000	0.12963	CTA	.	.	none		0.323	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197	
CAMTA1	23261	hgsc.bcm.edu	37	1	7797002	7797002	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:7797002C>T	ENST00000303635.7	+	14	3482	c.3275C>T	c.(3274-3276)gCg>gTg	p.A1092V	CAMTA1_ENST00000439411.2_Missense_Mutation_p.A1092V	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	1092					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(11)|lung(29)|ovary(5)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	85	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		ACAAAGCACGCGGATAGCATT	0.463			T	WWTR1	epitheliod hemangioendothelioma																																p.A1092V		Atlas-SNP	.		Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	CAMTA1,NS,carcinoma,+1,1	CAMTA1	226	1	0			c.C3275T						scavenged	.						127.0	114.0	119.0					1																	7797002		2203	4300	6503	SO:0001583	missense	23261	exon14			AGCACGCGGATAG	AB020640	CCDS30576.1, CCDS55574.1, CCDS55575.1	1p36.31-p36.23	2008-07-18			ENSG00000171735	ENSG00000171735			18806	protein-coding gene	gene with protein product		611501				11925432	Standard	NM_001195563		Approved	KIAA0833	uc001aoi.3	Q9Y6Y1	OTTHUMG00000001212	ENST00000303635.7:c.3275C>T	1.37:g.7797002C>T	ENSP00000306522:p.Ala1092Val	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	139	3	0.0215827	NM_015215	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	Missense_Mutation	SNP	ENST00000303635.7	37	CCDS30576.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.1|21.1	4.100289|4.100289	0.76983|0.76983	.|.	.|.	ENSG00000171735|ENSG00000171735	ENST00000303635;ENST00000439411;ENST00000414738;ENST00000303646|ENST00000495233	T;T|.	0.42513|.	0.97;0.97|.	5.61|5.61	5.61|5.61	0.85477|0.85477	Ankyrin repeat-containing domain (3);|.	0.053468|.	0.85682|.	D|.	0.000000|.	T|T	0.56381|0.56381	0.1981|0.1981	N|N	0.25060|0.25060	0.705|0.705	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.76494|.	0.997;0.982;0.998;0.999|.	D;B;P;D|.	0.66351|.	0.943;0.383;0.84;0.911|.	T|T	0.50224|0.50224	-0.8853|-0.8853	10|5	0.37606|.	T|.	0.19|.	-8.6758|-8.6758	19.6383|19.6383	0.95746|0.95746	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1092;179;48;1092|.	Q9Y6Y1-2;B4DXR3;Q7Z7P1;Q9Y6Y1|.	.;.;.;CMTA1_HUMAN|.	V|W	1092;1092;179;48|49	ENSP00000306522:A1092V;ENSP00000402561:A1092V|.	ENSP00000306522:A1092V|.	A|R	+|+	2|1	0|2	CAMTA1|CAMTA1	7719589|7719589	1.000000|1.000000	0.71417|0.71417	0.766000|0.766000	0.31476|0.31476	0.031000|0.031000	0.12232|0.12232	7.440000|7.440000	0.80464|0.80464	2.631000|2.631000	0.89168|0.89168	0.655000|0.655000	0.94253|0.94253	GCG|CGG	.	.	none		0.463	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003588.3	NM_015215	
CYP2D6	1565	hgsc.bcm.edu	37	22	42523636	42523636	+	Splice_Site	SNP	C	C	A	rs1135831|rs3915951		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr22:42523636C>A	ENST00000360608.5	-	7	1100	c.986G>T	c.(985-987)cGc>cTc	p.R329L	NDUFA6-AS1_ENST00000536447.2_RNA|NDUFA6-AS1_ENST00000451451.1_RNA|NDUFA6-AS1_ENST00000417327.1_RNA|NDUFA6-AS1_ENST00000439129.1_RNA|NDUFA6-AS1_ENST00000600968.1_RNA|CYP2D6_ENST00000389970.3_Splice_Site_p.R329L|NDUFA6-AS1_ENST00000416037.2_RNA|CYP2D6_ENST00000359033.4_Splice_Site_p.R278L|NDUFA6-AS1_ENST00000434834.1_RNA|NDUFA6-AS1_ENST00000595777.1_RNA|NDUFA6-AS1_ENST00000610250.1_RNA	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	329			R -> L (in dbSNP:rs3915951).		alkaloid catabolic process (GO:0009822)|alkaloid metabolic process (GO:0009820)|coumarin metabolic process (GO:0009804)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|heterocycle metabolic process (GO:0046483)|isoquinoline alkaloid metabolic process (GO:0033076)|monoterpenoid metabolic process (GO:0016098)|negative regulation of binding (GO:0051100)|negative regulation of cellular organofluorine metabolic process (GO:0090350)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)	p.R278L(5)|p.R329L(4)		NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(4)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21					Abiraterone(DB05812)|Acebutolol(DB01193)|Acetaminophen(DB00316)|Ajmaline(DB01426)|Almotriptan(DB00918)|Alogliptin(DB06203)|Alprenolol(DB00866)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amoxapine(DB00543)|Amphetamine(DB00182)|Amprenavir(DB00701)|Amsacrine(DB00276)|Antipyrine(DB01435)|Aprindine(DB01429)|Arformoterol(DB01274)|Aripiprazole(DB01238)|Artemether(DB06697)|Asenapine(DB06216)|Astemizole(DB00637)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzatropine(DB00245)|Benzyl alcohol(DB06770)|Bepridil(DB01244)|Betaxolol(DB00195)|Bicalutamide(DB01128)|Biperiden(DB00810)|Bisoprolol(DB00612)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Buspirone(DB00490)|Caffeine(DB00201)|Captopril(DB01197)|Carbinoxamine(DB00748)|Carteolol(DB00521)|Carvedilol(DB01136)|Celecoxib(DB00482)|Cephalexin(DB00567)|Cevimeline(DB00185)|Chlordiazepoxide(DB00475)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Cisapride(DB00604)|Citalopram(DB00215)|Clemastine(DB00283)|Clevidipine(DB04920)|Clomipramine(DB01242)|Clonidine(DB00575)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Codeine(DB00318)|Cyclobenzaprine(DB00924)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Darifenacin(DB00496)|Debrisoquin(DB04840)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dihydrocodeine(DB01551)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dolasetron(DB00757)|Domperidone(DB01184)|Donepezil(DB00843)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronedarone(DB04855)|Duloxetine(DB00476)|Efavirenz(DB00625)|Eletriptan(DB00216)|Encainide(DB01228)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erlotinib(DB00530)|Escitalopram(DB01175)|Ethylmorphine(DB01466)|Etoricoxib(DB01628)|Felodipine(DB01023)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fingolimod(DB08868)|Flecainide(DB01195)|Flunarizine(DB04841)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Galantamine(DB00674)|Gefitinib(DB00317)|Glutethimide(DB01437)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Halothane(DB01159)|Histamine Phosphate(DB00667)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Hydroxychloroquine(DB01611)|Hydroxyurea(DB01005)|Hydroxyzine(DB00557)|Idarubicin(DB01177)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Ipratropium bromide(DB00332)|Irbesartan(DB01029)|Isoniazid(DB00951)|Itraconazole(DB01167)|Ketoconazole(DB01026)|L-DOPA(DB01235)|Labetalol(DB00598)|Lansoprazole(DB00448)|Lercanidipine(DB00528)|Levomilnacipran(DB08918)|Lidocaine(DB00281)|Lisuride(DB00589)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Lovastatin(DB00227)|Lumefantrine(DB06708)|Maprotiline(DB00934)|Mefloquine(DB00358)|Mepyramine(DB06691)|Mequitazine(DB01071)|Mesoridazine(DB00933)|Methadone(DB00333)|Methamphetamine(DB01577)|Methazolamide(DB00703)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxyflurane(DB01028)|Methylnaltrexone(DB06800)|Methylphenidate(DB00422)|Methyprylon(DB01107)|Metoclopramide(DB01233)|Metoprolol(DB00264)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midodrine(DB00211)|Mifepristone(DB00834)|Minaprine(DB00805)|Mirabegron(DB08893)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Morphine(DB00295)|Nateglinide(DB00731)|Nebivolol(DB04861)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niacin(DB00627)|Nicardipine(DB00622)|Nicergoline(DB00699)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitrofural(DB00336)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxamniquine(DB01096)|Oxprenolol(DB01580)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Paliperidone(DB01267)|Palonosetron(DB00377)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Pergolide(DB01186)|Perhexiline(DB01074)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenformin(DB00914)|Phentermine(DB00191)|Pimozide(DB01100)|Pindolol(DB00960)|Pioglitazone(DB01132)|Piperazine(DB00592)|Pipotiazine(DB01621)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Primaquine(DB01087)|Procainamide(DB01035)|Prochlorperazine(DB00433)|Progesterone(DB00396)|Proguanil(DB01131)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Pyrimethamine(DB00205)|Quetiapine(DB01224)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ranitidine(DB00863)|Ranolazine(DB00243)|Reboxetine(DB00234)|Remoxipride(DB00409)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivastigmine(DB00989)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertindole(DB06144)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tamsulosin(DB00706)|Tapentadol(DB06204)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Terbinafine(DB00857)|Tetrabenazine(DB04844)|Theophylline(DB00277)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Timolol(DB00373)|Tiotropium(DB01409)|Tipranavir(DB00932)|Tolterodine(DB01036)|Trabectedin(DB05109)|Tramadol(DB00193)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Trimipramine(DB00726)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Trospium(DB00209)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)|Vinblastine(DB00570)|Vinorelbine(DB00361)|Yohimbine(DB01392)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Ziprasidone(DB00246)|Zolpidem(DB00425)	TTGGACACGGCCTGGACAGAC	0.602																																					p.R329L		Atlas-SNP	.											CYP2D6_ENST00000360608,NS,carcinoma,0,11	CYP2D6	104	11	9	Substitution - Missense(9)	prostate(6)|large_intestine(2)|NS(1)	c.G986T						scavenged	.						73.0	56.0	62.0					22																	42523636		2201	4299	6500	SO:0001630	splice_region_variant	1565	exon7			ACACGGCCTGGAC	M20403	CCDS33657.1, CCDS46721.1	22q13.1	2014-09-17	2003-01-14		ENSG00000100197	ENSG00000100197		"""Cytochrome P450s"""	2625	protein-coding gene	gene with protein product		124030	"""cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolizing), polypeptide 6"", ""cytochrome P450, family 2, subfamily D, polypeptide 7 pseudogene 2"", ""cytochrome P450, subfamily II (debrisoquine, sparteine, etc., -metabolising), polypeptide 7 pseudogene 2"", ""cytochrome P450, family 2, subfamily D, polypeptide 8 pseudogene 2"", ""cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolising), polypeptide 8 pseudogene 2"""	CYP2DL1, CYP2D7P2, CYP2D7BP, CYP2D8P2, CYP2D7AP		8449513	Standard	NM_000106		Approved	CPD6, P450-DB1, CYP2D, P450C2D	uc003bce.3	P10635	OTTHUMG00000150918	ENST00000360608.5:c.986-1G>T	22.37:g.42523636C>A		Somatic	154	1	0.00649351		WXS	Illumina HiSeq	Phase_I	134	3	0.0223881	NM_000106	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	Missense_Mutation	SNP	ENST00000360608.5	37	CCDS46721.1	.	.	.	.	.	.	.	.	.	.	C	14.89	2.669463	0.47677	.	.	ENSG00000100197	ENST00000360608;ENST00000389970;ENST00000413640;ENST00000359033;ENST00000542856	T;T;T	0.79940	-1.32;-1.32;4.99	4.93	3.91	0.45181	.	.	.	.	.	T	0.76435	0.3987	M	0.67953	2.075	0.41700	D	0.989391	B;B;B	0.15473	0.004;0.013;0.002	B;B;B	0.26693	0.013;0.072;0.013	T	0.72174	-0.4370	9	0.48119	T	0.1	.	5.5275	0.16967	0.1599:0.672:0.0:0.1681	rs3915951	329;278;329	C1ID54;Q6NXU8;Q6NWU0	.;.;.	L	329;329;275;278;278	ENSP00000353820:R329L;ENSP00000374620:R329L;ENSP00000351927:R278L	ENSP00000351927:R278L	R	-	2	0	CYP2D6	40853580	0.444000	0.25649	0.954000	0.39281	0.844000	0.47949	0.448000	0.21726	1.070000	0.40811	0.555000	0.69702	CGC	C|0.500;A|0.500	0.500	weak		0.602	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320525.1		Missense_Mutation
CFAP53	220136	hgsc.bcm.edu	37	18	47753972	47753972	+	Missense_Mutation	SNP	G	G	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr18:47753972G>T	ENST00000398545.4	-	8	1441	c.1324C>A	c.(1324-1326)Cgt>Agt	p.R442S		NM_145020.3	NP_659457.2												p.R442C(1)		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)		TGGGCTAAACGTTGGCGTCTA	0.373																																					p.R442S		Atlas-SNP	.											CCDC11,caecum,carcinoma,0,1	CCDC11	59	1	1	Substitution - Missense(1)	large_intestine(1)	c.C1324A						scavenged	.						177.0	167.0	171.0					18																	47753972		1914	4136	6050	SO:0001583	missense	220136	exon8			CTAAACGTTGGCG																												ENST00000398545.4:c.1324C>A	18.37:g.47753972G>T	ENSP00000381553:p.Arg442Ser	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	208	3	0.0144231	NM_145020		Missense_Mutation	SNP	ENST00000398545.4	37	CCDS11940.2	.	.	.	.	.	.	.	.	.	.	G	1.393	-0.580189	0.03854	.	.	ENSG00000172361	ENST00000398545	T	0.09538	2.97	5.5	-11.0	0.00169	.	2.891430	0.00961	N	0.003101	T	0.02455	0.0075	N	0.02011	-0.69	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.36383	-0.9750	10	0.10377	T	0.69	21.8414	1.6502	0.02770	0.1564:0.2326:0.3121:0.2989	.	442	Q96M91	CCD11_HUMAN	S	442	ENSP00000381553:R442S	ENSP00000381553:R442S	R	-	1	0	CCDC11	46007970	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-2.318000	0.01121	-2.485000	0.00520	-1.899000	0.00529	CGT	.	.	none		0.373	CCDC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255922.3		
PRAC1	84366	hgsc.bcm.edu	37	17	46799191	46799191	+	Missense_Mutation	SNP	G	G	A	rs554311327	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr17:46799191G>A	ENST00000290294.3	-	2	275	c.146C>T	c.(145-147)tCg>tTg	p.S49L	MIR3185_ENST00000583892.1_RNA|PRAC2_ENST00000432056.1_RNA|PRAC2_ENST00000422730.2_RNA	NM_032391.2	NP_115767.1	Q96KF2	PRAC1_HUMAN	prostate cancer susceptibility candidate 1	49						nucleus (GO:0005634)											tcggcctcccgaaattccaga	0.398													G|||	4	0.000798722	0.0	0.0043	5008	,	,		13775	0.0		0.001	False		,,,				2504	0.0				p.S49L		Atlas-SNP	.											.	PRAC	6	.	0			c.C146T						PASS	.						33.0	41.0	38.0					17																	46799191		1327	2309	3636	SO:0001583	missense	84366	exon2			CCTCCCGAAATTC	AF331165	CCDS11535.1	17q21	2013-08-29	2013-08-29	2013-08-29	ENSG00000159182	ENSG00000159182			30591	protein-coding gene	gene with protein product	"""prostate, rectum and colon"""	609819	"""chromosome 17 open reading frame 92"", ""prostate cancer susceptibility candidate"""	C17orf92, PRAC		11340635	Standard	NM_032391		Approved		uc002iny.3	Q96KF2	OTTHUMG00000159899	ENST00000290294.3:c.146C>T	17.37:g.46799191G>A	ENSP00000290294:p.Ser49Leu	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	181	60	0.331492	NM_032391		Missense_Mutation	SNP	ENST00000290294.3	37	CCDS11535.1	.	.	.	.	.	.	.	.	.	.	G	5.599	0.295270	0.10622	.	.	ENSG00000159182	ENST00000290294	T	0.58652	0.32	0.664	-1.33	0.09172	.	.	.	.	.	T	0.40815	0.1132	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33548	-0.9864	7	0.87932	D	0	.	.	.	.	.	49	Q96KF2	PRAC_HUMAN	L	49	ENSP00000290294:S49L	ENSP00000290294:S49L	S	-	2	0	PRAC	44154190	0.001000	0.12720	0.002000	0.10522	0.001000	0.01503	-0.678000	0.05209	-0.355000	0.08199	-0.752000	0.03492	TCG	.	.	none		0.398	PRAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358086.1	NM_032391	
RASSF2	9770	hgsc.bcm.edu	37	20	4768377	4768377	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr20:4768377C>T	ENST00000379400.3	-	10	910	c.715G>A	c.(715-717)Gat>Aat	p.D239N	RASSF2_ENST00000379376.2_Missense_Mutation_p.D239N|RASSF2_ENST00000478553.1_Intron	NM_014737.2	NP_055552.1	P50749	RASF2_HUMAN	Ras association (RalGDS/AF-6) domain family member 2	239	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				bone remodeling (GO:0046849)|cell cycle (GO:0007049)|epidermal growth factor receptor signaling pathway via I-kappaB kinase/NF-kappaB cascade (GO:0038168)|homeostasis of number of cells (GO:0048872)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|ossification (GO:0001503)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(3)|kidney(2)|large_intestine(8)|lung(12)|ovary(3)|pancreas(2)|prostate(2)|skin(2)	34						AGCGGGTAATCGGTGGCCTTC	0.537																																					p.D239N	Melanoma(158;1891 3343 50738)	Atlas-SNP	.											RASSF2,NS,carcinoma,0,1	RASSF2	75	1	0			c.G715A						scavenged	.						137.0	115.0	123.0					20																	4768377		2203	4300	6503	SO:0001583	missense	9770	exon10			GGTAATCGGTGGC	D79990	CCDS13083.1	20p13	2011-08-12	2008-02-22		ENSG00000101265	ENSG00000101265			9883	protein-coding gene	gene with protein product	"""centromere protein 34"""	609492				8724849, 15806169	Standard	NM_014737		Approved	KIAA0168, CENP-34	uc002wld.3	P50749	OTTHUMG00000031790	ENST00000379400.3:c.715G>A	20.37:g.4768377C>T	ENSP00000368710:p.Asp239Asn	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	142	2	0.0140845	NM_014737	A6NIX9|A8K5Z3|Q17S06|Q53HD0|Q6AHZ2|Q8IZA5	Missense_Mutation	SNP	ENST00000379400.3	37	CCDS13083.1	.	.	.	.	.	.	.	.	.	.	C	35	5.426218	0.96131	.	.	ENSG00000101265	ENST00000379400;ENST00000379376	T;T	0.32753	1.44;1.44	5.41	5.41	0.78517	Ras-association (3);	0.000000	0.85682	D	0.000000	T	0.59972	0.2233	M	0.80982	2.52	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.63453	-0.6634	10	0.87932	D	0	.	17.9201	0.88963	0.0:1.0:0.0:0.0	.	239	P50749	RASF2_HUMAN	N	239	ENSP00000368710:D239N;ENSP00000368684:D239N	ENSP00000368684:D239N	D	-	1	0	RASSF2	4716377	1.000000	0.71417	0.951000	0.38953	0.995000	0.86356	7.247000	0.78257	2.815000	0.96918	0.561000	0.74099	GAT	.	.	none		0.537	RASSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077828.1	NM_014737	
KRTAP5-4	387267	hgsc.bcm.edu	37	11	1643066	1643066	+	Silent	SNP	A	A	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	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	188	8	0.0425532		WXS	Illumina HiSeq	Phase_I	189	11	0.0582011	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	
ZNF845	91664	hgsc.bcm.edu	37	19	53855284	53855284	+	Silent	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:53855284G>A	ENST00000595091.1	+	5	1575	c.1356G>A	c.(1354-1356)tcG>tcA	p.S452S	ZNF845_ENST00000458035.1_Silent_p.S452S			Q96IR2	ZN845_HUMAN	zinc finger protein 845	452					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S452S(2)		endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						GTTTCAAATCGAACCTTGAAA	0.398																																					p.S452S		Atlas-SNP	.											ZNF845,NS,carcinoma,0,1	ZNF845	101	1	2	Substitution - coding silent(2)	prostate(1)|kidney(1)	c.G1356A						scavenged	.						26.0	24.0	25.0					19																	53855284		692	1590	2282	SO:0001819	synonymous_variant	91664	exon4			CAAATCGAACCTT	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.1356G>A	19.37:g.53855284G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	77	4	0.0519481	NM_138374		Silent	SNP	ENST00000595091.1	37	CCDS46170.1																																																																																			.	.	none		0.398	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908	
VPS16	64601	hgsc.bcm.edu	37	20	2842741	2842741	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr20:2842741G>A	ENST00000380445.3	+	11	1108	c.1036G>A	c.(1036-1038)Ggg>Agg	p.G346R	VPS16_ENST00000380443.3_5'Flank|PTPRA_ENST00000380393.3_5'Flank|VPS16_ENST00000481812.2_Intron|VPS16_ENST00000380469.3_Intron	NM_022575.2	NP_072097.2	Q9H269	VPS16_HUMAN	vacuolar protein sorting 16 homolog (S. cerevisiae)	346					intracellular protein transport (GO:0006886)|viral entry into host cell (GO:0046718)	actin filament (GO:0005884)|axon (GO:0030424)|early endosome (GO:0005769)|HOPS complex (GO:0030897)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|recycling endosome (GO:0055037)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	37						AATGGCCCCCGGGGCGCTGCT	0.607																																					p.G346R		Atlas-SNP	.											VPS16,NS,carcinoma,0,1	VPS16	76	1	0			c.G1036A						scavenged	.						27.0	30.0	29.0					20																	2842741		2203	4300	6503	SO:0001583	missense	64601	exon11			GCCCCCGGGGCGC	AF308801	CCDS13036.1, CCDS13037.1	20p13	2009-07-07	2009-07-07	2009-07-07	ENSG00000215305	ENSG00000215305			14584	protein-coding gene	gene with protein product		608550					Standard	NM_022575		Approved		uc002whe.3	Q9H269	OTTHUMG00000031714	ENST00000380445.3:c.1036G>A	20.37:g.2842741G>A	ENSP00000369810:p.Gly346Arg	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	152	4	0.0263158	NM_022575	Q5JUB1|Q8WU31|Q96EE7|Q96N92|Q9H1Q4|Q9H1Q5	Missense_Mutation	SNP	ENST00000380445.3	37	CCDS13036.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.392024	0.83011	.	.	ENSG00000215305	ENST00000380445	T	0.53206	0.63	4.93	3.97	0.46021	Vps16, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.67353	0.2884	M	0.80982	2.52	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.70828	-0.4766	10	0.72032	D	0.01	-11.1107	10.4343	0.44426	0.0:0.0:0.8056:0.1944	.	346	Q9H269	VPS16_HUMAN	R	346	ENSP00000369810:G346R	ENSP00000369810:G346R	G	+	1	0	VPS16	2790741	1.000000	0.71417	0.983000	0.44433	0.922000	0.55478	8.160000	0.89653	1.291000	0.44653	0.561000	0.74099	GGG	.	.	none		0.607	VPS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077658.2	NM_022575	
ARFRP1	10139	hgsc.bcm.edu	37	20	62333231	62333231	+	Missense_Mutation	SNP	G	G	A	rs139547982	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr20:62333231G>A	ENST00000359715.5	-	5	934	c.368C>T	c.(367-369)gCg>gTg	p.A123V	ARFRP1_ENST00000324228.2_Missense_Mutation_p.A123V|ARFRP1_ENST00000485858.1_5'Flank|ARFRP1_ENST00000607873.1_Missense_Mutation_p.A76V|ARFRP1_ENST00000440854.1_Missense_Mutation_p.A123V|ARFRP1_ENST00000609142.1_Missense_Mutation_p.A123V			Q13795	ARFRP_HUMAN	ADP-ribosylation factor related protein 1	123					gastrulation (GO:0007369)|Golgi to plasma membrane protein transport (GO:0043001)|GTP catabolic process (GO:0006184)|protein localization to Golgi apparatus (GO:0034067)|retrograde transport, endosome to Golgi (GO:0042147)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(1)	7	all_cancers(38;9.53e-13)|all_epithelial(29;2.64e-14)|Lung NSC(23;7e-10)|all_lung(23;2.53e-09)		Epithelial(9;4.09e-08)|all cancers(9;1.7e-07)|OV - Ovarian serous cystadenocarcinoma(5;0.0102)			ACCGCACAGCGCCTCGCTGGT	0.687													G|||	2	0.000399361	0.0	0.0014	5008	,	,		15284	0.001		0.0	False		,,,				2504	0.0				p.A123V		Atlas-SNP	.											ARFRP1,colon,carcinoma,+1,1	ARFRP1	17	1	0			c.C368T						scavenged	.	G	VAL/ALA,VAL/ALA	1,4167		0,1,2083	48.0	28.0	35.0		368,368	4.6	0.6	20	dbSNP_134	35	10,8152		0,10,4071	yes	missense,missense	ARFRP1	NM_001134758.1,NM_003224.3	64,64	0,11,6154	AA,AG,GG		0.1225,0.024,0.0892	benign,benign	123/174,123/202	62333231	11,12319	2084	4081	6165	SO:0001583	missense	10139	exon6			CACAGCGCCTCGC	X91504	CCDS13533.1, CCDS46630.1, CCDS68172.1, CCDS68173.1	20q13.3	2014-05-09			ENSG00000101246	ENSG00000101246		"""ADP-ribosylation factors"""	662	protein-coding gene	gene with protein product		604699				8530503	Standard	NM_003224		Approved	ARP, Arp1, ARL18	uc031rup.1	Q13795	OTTHUMG00000032993	ENST00000359715.5:c.368C>T	20.37:g.62333231G>A	ENSP00000352746:p.Ala123Val	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	171	4	0.0233918	NM_001134758	B7ZKX7|E1P5J9|Q6IBQ0	Missense_Mutation	SNP	ENST00000359715.5	37	CCDS13533.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	2	0.0034965034965034965	1	0.0013192612137203166	G	11.15	1.552881	0.27739	2.4E-4	0.001225	ENSG00000101246	ENST00000440854;ENST00000359715;ENST00000324228	T;T;T	0.63913	-0.07;-0.07;-0.07	5.53	4.57	0.56435	Small GTP-binding protein domain (1);	0.234257	0.42053	D	0.000776	T	0.41351	0.1155	L	0.33624	1.015	0.50467	D	0.999877	B	0.12630	0.006	B	0.12156	0.007	T	0.44757	-0.9307	10	0.51188	T	0.08	-29.5252	10.3719	0.44060	0.1489:0.0:0.8511:0.0	.	123	Q13795	ARFRP_HUMAN	V	123	ENSP00000403942:A123V;ENSP00000352746:A123V;ENSP00000326884:A123V	ENSP00000326884:A123V	A	-	2	0	ARFRP1	61803675	0.992000	0.36948	0.594000	0.28785	0.597000	0.36814	2.904000	0.48719	2.590000	0.87494	0.462000	0.41574	GCG	G|0.999;A|0.001	0.001	strong		0.687	ARFRP1-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472024.1		
CEACAM18	729767	hgsc.bcm.edu	37	19	51983701	51983701	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:51983701T>C	ENST00000396477.4	+	2	188	c.167T>C	c.(166-168)gTt>gCt	p.V56A	CEACAM18_ENST00000451626.1_Missense_Mutation_p.V117A	NM_001278392.1	NP_001265321.1	A8MTB9	CEA18_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 18	56										breast(1)|endometrium(4)|large_intestine(3)|lung(8)|skin(1)	17		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		CCTGAGGATGTTCAGGAATAC	0.562																																					p.V117A		Atlas-SNP	.											CEACAM18_ENST00000451626,NS,carcinoma,0,2	CEACAM18	96	2	0			c.T350C						scavenged	.						59.0	58.0	58.0					19																	51983701		2022	4180	6202	SO:0001583	missense	729767	exon3			AGGATGTTCAGGA			19q13.41	2013-01-29				ENSG00000213822		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	31949	protein-coding gene	gene with protein product							Standard	NM_001278392		Approved		uc002pwv.1	A8MTB9		ENST00000396477.4:c.167T>C	19.37:g.51983701T>C	ENSP00000379738:p.Val56Ala	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	120	2	0.0166667	NM_001080405	C9JN24	Missense_Mutation	SNP	ENST00000396477.4	37		.	.	.	.	.	.	.	.	.	.	.	7.510	0.654499	0.14580	.	.	ENSG00000213822	ENST00000451626;ENST00000451086;ENST00000396477	T	0.65916	-0.18	2.79	-3.87	0.04218	Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.49287	0.1548	L	0.34521	1.04	0.09310	N	1	B	0.23442	0.085	B	0.33960	0.173	T	0.47407	-0.9120	9	0.32370	T	0.25	-2.777	9.3296	0.38014	0.0:0.6389:0.0:0.3611	.	117	A8MTB9	CEA18_HUMAN	A	117;56;56	ENSP00000402203:V117A	ENSP00000379738:V56A	V	+	2	0	CEACAM18	56675513	0.001000	0.12720	0.000000	0.03702	0.005000	0.04900	-0.582000	0.05814	-1.005000	0.03417	-0.296000	0.09543	GTT	.	.	none		0.562	CEACAM18-001	PUTATIVE	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000323114.2		
KRT8	3856	hgsc.bcm.edu	37	12	53298699	53298699	+	Missense_Mutation	SNP	G	G	A	rs201807576	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:53298699G>A	ENST00000552551.1	-	2	499	c.67C>T	c.(67-69)Cgc>Tgc	p.R23C	KRT8_ENST00000546897.1_Missense_Mutation_p.R23C|KRT8_ENST00000293308.6_Missense_Mutation_p.R23C|KRT8_ENST00000552150.1_Missense_Mutation_p.R51C			P05787	K2C8_HUMAN	keratin 8	23	Head.|Ser-rich.				cell differentiation involved in embryonic placenta development (GO:0060706)|extrinsic apoptotic signaling pathway (GO:0097191)|hepatocyte apoptotic process (GO:0097284)|response to hydrostatic pressure (GO:0051599)|response to other organism (GO:0051707)|sarcomere organization (GO:0045214)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|viral process (GO:0016032)	cell-cell junction (GO:0005911)|costamere (GO:0043034)|cytoplasm (GO:0005737)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	scaffold protein binding (GO:0097110)|structural molecule activity (GO:0005198)			endometrium(5)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	13				BRCA - Breast invasive adenocarcinoma(357;0.108)	Tenecteplase(DB00031)	GTGTAGGAGCGGCTGCTGAAG	0.667																																					p.R51C		Atlas-SNP	.											KRT8,colon,carcinoma,0,2	KRT8	41	2	0			c.C151T						scavenged	.						11.0	13.0	13.0					12																	53298699		1953	3904	5857	SO:0001583	missense	3856	exon2			AGGAGCGGCTGCT	BC000654	CCDS8841.1, CCDS58234.1	12q13.13	2013-01-16			ENSG00000170421	ENSG00000170421		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6446	protein-coding gene	gene with protein product		148060				2434381, 1705144, 16831889	Standard	NM_002273		Approved	CARD2, K8, CK8, CYK8, K2C8, KO	uc009zmk.1	P05787	OTTHUMG00000169881	ENST00000552551.1:c.67C>T	12.37:g.53298699G>A	ENSP00000447566:p.Arg23Cys	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	95	5	0.0526316	NM_001256282	A8K4H3|B0AZN5|F8VXB4|Q14099|Q14716|Q14717|Q53GJ0|Q6DHW5|Q6GMY0|Q6P4C7|Q96J60	Missense_Mutation	SNP	ENST00000552551.1	37	CCDS8841.1	.	.	.	.	.	.	.	.	.	.	-	13.69	2.312705	0.40895	.	.	ENSG00000170421	ENST00000552551;ENST00000293308;ENST00000547916;ENST00000546897;ENST00000552150;ENST00000546826;ENST00000548998;ENST00000547413;ENST00000546542	D;D;D;D;D;D;D;T	0.84944	-1.92;-1.92;-1.92;-1.92;-1.92;-1.92;-1.92;-0.98	4.71	4.71	0.59529	.	0.431059	0.26883	N	0.022003	T	0.75824	0.3902	L	0.33293	1	0.41950	D	0.99065	B;B;B	0.12630	0.006;0.003;0.003	B;B;B	0.15484	0.013;0.005;0.002	T	0.69450	-0.5142	10	0.27082	T	0.32	.	9.653	0.39908	0.0974:0.0:0.9026:0.0	.	51;23;23	F8VXB4;F8VU64;P05787	.;.;K2C8_HUMAN	C	23;23;23;23;51;23;63;23;101	ENSP00000447566:R23C;ENSP00000293308:R23C;ENSP00000447402:R23C;ENSP00000449404:R51C;ENSP00000447881:R23C;ENSP00000447040:R63C;ENSP00000448681:R23C;ENSP00000450228:R101C	ENSP00000293308:R23C	R	-	1	0	KRT8	51584966	0.070000	0.21116	1.000000	0.80357	0.819000	0.46315	0.097000	0.15168	2.582000	0.87167	0.531000	0.56144	CGC	G|0.944;A|0.055	0.055	strong		0.667	KRT8-001	KNOWN	alternative_5_UTR|overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406385.1	NM_002273	
HTR1F	3355	hgsc.bcm.edu	37	3	88040470	88040470	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:88040470T>C	ENST00000319595.4	+	1	625	c.571T>C	c.(571-573)Tac>Cac	p.Y191H		NM_000866.3	NP_000857.1	P30939	5HT1F_HUMAN	5-hydroxytryptamine (serotonin) receptor 1F, G protein-coupled	191					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)	TGGAGCTTTCTACATCCCACT	0.408																																					p.Y191H		Atlas-SNP	.											HTR1F,right_upper_lobe,carcinoma,-2,1	HTR1F	66	1	0			c.T571C						scavenged	.						77.0	82.0	80.0					3																	88040470		2203	4300	6503	SO:0001583	missense	3355	exon2			GCTTTCTACATCC	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.571T>C	3.37:g.88040470T>C	ENSP00000322924:p.Tyr191His	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	188	2	0.0106383	NM_000866		Missense_Mutation	SNP	ENST00000319595.4	37	CCDS2920.1	.	.	.	.	.	.	.	.	.	.	T	18.21	3.573696	0.65765	.	.	ENSG00000179097	ENST00000319595	T	0.74421	-0.84	5.01	5.01	0.66863	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.90511	0.7027	H	0.97707	4.06	0.54753	D	0.999982	D	0.89917	1.0	D	0.97110	1.0	D	0.93226	0.6613	10	0.87932	D	0	.	12.7021	0.57038	0.0:0.0:0.0:1.0	.	191	P30939	5HT1F_HUMAN	H	191	ENSP00000322924:Y191H	ENSP00000322924:Y191H	Y	+	1	0	HTR1F	88123160	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.004000	0.88535	1.897000	0.54924	0.377000	0.23210	TAC	.	.	none		0.408	HTR1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352890.1	NM_000866	
PIK3AP1	118788	hgsc.bcm.edu	37	10	98369476	98369476	+	Silent	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr10:98369476G>A	ENST00000339364.5	-	14	2282	c.2163C>T	c.(2161-2163)agC>agT	p.S721S	PIK3AP1_ENST00000371110.2_Silent_p.S543S|PIK3AP1_ENST00000371109.3_Silent_p.S320S	NM_152309.2	NP_689522.2	Q6ZUJ8	BCAP_HUMAN	phosphoinositide-3-kinase adaptor protein 1	721					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)		CACTTGCTGTGCTGGAGGTGC	0.572																																					p.S721S		Atlas-SNP	.											.	PIK3AP1	111	.	0			c.C2163T						PASS	.						99.0	106.0	104.0					10																	98369476		2203	4300	6503	SO:0001819	synonymous_variant	118788	exon14			TGCTGTGCTGGAG	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.2163C>T	10.37:g.98369476G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	111	48	0.432432	NM_152309	Q5TB56|Q5VXJ9|Q8N6J6|Q8NAC8	Silent	SNP	ENST00000339364.5	37	CCDS31259.1																																																																																			.	.	none		0.572	PIK3AP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049619.2	NM_152309	
OR51A2	401667	hgsc.bcm.edu	37	11	4976671	4976671	+	Silent	SNP	G	G	A	rs2595984	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:4976671G>A	ENST00000380371.1	-	1	272	c.273C>T	c.(271-273)gcC>gcT	p.A91A	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001004748.1	NP_001004748.1	Q8NGJ7	O51A2_HUMAN	olfactory receptor, family 51, subfamily A, member 2	91						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A91A(1)		endometrium(4)|kidney(1)|large_intestine(3)|lung(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.22e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		AAGTTTCAGGGGCATTGAACA	0.438													A|||	746	0.148962	0.1036	0.2061	5008	,	,		14045	0.2183		0.1918	False		,,,				2504	0.0542				p.A91A		Atlas-SNP	.											OR51A2,rectum,carcinoma,0,1	OR51A2	40	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C273T						scavenged	.						132.0	99.0	111.0					11																	4976671		1918	3466	5384	SO:0001819	synonymous_variant	401667	exon1			TTCAGGGGCATTG	AB065797	CCDS31368.1	11p15.4	2012-08-09			ENSG00000205496	ENSG00000205496		"""GPCR / Class A : Olfactory receptors"""	14764	protein-coding gene	gene with protein product							Standard	NM_001004748		Approved		uc010qyt.2	Q8NGJ7	OTTHUMG00000066602	ENST00000380371.1:c.273C>T	11.37:g.4976671G>A		Somatic	302	3	0.00993378		WXS	Illumina HiSeq	Phase_I	417	11	0.0263789	NM_001004748		Silent	SNP	ENST00000380371.1	37	CCDS31368.1																																																																																			G|0.880;A|0.120	0.120	strong		0.438	OR51A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142809.1	NM_001004748	
UBE2A	7319	hgsc.bcm.edu	37	X	118715490	118715490	+	Nonsense_Mutation	SNP	G	G	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:118715490G>T	ENST00000371558.2	+	4	346	c.172G>T	c.(172-174)Gaa>Taa	p.E58*	UBE2A_ENST00000346330.3_Intron|UBE2A_ENST00000371569.5_5'UTR	NM_001282161.1|NM_003336.2|NM_181762.1	NP_001269090.1|NP_003327.2|NP_861427.1	P49459	UBE2A_HUMAN	ubiquitin-conjugating enzyme E2A	58					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|DNA repair (GO:0006281)|histone H2A ubiquitination (GO:0033522)|in utero embryonic development (GO:0001701)|maternal process involved in female pregnancy (GO:0060135)|positive regulation of cell proliferation (GO:0008284)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K11-linked ubiquitination (GO:0070979)|protein K48-linked ubiquitination (GO:0070936)|protein polyubiquitination (GO:0000209)|response to UV (GO:0009411)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|cytosol (GO:0005829)|HULC complex (GO:0033503)|nuclear chromatin (GO:0000790)|XY body (GO:0001741)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)	p.E58*(1)		haematopoietic_and_lymphoid_tissue(1)|lung(7)	8						ACTTACAATAGAATTCACTGA	0.299								Rad6 pathway																													p.E58X		Atlas-SNP	.											.	UBE2A	43	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G172T						PASS	.						81.0	79.0	80.0					X																	118715490		2202	4298	6500	SO:0001587	stop_gained	7319	exon4			ACAATAGAATTCA	AK223045	CCDS14580.1, CCDS14581.1	Xq24	2011-05-19	2011-05-19		ENSG00000077721	ENSG00000077721		"""Ubiquitin-conjugating enzymes E2"""	12472	protein-coding gene	gene with protein product		312180	"""ubiquitin-conjugating enzyme E2A (RAD6 homolog)"""			1559696	Standard	NM_003336		Approved	UBC2, HHR6A, RAD6A	uc004erl.3	P49459	OTTHUMG00000022275	ENST00000371558.2:c.172G>T	X.37:g.118715490G>T	ENSP00000360613:p.Glu58*	Somatic	383	1	0.00261097		WXS	Illumina HiSeq	Phase_I	508	203	0.399606	NM_003336	A6NFE9|A6NGR2|A6NMF5|B2R7R9|D3DWI1|Q4TTG1|Q96FX4	Nonsense_Mutation	SNP	ENST00000371558.2	37	CCDS14580.1	.	.	.	.	.	.	.	.	.	.	G	38	7.024582	0.98010	.	.	ENSG00000077721	ENST00000371558	.	.	.	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	-0.6356	17.9034	0.88911	0.0:0.0:1.0:0.0	.	.	.	.	X	58	.	ENSP00000360613:E58X	E	+	1	0	UBE2A	118599518	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.858000	0.99539	2.448000	0.82819	0.600000	0.82982	GAA	.	.	none		0.299	UBE2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058036.1	NM_003336	
AURKAIP1	54998	hgsc.bcm.edu	37	1	1309461	1309461	+	Silent	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:1309461G>A	ENST00000338370.3	-	2	817	c.417C>T	c.(415-417)aaC>aaT	p.N139N	AURKAIP1_ENST00000321751.5_Silent_p.N139N|AURKAIP1_ENST00000378853.3_Silent_p.N139N|AURKAIP1_ENST00000338338.5_Silent_p.N139N|AURKAIP1_ENST00000489799.1_5'Flank			Q9NWT8	AKIP_HUMAN	aurora kinase A interacting protein 1	139					negative regulation of mitosis (GO:0045839)|positive regulation of proteolysis (GO:0045862)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				kidney(1)|lung(2)	3	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;5.82e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		ACTTGTGGTGGTTCATCTTCC	0.617																																					p.N139N		Atlas-SNP	.											.	AURKAIP1	12	.	0			c.C417T						PASS	.						101.0	100.0	100.0					1																	1309461		2203	4296	6499	SO:0001819	synonymous_variant	54998	exon3			GTGGTGGTTCATC		CCDS25.1	1p36.33	2014-02-12			ENSG00000175756	ENSG00000175756			24114	protein-coding gene	gene with protein product		609183				12244051	Standard	NM_017900		Approved	AKIP, AIP, FLJ20608	uc009vkb.1	Q9NWT8	OTTHUMG00000001413	ENST00000338370.3:c.417C>T	1.37:g.1309461G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	73	29	0.39726	NM_001127230	Q5TA36|Q8TBD3	Silent	SNP	ENST00000338370.3	37	CCDS25.1																																																																																			.	.	none		0.617	AURKAIP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008273.1	NM_017900	
DRP2	1821	hgsc.bcm.edu	37	X	100509422	100509422	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:100509422C>T	ENST00000395209.3	+	18	2513	c.1986C>T	c.(1984-1986)tcC>tcT	p.S662S	DRP2_ENST00000538510.1_Silent_p.S662S|DRP2_ENST00000541709.1_Silent_p.S584S|DRP2_ENST00000402866.1_Silent_p.S662S	NM_001939.2	NP_001930.2	Q13474	DRP2_HUMAN	dystrophin related protein 2	662					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						AGACCACATCCAGTGAGAACA	0.507																																					p.S662S		Atlas-SNP	.											.	DRP2	98	.	0			c.C1986T						PASS	.						110.0	81.0	90.0					X																	100509422		2203	4300	6503	SO:0001819	synonymous_variant	1821	exon18			CACATCCAGTGAG	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.1986C>T	X.37:g.100509422C>T		Somatic	314	0	0		WXS	Illumina HiSeq	Phase_I	351	67	0.190883	NM_001939	A6ZKI5|A8K1B0|B1B1F3|B4DIZ0	Silent	SNP	ENST00000395209.3	37	CCDS14480.2																																																																																			.	.	none		0.507	DRP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057522.3	NM_001939	
C5orf38	153571	hgsc.bcm.edu	37	5	2752510	2752510	+	Silent	SNP	G	G	A	rs181498861	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:2752510G>A	ENST00000334000.3	+	1	249	c.132G>A	c.(130-132)gcG>gcA	p.A44A	C5orf38_ENST00000515640.1_Silent_p.A44A|IRX2_ENST00000382611.6_5'Flank|C5orf38_ENST00000397835.4_Silent_p.A44A|IRX2_ENST00000502957.1_Intron|IRX2_ENST00000302057.5_5'Flank|C5orf38_ENST00000505778.1_Silent_p.A44A|C5orf38_ENST00000457752.2_Silent_p.A44A	NM_178569.2	NP_848664.1	Q86SI9	CEI_HUMAN	chromosome 5 open reading frame 38	44						extracellular region (GO:0005576)				endometrium(2)|large_intestine(1)|lung(1)	4				GBM - Glioblastoma multiforme(108;0.205)		TACCCCTCGCGGTCCACTCCG	0.701																																					p.A44A		Atlas-SNP	.											.	C5orf38	20	.	0			c.G132A						PASS	.						14.0	16.0	15.0					5																	2752510		2199	4294	6493	SO:0001819	synonymous_variant	153571	exon1			CCTCGCGGTCCAC	AY249324	CCDS34131.1	5p15.33	2014-06-02			ENSG00000186493	ENSG00000186493			24226	protein-coding gene	gene with protein product	"""coordinated expression to IRX2"", ""IRX2 neighbor"""	610522				16515847, 16750006	Standard	XM_005248256		Approved	CEI, IRX2NB	uc003jdc.3	Q86SI9	OTTHUMG00000161741	ENST00000334000.3:c.132G>A	5.37:g.2752510G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	51	17	0.333333	NM_178569		Silent	SNP	ENST00000334000.3	37	CCDS34131.1																																																																																			G|0.999;C|0.001	.	alt		0.701	C5orf38-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365956.2	NM_178569	
FNIP1	96459	hgsc.bcm.edu	37	5	131013444	131013444	+	Missense_Mutation	SNP	C	C	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:131013444C>G	ENST00000510461.1	-	13	1566	c.1471G>C	c.(1471-1473)Gac>Cac	p.D491H	CTC-432M15.3_ENST00000514667.1_Intron|FNIP1_ENST00000307954.8_Missense_Mutation_p.D446H|FNIP1_ENST00000307968.7_Missense_Mutation_p.D463H|FNIP1_ENST00000511848.1_Missense_Mutation_p.D491H	NM_133372.2	NP_588613	Q8TF40	FNIP1_HUMAN	folliculin interacting protein 1	491					cellular response to starvation (GO:0009267)|immature B cell differentiation (GO:0002327)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell apoptotic process (GO:0002904)|positive regulation of GTPase activity (GO:0043547)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein phosphorylation (GO:0001934)|regulation of pro-B cell differentiation (GO:2000973)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(11)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34		all_cancers(142;0.00347)|Lung NSC(810;0.106)|all_lung(232;0.123)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0665)		GCCAACATGTCCACACTCTGA	0.398																																					p.D491H		Atlas-SNP	.											.	FNIP1	104	.	0			c.G1471C						PASS	.						128.0	124.0	125.0					5																	131013444		2203	4300	6503	SO:0001583	missense	96459	exon13			ACATGTCCACACT	DQ145719	CCDS34226.1, CCDS34227.1	5q23.3	2014-01-28				ENSG00000217128			29418	protein-coding gene	gene with protein product		610594				11853319, 17028174	Standard	NM_001008738		Approved	KIAA1961		Q8TF40		ENST00000510461.1:c.1471G>C	5.37:g.131013444C>G	ENSP00000421985:p.Asp491His	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	126	37	0.293651	NM_133372	D6RJH5|Q86T47|Q9BUT0	Missense_Mutation	SNP	ENST00000510461.1	37	CCDS34227.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.756687	0.89843	.	.	ENSG00000217128	ENST00000307968;ENST00000307954;ENST00000544351;ENST00000510461;ENST00000511848	T;T;T;T	0.31769	1.48;1.48;1.48;1.48	5.45	5.45	0.79879	.	.	.	.	.	T	0.53981	0.1830	L	0.55481	1.735	0.80722	D	1	D;D;D;P	0.89917	0.997;1.0;0.997;0.855	P;D;D;P	0.91635	0.858;0.999;0.91;0.667	T	0.53251	-0.8465	9	0.72032	D	0.01	-1.7286	19.6467	0.95778	0.0:1.0:0.0:0.0	.	491;491;463;491	A8K8V8;Q8TF40-2;Q8TF40-3;Q8TF40	.;.;.;FNIP1_HUMAN	H	463;446;251;491;491	ENSP00000309266:D463H;ENSP00000310453:D446H;ENSP00000421985:D491H;ENSP00000425619:D491H	ENSP00000310453:D446H	D	-	1	0	FNIP1	131041343	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.445000	0.80570	2.716000	0.92895	0.655000	0.94253	GAC	.	.	none		0.398	FNIP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370077.1	NM_133372	
PCDHGB4	8641	hgsc.bcm.edu	37	5	140768636	140768636	+	Silent	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:140768636T>C	ENST00000519479.1	+	1	1185	c.1185T>C	c.(1183-1185)tcT>tcC	p.S395S	PCDHGA3_ENST00000253812.6_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron	NM_003736.2|NM_018925.2|NM_032098.1	NP_003727.1|NP_061748.1|NP_115269.1	Q9UN71	PCDGG_HUMAN	protocadherin gamma subfamily B, 4	395	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(9)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(2)	37			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TATTAACTTCTTCAAGAAACA	0.413																																					p.S395S		Atlas-SNP	.											PCDHGB4,NS,carcinoma,+1,1	PCDHGB4	125	1	0			c.T1185C						scavenged	.						116.0	117.0	117.0					5																	140768636		1901	4123	6024	SO:0001819	synonymous_variant	8641	exon1			AACTTCTTCAAGA	AF152520	CCDS54928.1, CCDS75337.1	5q31	2010-01-26				ENSG00000253953		"""Cadherins / Protocadherins : Clustered"""	8711	other	protocadherin	"""fibroblast cadherin FIB2"", ""cadherin 20"""	603058				10380929	Standard	NM_003736		Approved	FIB2, CDH20, PCDH-GAMMA-B4		Q9UN71		ENST00000519479.1:c.1185T>C	5.37:g.140768636T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	112	3	0.0267857	NM_032098	O15099|Q2M267|Q9UN64	Silent	SNP	ENST00000519479.1	37	CCDS54928.1																																																																																			.	.	none		0.413	PCDHGB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374745.1	NM_003736	
ALDH8A1	64577	hgsc.bcm.edu	37	6	135271176	135271176	+	Missense_Mutation	SNP	C	C	T	rs150345681	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr6:135271176C>T	ENST00000265605.2	-	1	84	c.16G>A	c.(16-18)Gca>Aca	p.A6T	ALDH8A1_ENST00000367847.2_Missense_Mutation_p.A6T|ALDH8A1_ENST00000367845.2_Missense_Mutation_p.A6T	NM_022568.3	NP_072090.1	Q9H2A2	AL8A1_HUMAN	aldehyde dehydrogenase 8 family, member A1	6					9-cis-retinoic acid biosynthetic process (GO:0042904)|retinal metabolic process (GO:0042574)|retinoic acid metabolic process (GO:0042573)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	retinal dehydrogenase activity (GO:0001758)	p.A6T(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	36	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00401)|GBM - Glioblastoma multiforme(68;0.0058)		ATCAAAAGTGCGTTTGTTCCA	0.448													C|||	3	0.000599042	0.0	0.0	5008	,	,		19818	0.0		0.003	False		,,,				2504	0.0				p.A6T		Atlas-SNP	.											ALDH8A1,colon,carcinoma,0,1	ALDH8A1	68	1	1	Substitution - Missense(1)	large_intestine(1)	c.G16A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA	2,4404	4.2+/-10.8	0,2,2201	103.0	103.0	103.0		16,16,16	0.7	0.0	6	dbSNP_134	103	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense,missense	ALDH8A1	NM_001193480.1,NM_022568.3,NM_170771.2	58,58,58	0,8,6495	TT,TC,CC		0.0698,0.0454,0.0615	benign,benign,benign	6/438,6/488,6/434	135271176	8,12998	2203	4300	6503	SO:0001583	missense	64577	exon1			AAAGTGCGTTTGT	AL021939	CCDS5171.1, CCDS5172.1, CCDS55057.1	6q24.1-q25.1	2008-07-03			ENSG00000118514	ENSG00000118514		"""Aldehyde dehydrogenases"""	15471	protein-coding gene	gene with protein product		606467				11007799	Standard	NM_001193480		Approved	ALDH12	uc003qew.3	Q9H2A2	OTTHUMG00000015623	ENST00000265605.2:c.16G>A	6.37:g.135271176C>T	ENSP00000265605:p.Ala6Thr	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	109	5	0.0458716	NM_022568	B7Z521|O60793|Q24JS9|Q53GT3|Q5TI80	Missense_Mutation	SNP	ENST00000265605.2	37	CCDS5171.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	15.19	2.758936	0.49468	4.54E-4	6.98E-4	ENSG00000118514	ENST00000265605;ENST00000367845;ENST00000367847	T;T;T	0.76186	-1.0;-0.99;-1.0	6.14	0.675	0.17952	.	0.376195	0.27294	N	0.020038	T	0.30293	0.0760	N	0.17082	0.46	0.09310	N	1	B;B;B	0.12013	0.003;0.005;0.003	B;B;B	0.11329	0.004;0.006;0.003	T	0.31558	-0.9939	10	0.19147	T	0.46	.	7.8484	0.29440	0.0:0.5556:0.1117:0.3328	.	6;6;6	B7Z521;Q9H2A2-2;Q9H2A2	.;.;AL8A1_HUMAN	T	6	ENSP00000265605:A6T;ENSP00000356819:A6T;ENSP00000356821:A6T	ENSP00000265605:A6T	A	-	1	0	ALDH8A1	135312869	0.000000	0.05858	0.000000	0.03702	0.934000	0.57294	-0.277000	0.08502	0.128000	0.18479	0.650000	0.86243	GCA	C|0.999;T|0.001	0.001	strong		0.448	ALDH8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042334.2		
LRP1B	53353	hgsc.bcm.edu	37	2	141259273	141259273	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:141259273G>A	ENST00000389484.3	-	55	9804	c.8833C>T	c.(8833-8835)Ctt>Ttt	p.L2945F		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2945	EGF-like 11. {ECO:0000255|PROSITE- ProRule:PRU00076}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CTGACCGGAAGGTCTTGACAG	0.363										TSP Lung(27;0.18)																											p.L2945F	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.C8833T						PASS	.						112.0	115.0	114.0					2																	141259273		2203	4300	6503	SO:0001583	missense	53353	exon55			CCGGAAGGTCTTG	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.8833C>T	2.37:g.141259273G>A	ENSP00000374135:p.Leu2945Phe	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	63	31	0.492063	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	G	19.73	3.881949	0.72294	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.87887	-2.31	5.41	4.29	0.51040	Growth factor, receptor (1);EGF-like calcium-binding (1);	0.086330	0.45361	U	0.000370	D	0.83179	0.5198	M	0.73372	2.23	0.43347	D	0.995408	B	0.30664	0.289	B	0.26517	0.07	T	0.77130	-0.2701	10	0.10902	T	0.67	.	11.8149	0.52204	0.1088:0.0:0.8912:0.0	.	2945	Q9NZR2	LRP1B_HUMAN	F	2945;2883	ENSP00000374135:L2945F	ENSP00000374135:L2945F	L	-	1	0	LRP1B	140975743	1.000000	0.71417	0.996000	0.52242	0.937000	0.57800	5.559000	0.67326	1.080000	0.41073	0.585000	0.79938	CTT	.	.	none		0.363	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
APC	324	hgsc.bcm.edu	37	5	112176927	112176927	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:112176927C>T	ENST00000457016.1	+	16	6016	c.5636C>T	c.(5635-5637)gCt>gTt	p.A1879V	APC_ENST00000257430.4_Missense_Mutation_p.A1879V|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Missense_Mutation_p.A1879V			P25054	APC_HUMAN	adenomatous polyposis coli	1879	Highly charged.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AGGGAAAAGGCTGAATTAAGA	0.383		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											p.A1879V	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	Atlas-SNP	.	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	APC,colon,carcinoma,+1,1	APC	4158	1	2	Unknown(1)|Deletion - Frameshift(1)	soft_tissue(1)|skin(1)	c.C5636T						scavenged	.						83.0	80.0	81.0					5																	112176927		2202	4300	6502	SO:0001583	missense	324	exon17	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	AAAAGGCTGAATT	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.5636C>T	5.37:g.112176927C>T	ENSP00000413133:p.Ala1879Val	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	179	3	0.0167598	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	13.91	2.377824	0.42105	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.91686	-2.89;-2.89;-2.89	6.07	5.18	0.71444	.	0.065670	0.64402	D	0.000006	D	0.87865	0.6285	L	0.34521	1.04	0.58432	D	0.999999	P;B	0.38440	0.631;0.155	B;B	0.37422	0.249;0.183	D	0.86003	0.1496	9	.	.	.	-11.778	16.585	0.84725	0.1314:0.8685:0.0:0.0	.	1881;1879	Q4LE70;P25054	.;APC_HUMAN	V	1879	ENSP00000413133:A1879V;ENSP00000257430:A1879V;ENSP00000427089:A1879V	.	A	+	2	0	APC	112204826	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.576000	0.60915	1.539000	0.49286	0.650000	0.86243	GCT	.	.	none		0.383	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
TLE4	7091	hgsc.bcm.edu	37	9	82337469	82337469	+	Missense_Mutation	SNP	T	T	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr9:82337469T>G	ENST00000376552.2	+	18	3108	c.2090T>G	c.(2089-2091)cTa>cGa	p.L697R	TLE4_ENST00000265284.6_Missense_Mutation_p.L672R|TLE4_ENST00000376544.3_Missense_Mutation_p.L628R|TLE4_ENST00000376537.4_Missense_Mutation_p.L729R|TLE4_ENST00000376520.4_Missense_Mutation_p.L729R|TLE4_ENST00000376534.4_Missense_Mutation_p.L334R	NM_007005.3	NP_008936.2	Q04727	TLE4_HUMAN	transducin-like enhancer of split 4	697					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|Wnt signaling pathway (GO:0016055)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	39						AAATACCAACTACATCTTCAT	0.488																																					p.L697R		Atlas-SNP	.											.	TLE4	187	.	0			c.T2090G						PASS	.						142.0	139.0	140.0					9																	82337469		2032	4228	6260	SO:0001583	missense	7091	exon18			ACCAACTACATCT	M99439	CCDS43837.1, CCDS65069.1, CCDS65070.1, CCDS75851.1	9q21.32	2014-03-07	2014-03-07		ENSG00000106829	ENSG00000106829		"""WD repeat domain containing"""	11840	protein-coding gene	gene with protein product		605132	"""transducin-like enhancer of split 4, homolog of Drosophila E(sp1)"", ""transducin-like enhancer of split 4 (E(sp1) homolog, Drosophila)"""			8365415	Standard	XM_005252167		Approved	E(spI), ESG, GRG4	uc004alc.3	Q04727	OTTHUMG00000020072	ENST00000376552.2:c.2090T>G	9.37:g.82337469T>G	ENSP00000365735:p.Leu697Arg	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	129	46	0.356589	NM_007005	F8W6T6|Q3ZCS1|Q5T1Y2|Q6PCB3|Q9BZ07|Q9BZ08|Q9BZ09|Q9NSL3|Q9ULF9	Missense_Mutation	SNP	ENST00000376552.2	37	CCDS43837.1	.	.	.	.	.	.	.	.	.	.	T	30	5.049799	0.93740	.	.	ENSG00000106829	ENST00000376552;ENST00000376544;ENST00000376520;ENST00000376537;ENST00000376534;ENST00000265284	T;T;T;T;T;T	0.68331	-0.32;-0.32;-0.32;-0.32;-0.32;-0.32	6.17	6.17	0.99709	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.83119	0.5185	M	0.81682	2.555	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.997;1.0;1.0	D	0.85181	0.1004	10	0.87932	D	0	-13.1859	16.8222	0.85835	0.0:0.0:0.0:1.0	.	672;628;729;697	F8W6T6;Q04727-2;Q04727-3;Q04727	.;.;.;TLE4_HUMAN	R	697;628;729;729;334;672	ENSP00000365735:L697R;ENSP00000365727:L628R;ENSP00000365703:L729R;ENSP00000365720:L729R;ENSP00000365717:L334R;ENSP00000265284:L672R	ENSP00000265284:L672R	L	+	2	0	TLE4	81527289	1.000000	0.71417	0.980000	0.43619	0.992000	0.81027	8.040000	0.89188	2.371000	0.80710	0.533000	0.62120	CTA	.	.	none		0.488	TLE4-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052792.4	XM_212237	
MYO18B	84700	hgsc.bcm.edu	37	22	26164606	26164606	+	Silent	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr22:26164606G>A	ENST00000407587.2	+	4	892	c.723G>A	c.(721-723)gtG>gtA	p.V241V	MYO18B_ENST00000536101.1_Silent_p.V241V|MYO18B_ENST00000335473.7_Silent_p.V241V			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	241						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						AAAGCATAGTGGGGAAGGGGC	0.637																																					p.V241V		Atlas-SNP	.											.	MYO18B	322	.	0			c.G723A						PASS	.						27.0	33.0	31.0					22																	26164606		1893	4105	5998	SO:0001819	synonymous_variant	84700	exon4			CATAGTGGGGAAG	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.723G>A	22.37:g.26164606G>A		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	32	7	0.21875	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	37																																																																																				.	.	none		0.637	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
RHPN2	85415	hgsc.bcm.edu	37	19	33493842	33493842	+	Missense_Mutation	SNP	C	C	A	rs137892450	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:33493842C>A	ENST00000254260.3	-	8	860	c.825G>T	c.(823-825)atG>atT	p.M275I	RHPN2_ENST00000400226.4_Missense_Mutation_p.M124I	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	275	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(5)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(3)|skin(3)|urinary_tract(1)	44	Esophageal squamous(110;0.137)					GCACGCTGAGCATGGCAGGGC	0.448																																					p.M275I		Atlas-SNP	.											RHPN2,NS,neuroblastoma,0,1	RHPN2	107	1	0			c.G825T						scavenged	.						54.0	49.0	50.0					19																	33493842		2203	4300	6503	SO:0001583	missense	85415	exon8			GCTGAGCATGGCA	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.825G>T	19.37:g.33493842C>A	ENSP00000254260:p.Met275Ile	Somatic	90	3	0.0333333		WXS	Illumina HiSeq	Phase_I	92	8	0.0869565	NM_033103	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Missense_Mutation	SNP	ENST00000254260.3	37	CCDS12427.1	.	.	.	.	.	.	.	.	.	.	C	17.99	3.524256	0.64747	.	.	ENSG00000131941	ENST00000254260;ENST00000544458;ENST00000400226	T;T	0.16324	2.35;2.35	4.9	4.9	0.64082	BRO1 domain (3);	0.035852	0.85682	D	0.000000	T	0.23370	0.0565	M	0.72576	2.205	0.80722	D	1	P	0.41475	0.751	B	0.36959	0.237	T	0.07158	-1.0787	10	0.44086	T	0.13	-4.5596	18.4946	0.90860	0.0:1.0:0.0:0.0	.	275	Q8IUC4	RHPN2_HUMAN	I	275;5;124	ENSP00000254260:M275I;ENSP00000402244:M124I	ENSP00000254260:M275I	M	-	3	0	RHPN2	38185682	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	7.752000	0.85141	2.432000	0.82394	0.478000	0.44815	ATG	A|0.000;C|0.999;T|0.000	0.000	strong		0.448	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103	
CDH4	1002	hgsc.bcm.edu	37	20	60427856	60427856	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr20:60427856C>T	ENST00000360469.5	+	6	867	c.779C>T	c.(778-780)cCc>cTc	p.P260L	CDH4_ENST00000543233.1_Missense_Mutation_p.P186L	NM_001794.3	NP_001785.2	P55283	CADH4_HUMAN	cadherin 4, type 1, R-cadherin (retinal)	260	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(2)|lung(25)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			GTGGAGAACCCCATCGACCTG	0.592																																					p.P260L		Atlas-SNP	.											.	CDH4	172	.	0			c.C779T						PASS	.						163.0	123.0	136.0					20																	60427856		2203	4300	6503	SO:0001583	missense	1002	exon6			AGAACCCCATCGA	L34059	CCDS13488.1, CCDS58784.1	20q13.3	2010-01-26			ENSG00000179242	ENSG00000179242		"""Cadherins / Major cadherins"""	1763	protein-coding gene	gene with protein product	"""R-Cadherin"""	603006				10191097, 10516427	Standard	NM_001794		Approved		uc002ybn.2	P55283	OTTHUMG00000032890	ENST00000360469.5:c.779C>T	20.37:g.60427856C>T	ENSP00000353656:p.Pro260Leu	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	133	45	0.338346	NM_001794	B3KWB8|G3V1P8|Q2M208|Q5VZ44|Q9BZ05	Missense_Mutation	SNP	ENST00000360469.5	37	CCDS13488.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.927112	0.92389	.	.	ENSG00000179242	ENST00000360469;ENST00000536643;ENST00000543233	T;T	0.51817	0.69;0.69	4.76	4.76	0.60689	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.69771	0.3148	M	0.78801	2.425	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	T	0.72802	-0.4183	9	.	.	.	.	17.758	0.88455	0.0:1.0:0.0:0.0	.	260	P55283	CADH4_HUMAN	L	260;168;186	ENSP00000353656:P260L;ENSP00000443301:P186L	.	P	+	2	0	CDH4	59861251	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.549000	0.82163	2.202000	0.70862	0.561000	0.74099	CCC	.	.	none		0.592	CDH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079965.2	NM_001794	
HMCN1	83872	hgsc.bcm.edu	37	1	186008085	186008085	+	Silent	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:186008085G>A	ENST00000271588.4	+	38	6205	c.5976G>A	c.(5974-5976)gtG>gtA	p.V1992V	HMCN1_ENST00000367492.2_Silent_p.V1992V	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	1992	Ig-like C2-type 17.				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						ATAAATGCGTGGCCATCAACT	0.433																																					p.V1992V		Atlas-SNP	.											HMCN1,NS,carcinoma,+2,1	HMCN1	797	1	0			c.G5976A						scavenged	.						109.0	101.0	104.0					1																	186008085		2203	4300	6503	SO:0001819	synonymous_variant	83872	exon38			ATGCGTGGCCATC	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.5976G>A	1.37:g.186008085G>A		Somatic	353	0	0		WXS	Illumina HiSeq	Phase_I	362	4	0.0110497	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	37	CCDS30956.1																																																																																			.	.	none		0.433	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
CALR	811	hgsc.bcm.edu	37	19	13050364	13050364	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:13050364G>A	ENST00000316448.5	+	3	389	c.316G>A	c.(316-318)Ggg>Agg	p.G106R		NM_004343.3	NP_004334.1	P27797	CALR_HUMAN	calreticulin	106	N-domain.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|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)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cellular calcium ion homeostasis (GO:0006874)|cellular protein metabolic process (GO:0044267)|cellular response to lithium ion (GO:0071285)|cellular senescence (GO:0090398)|chaperone-mediated protein folding (GO:0061077)|cortical actin cytoskeleton organization (GO:0030866)|endoplasmic reticulum unfolded protein response (GO:0030968)|glucocorticoid receptor signaling pathway (GO:0042921)|negative regulation of intracellular steroid hormone receptor signaling pathway (GO:0033144)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|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)|peptide antigen assembly with MHC class I protein complex (GO:0002502)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of dendritic cell chemotaxis (GO:2000510)|positive regulation of DNA replication (GO:0045740)|positive regulation of gene expression (GO:0010628)|positive regulation of phagocytosis (GO:0050766)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|post-translational protein modification (GO:0043687)|protein export from nucleus (GO:0006611)|protein folding (GO:0006457)|protein localization to nucleus (GO:0034504)|protein maturation by protein folding (GO:0022417)|protein N-linked glycosylation via asparagine (GO:0018279)|protein stabilization (GO:0050821)|regulation of apoptotic process (GO:0042981)|regulation of meiosis (GO:0040020)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to testosterone (GO:0033574)|sequestering of calcium ion (GO:0051208)|spermatogenesis (GO:0007283)	acrosomal vesicle (GO:0001669)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|intracellular (GO:0005622)|membrane (GO:0016020)|MHC class I peptide loading complex (GO:0042824)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|proteinaceous extracellular matrix (GO:0005578)|sarcoplasmic reticulum (GO:0016529)	androgen receptor binding (GO:0050681)|calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|chaperone binding (GO:0051087)|complement component C1q binding (GO:0001849)|DNA binding (GO:0003677)|glycoprotein binding (GO:0001948)|hormone binding (GO:0042562)|integrin binding (GO:0005178)|iron ion binding (GO:0005506)|mRNA binding (GO:0003729)|peptide binding (GO:0042277)|poly(A) RNA binding (GO:0044822)|protein binding involved in protein folding (GO:0044183)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(3)|lung(5)|ovary(1)	10					Antihemophilic Factor(DB00025)|Melatonin(DB01065)|Tenecteplase(DB00031)	CATCGACTGTGGGGGCGGCTA	0.517																																					p.G106R		Atlas-SNP	.											CALR,colon,carcinoma,-2,1	CALR	31	1	0			c.G316A						scavenged	.						178.0	175.0	176.0					19																	13050364		2203	4300	6503	SO:0001583	missense	811	exon3			GACTGTGGGGGCG	M84739	CCDS12288.1	19p13.3-p13.2	2014-09-17				ENSG00000179218			1455	protein-coding gene	gene with protein product	"""Sicca syndrome antigen A (autoantigen Ro; calreticulin)"", ""autoantigen Ro"""	109091				2365822	Standard	NM_004343		Approved	RO, SSA, cC1qR, CRT, FLJ26680	uc002mvu.2	P27797		ENST00000316448.5:c.316G>A	19.37:g.13050364G>A	ENSP00000320866:p.Gly106Arg	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	137	2	0.0145985	NM_004343	Q6IAT4|Q9UDG2	Missense_Mutation	SNP	ENST00000316448.5	37	CCDS12288.1	.	.	.	.	.	.	.	.	.	.	G	34	5.336975	0.95758	.	.	ENSG00000179218	ENST00000316448	T	0.67865	-0.29	5.56	4.52	0.55395	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Calreticulin/calnexin, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.88706	0.6509	H	0.99042	4.41	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92506	0.6012	10	0.87932	D	0	-40.3969	13.4526	0.61180	0.0772:0.0:0.9227:0.0	.	106	P27797	CALR_HUMAN	R	106	ENSP00000320866:G106R	ENSP00000320866:G106R	G	+	1	0	CALR	12911364	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.808000	0.99193	1.341000	0.45600	0.561000	0.74099	GGG	.	.	none		0.517	CALR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451952.1	NM_004343	
IFITM3	10410	hgsc.bcm.edu	37	11	320606	320606	+	Missense_Mutation	SNP	G	G	T	rs199749095	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:320606G>T	ENST00000399808.4	-	1	444	c.208C>A	c.(208-210)Ccc>Acc	p.P70T	RP11-326C3.11_ENST00000602756.1_RNA|RP11-326C3.11_ENST00000508004.2_RNA|IFITM3_ENST00000602735.1_Missense_Mutation_p.P49T|RP11-326C3.14_ENST00000602809.1_lincRNA|RP11-326C3.10_ENST00000534271.1_RNA|IFITM3_ENST00000526811.1_Missense_Mutation_p.P49T|RP11-326C3.11_ENST00000602429.1_RNA	NM_021034.2	NP_066362.2	Q01628	IFM3_HUMAN	interferon induced transmembrane protein 3	70	Interaction with SPP1.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|immune response (GO:0006955)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral genome replication (GO:0045071)|negative regulation of viral transcription (GO:0032897)|response to interferon-alpha (GO:0035455)|response to interferon-beta (GO:0035456)|response to interferon-gamma (GO:0034341)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)		p.P70T(3)		central_nervous_system(7)|endometrium(7)|kidney(2)|large_intestine(1)|lung(1)	18		all_cancers(49;2e-09)|all_epithelial(84;3.36e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;8.85e-28)|Epithelial(43;5.52e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)		AGGCAGCAGGGGTTCATGAAG	0.632																																					p.P70T		Atlas-SNP	.											IFITM3,caecum,carcinoma,0,13	IFITM3	132	13	3	Substitution - Missense(3)	endometrium(2)|central_nervous_system(1)	c.C208A						scavenged	.						89.0	95.0	93.0					11																	320606		2101	4210	6311	SO:0001583	missense	10410	exon1			AGCAGGGGTTCAT	X57352	CCDS41585.1	11p15.5	2011-05-24	2011-05-24		ENSG00000142089	ENSG00000142089			5414	protein-coding gene	gene with protein product		605579	"""interferon induced transmembrane protein 3 (1-8U)"""			1906403, 16326387	Standard	NM_021034		Approved	1-8U	uc001lpa.2	Q01628		ENST00000399808.4:c.208C>A	11.37:g.320606G>T	ENSP00000382707:p.Pro70Thr	Somatic	148	6	0.0405405		WXS	Illumina HiSeq	Phase_I	162	6	0.037037	NM_021034	Q53Y76|Q96HK8|Q96J15	Missense_Mutation	SNP	ENST00000399808.4	37	CCDS41585.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|G	0.076|0.076	-1.193620|-1.193620	0.01594|0.01594	.|.	.|.	ENSG00000142089|ENSG00000142089	ENST00000270031|ENST00000399808;ENST00000526811	.|T;T	.|0.78595	.|-0.94;-1.19	4.65|4.65	-9.3|-9.3	0.00649|0.00649	.|.	.|.	.|.	.|.	.|.	.|T	.|0.54447	.|0.1859	L|L	0.29908|0.29908	0.895|0.895	0.09310|0.09310	N|N	0.999999|0.999999	.|B	.|0.02656	.|0.0	.|B	.|0.04013	.|0.001	.|T	.|0.32375	.|-0.9909	.|9	.|0.22109	.|T	.|0.4	.|.	2.5632|2.5632	0.04777|0.04777	0.1587:0.0951:0.2785:0.4676|0.1587:0.0951:0.2785:0.4676	.|.	.|70	.|Q01628	.|IFM3_HUMAN	.|T	-1|70;49	.|ENSP00000382707:P70T;ENSP00000432108:P49T	.|ENSP00000382707:P70T	.|P	-|-	.|1	.|0	IFITM3|IFITM3	310606|310606	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.022000|0.022000	0.10575|0.10575	-1.460000|-1.460000	0.02368|0.02368	-3.272000|-3.272000	0.00199|0.00199	-2.532000|-2.532000	0.00182|0.00182	.|CCC	G|0.936;T|0.064	0.064	strong		0.632	IFITM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384765.1	NM_021034	
CTPS2	56474	hgsc.bcm.edu	37	X	16711587	16711587	+	Silent	SNP	G	G	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:16711587G>T	ENST00000443824.1	-	5	1205	c.462C>A	c.(460-462)atC>atA	p.I154I	CTPS2_ENST00000359276.4_Silent_p.I154I|CTPS2_ENST00000380241.3_Silent_p.I154I	NM_001144002.1	NP_001137474.1	Q9NRF8	PYRG2_HUMAN	CTP synthase 2	154					'de novo' CTP biosynthetic process (GO:0044210)|glutamine metabolic process (GO:0006541)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleotide metabolic process (GO:0006220)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|CTP synthase activity (GO:0003883)			breast(1)|endometrium(3)|large_intestine(4)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	Hepatocellular(33;0.0997)					GCATTCCTTCGATGTCTCCAA	0.438																																					p.I154I		Atlas-SNP	.											.	CTPS2	49	.	0			c.C462A						PASS	.						104.0	96.0	99.0					X																	16711587		2203	4300	6503	SO:0001819	synonymous_variant	56474	exon5			TCCTTCGATGTCT	AF086422	CCDS14175.1	Xp22	2012-05-02	2012-05-02		ENSG00000047230	ENSG00000047230	6.3.4.2		2520	protein-coding gene	gene with protein product		300380	"""CTP synthase II"""			10899599	Standard	NM_001144002		Approved		uc004cxm.3	Q9NRF8	OTTHUMG00000021193	ENST00000443824.1:c.462C>A	X.37:g.16711587G>T		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	156	44	0.282051	NM_001144002	B3KWM2|Q9BRI0|Q9H809|Q9H8K9	Silent	SNP	ENST00000443824.1	37	CCDS14175.1																																																																																			.	.	none		0.438	CTPS2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055906.1	NM_019857	
MYOM1	8736	hgsc.bcm.edu	37	18	3094190	3094190	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr18:3094190T>C	ENST00000356443.4	-	26	4175	c.3842A>G	c.(3841-3843)gAg>gGg	p.E1281G	MYOM1_ENST00000261606.7_Missense_Mutation_p.E1185G|MYOM1_ENST00000400569.3_Missense_Mutation_p.E1281G|RNU7-25P_ENST00000516544.1_RNA	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	1281					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						AATTTCCTTCTCGTTAAATAT	0.408																																					p.E1281G		Atlas-SNP	.											MYOM1,NS,carcinoma,-1,1	MYOM1	192	1	0			c.A3842G						scavenged	.						76.0	73.0	74.0					18																	3094190		1810	4079	5889	SO:0001583	missense	8736	exon26			TCCTTCTCGTTAA	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.3842A>G	18.37:g.3094190T>C	ENSP00000348821:p.Glu1281Gly	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	83	2	0.0240964	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	37	CCDS45824.1	.	.	.	.	.	.	.	.	.	.	T	19.54	3.847199	0.71603	.	.	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.03094	4.05;4.05;4.05	5.55	5.55	0.83447	Immunoglobulin-like fold (1);	0.350509	0.35040	N	0.003491	T	0.04815	0.0130	L	0.29908	0.895	0.43287	D	0.995269	B;B	0.27229	0.172;0.107	B;B	0.33196	0.159;0.059	T	0.53549	-0.8423	10	0.26408	T	0.33	.	15.8615	0.79026	0.0:0.0:0.0:1.0	.	1185;1281	P52179-2;P52179	.;MYOM1_HUMAN	G	1281;1281;1185	ENSP00000348821:E1281G;ENSP00000383413:E1281G;ENSP00000261606:E1185G	ENSP00000261606:E1185G	E	-	2	0	MYOM1	3084190	1.000000	0.71417	0.723000	0.30687	0.985000	0.73830	7.843000	0.86859	2.333000	0.79357	0.533000	0.62120	GAG	.	.	none		0.408	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
ZNF846	162993	hgsc.bcm.edu	37	19	9873975	9873975	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:9873975T>C	ENST00000397902.2	-	3	538	c.125A>G	c.(124-126)aAg>aGg	p.K42R	ZNF846_ENST00000586293.1_Missense_Mutation_p.K42R|ZNF846_ENST00000588267.1_5'UTR|ZNF846_ENST00000592859.1_Intron	NM_001077624.1	NP_001071092.1	Q147U1	ZN846_HUMAN	zinc finger protein 846	42	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)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	22						AATGAGATTCTTGTAGTTCTC	0.413																																					p.K42R		Atlas-SNP	.											ZNF846,NS,carcinoma,0,1	ZNF846	61	1	0			c.A125G						PASS	.						109.0	114.0	113.0					19																	9873975		2202	4300	6502	SO:0001583	missense	162993	exon3			AGATTCTTGTAGT	AK097652	CCDS42496.1	19p13.2	2013-01-08			ENSG00000196605	ENSG00000196605		"""Zinc fingers, C2H2-type"", ""-"""	27260	protein-coding gene	gene with protein product							Standard	NM_001077624		Approved		uc002mmb.1	Q147U1		ENST00000397902.2:c.125A>G	19.37:g.9873975T>C	ENSP00000380999:p.Lys42Arg	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	95	4	0.0421053	NM_001077624	A8K0H1|B3KUP1	Missense_Mutation	SNP	ENST00000397902.2	37	CCDS42496.1	.	.	.	.	.	.	.	.	.	.	.	0.313	-0.966567	0.02232	.	.	ENSG00000196605	ENST00000397902	T	0.01516	4.81	2.17	-1.17	0.09648	Krueppel-associated box (4);	.	.	.	.	T	0.01156	0.0038	N	0.13168	0.305	0.09310	N	1	B	0.06786	0.001	B	0.12156	0.007	T	0.48547	-0.9026	8	.	.	.	.	5.7018	0.17887	0.0:0.5061:0.0:0.4938	.	42	Q147U1	ZN846_HUMAN	R	42	ENSP00000380999:K42R	.	K	-	2	0	ZNF846	9734975	0.001000	0.12720	0.313000	0.25210	0.740000	0.42216	0.078000	0.14761	-0.400000	0.07656	0.421000	0.28195	AAG	.	.	none		0.413	ZNF846-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450253.1	NM_001077624	
MUC6	4588	hgsc.bcm.edu	37	11	1017566	1017566	+	Silent	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	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	632	30	0.0474684		WXS	Illumina HiSeq	Phase_I	636	27	0.0424528	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	
PLXNC1	10154	hgsc.bcm.edu	37	12	94543629	94543629	+	Silent	SNP	C	C	T	rs560001465	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:94543629C>T	ENST00000258526.4	+	1	1131	c.882C>T	c.(880-882)ctC>ctT	p.L294L		NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1	294	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(12)|lung(30)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						GCCGCCTGCTCCTCTCCTCCA	0.746													C|||	4	0.000798722	0.0	0.0	5008	,	,		13674	0.0		0.0	False		,,,				2504	0.0041				p.L294L		Atlas-SNP	.											.	PLXNC1	135	.	0			c.C882T						PASS	.						5.0	7.0	6.0					12																	94543629		2040	4096	6136	SO:0001819	synonymous_variant	10154	exon1			CCTGCTCCTCTCC	AF030339	CCDS9049.1	12q23	2009-04-17				ENSG00000136040		"""CD molecules"", ""Plexins"""	9106	protein-coding gene	gene with protein product		604259					Standard	NR_037687		Approved	VESPR, CD232	uc001tdc.3	O60486	OTTHUMG00000170235	ENST00000258526.4:c.882C>T	12.37:g.94543629C>T		Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	9	6	0.666667	NM_005761	Q59H25	Silent	SNP	ENST00000258526.4	37	CCDS9049.1																																																																																			.	.	none		0.746	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2		
MBD1	4152	hgsc.bcm.edu	37	18	47799097	47799097	+	Silent	SNP	A	A	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr18:47799097A>G	ENST00000591416.1	-	15	2159	c.1728T>C	c.(1726-1728)atT>atC	p.I576I	MBD1_ENST00000347968.3_Silent_p.I520I|MBD1_ENST00000269471.5_Silent_p.I507I|MBD1_ENST00000398488.1_Silent_p.I474I|MBD1_ENST00000353909.3_Silent_p.I527I|MBD1_ENST00000587605.1_Silent_p.I474I|MBD1_ENST00000591535.1_Silent_p.I507I|MBD1_ENST00000382948.5_Silent_p.I576I|MBD1_ENST00000349085.2_Silent_p.I474I|MBD1_ENST00000436910.1_Silent_p.I507I|MBD1_ENST00000590208.1_Silent_p.I576I|MBD1_ENST00000339998.6_Intron|MBD1_ENST00000588937.1_Silent_p.I507I|MBD1_ENST00000585672.1_Silent_p.I526I|MBD1_ENST00000269468.5_Silent_p.I576I|MBD1_ENST00000457839.2_Silent_p.I601I|MBD1_ENST00000424334.2_Silent_p.I627I|MBD1_ENST00000398495.2_Silent_p.I537I|MBD1_ENST00000398493.1_Silent_p.I520I|MBD1_ENST00000585595.1_Silent_p.I601I			Q9UIS9	MBD1_HUMAN	methyl-CpG binding domain protein 1	576	TRD.				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						CCAGGCTGAAAATCTCCGTGA	0.577																																					p.I601I		Atlas-SNP	.											.	MBD1	228	.	0			c.T1803C						PASS	.						141.0	146.0	144.0					18																	47799097		2203	4300	6503	SO:0001819	synonymous_variant	4152	exon16			GCTGAAAATCTCC	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.1728T>C	18.37:g.47799097A>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	105	27	0.257143	NM_001204137	A4UTZ0|B4DXJ5|E9PEC5|K7ELI2|K7EQZ4|K7ESN0|O15248|O95241|Q7Z7B5|Q8N4W4|Q9UNZ6|Q9UNZ7|Q9UNZ8|Q9UNZ9	Silent	SNP	ENST00000591416.1	37	CCDS11943.1																																																																																			.	.	none		0.577	MBD1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255926.3	NM_015846	
CRISPLD1	83690	hgsc.bcm.edu	37	8	75898242	75898242	+	Missense_Mutation	SNP	A	A	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr8:75898242A>T	ENST00000262207.4	+	2	488	c.20A>T	c.(19-21)gAg>gTg	p.E7V	CRISPLD1_ENST00000519798.1_3'UTR	NM_031461.5	NP_113649.1	Q9H336	CRLD1_HUMAN	cysteine-rich secretory protein LCCL domain containing 1	7					face morphogenesis (GO:0060325)	extracellular vesicular exosome (GO:0070062)				biliary_tract(1)|central_nervous_system(1)|endometrium(3)|kidney(7)|large_intestine(10)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(64;0.0799)		Epithelial(68;0.155)|BRCA - Breast invasive adenocarcinoma(89;0.161)			ACCGCGCGGGAGTGGCTCAGA	0.463																																					p.E7V		Atlas-SNP	.											.	CRISPLD1	94	.	0			c.A20T						PASS	.						139.0	150.0	146.0					8																	75898242		2203	4300	6503	SO:0001583	missense	83690	exon2			CGCGGGAGTGGCT	AL834301	CCDS6219.1, CCDS69497.1, CCDS75754.1	8q21.13	2005-09-23	2005-02-16	2005-02-16	ENSG00000121005	ENSG00000121005			18206	protein-coding gene	gene with protein product			"""LCCL domain containing cysteine-rich secretory protein 1"""	LCRISP1			Standard	NM_031461		Approved	Cocoacrisp, DKFZp762F133	uc003yan.3	Q9H336	OTTHUMG00000164529	ENST00000262207.4:c.20A>T	8.37:g.75898242A>T	ENSP00000262207:p.Glu7Val	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	79	19	0.240506	NM_031461	B2RA60|B7Z929	Missense_Mutation	SNP	ENST00000262207.4	37	CCDS6219.1	.	.	.	.	.	.	.	.	.	.	A	14.60	2.583707	0.46006	.	.	ENSG00000121005	ENST00000262207;ENST00000520277	T;T	0.60299	0.2;1.85	5.37	5.37	0.77165	.	0.261213	0.39985	N	0.001208	T	0.48519	0.1504	L	0.47716	1.5	0.80722	D	1	B	0.20671	0.047	B	0.19946	0.027	T	0.41787	-0.9489	10	0.25751	T	0.34	.	10.6874	0.45852	0.9261:0.0:0.0738:0.0	.	7	Q9H336	CRLD1_HUMAN	V	7	ENSP00000262207:E7V;ENSP00000430504:E7V	ENSP00000262207:E7V	E	+	2	0	CRISPLD1	76060797	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.642000	0.54367	2.254000	0.74563	0.460000	0.39030	GAG	.	.	none		0.463	CRISPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379117.1	NM_031461	
CIB3	117286	hgsc.bcm.edu	37	19	16275678	16275678	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:16275678C>T	ENST00000269878.4	-	5	442	c.393G>A	c.(391-393)acG>acA	p.T131T	CIB3_ENST00000541493.1_5'UTR|CIB3_ENST00000379859.3_Silent_p.T82T	NM_054113.2	NP_473454.1	Q96Q77	CIB3_HUMAN	calcium and integrin binding family member 3	131	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|skin(2)	16						GTTTGGTCACCGTCTGCTCCA	0.602																																					p.T131T		Atlas-SNP	.											CIB3,colon,carcinoma,-1,1	CIB3	35	1	0			c.G393A						scavenged	.						125.0	114.0	118.0					19																	16275678		2203	4300	6503	SO:0001819	synonymous_variant	117286	exon5			GGTCACCGTCTGC	AB050868	CCDS12340.1, CCDS74305.1	19p13.12	2013-01-10						"""EF-hand domain containing"""	24580	protein-coding gene	gene with protein product		610645					Standard	XM_005259728		Approved	KIP3	uc002nds.3	Q96Q77		ENST00000269878.4:c.393G>A	19.37:g.16275678C>T		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	199	2	0.0100503	NM_054113	E7EUX1|Q2M1W0|Q6ISP1	Silent	SNP	ENST00000269878.4	37	CCDS12340.1																																																																																			.	.	none		0.602	CIB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460351.1	NM_054113	
ZNF462	58499	hgsc.bcm.edu	37	9	109691621	109691621	+	Missense_Mutation	SNP	G	G	A	rs376844260		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr9:109691621G>A	ENST00000277225.5	+	3	5717	c.5428G>A	c.(5428-5430)Gtc>Atc	p.V1810I	ZNF462_ENST00000457913.1_Missense_Mutation_p.V1810I|ZNF462_ENST00000441147.2_Missense_Mutation_p.V655I			Q96JM2	ZN462_HUMAN	zinc finger protein 462	1810					chromatin organization (GO:0006325)|negative regulation of DNA binding (GO:0043392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.V1810I(1)		NS(2)|autonomic_ganglia(2)|breast(5)|central_nervous_system(4)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(20)|lung(32)|ovary(5)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	119						CTTCACGGCCGTCTATGCAGA	0.547																																					p.V1810I		Atlas-SNP	.											ZNF462,NS,carcinoma,0,1	ZNF462	322	1	1	Substitution - Missense(1)	breast(1)	c.G5428A						PASS	.	G	ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	92.0	94.0	93.0		5428	5.1	1.0	9		93	1,8599	1.2+/-3.3	0,1,4299	no	missense	ZNF462	NM_021224.4	29	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	benign	1810/2507	109691621	2,13004	2203	4300	6503	SO:0001583	missense	58499	exon3			ACGGCCGTCTATG	AB058706	CCDS35096.1	9q31.3	2008-02-05			ENSG00000148143	ENSG00000148143		"""Zinc fingers, C2H2-type"""	21684	protein-coding gene	gene with protein product							Standard	NM_021224		Approved	DKFZP762N2316, KIAA1803, Zfp462	uc004bcz.3	Q96JM2	OTTHUMG00000020438	ENST00000277225.5:c.5428G>A	9.37:g.109691621G>A	ENSP00000277225:p.Val1810Ile	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	100	20	0.2	NM_021224	Q5T0T4|Q8N408	Missense_Mutation	SNP	ENST00000277225.5	37	CCDS35096.1	.	.	.	.	.	.	.	.	.	.	G	13.20	2.166219	0.38217	2.27E-4	1.16E-4	ENSG00000148143	ENST00000277225;ENST00000457913;ENST00000374686;ENST00000441147	T;T;T;T	0.05319	3.46;3.89;4.01;4.01	5.97	5.07	0.68467	.	0.110994	0.64402	N	0.000008	T	0.02727	0.0082	N	0.04508	-0.205	0.80722	D	1	P;B	0.39748	0.686;0.016	B;B	0.26094	0.066;0.008	T	0.60016	-0.7345	10	0.19590	T	0.45	.	15.0554	0.71910	0.068:0.0:0.932:0.0	.	1810;1810	Q96JM2-3;Q96JM2	.;ZN462_HUMAN	I	1810;1810;693;655	ENSP00000277225:V1810I;ENSP00000414570:V1810I;ENSP00000363818:V693I;ENSP00000397306:V655I	ENSP00000277225:V1810I	V	+	1	0	ZNF462	108731442	1.000000	0.71417	0.998000	0.56505	0.968000	0.65278	5.989000	0.70587	1.524000	0.49035	0.591000	0.81541	GTC	.	.	weak		0.547	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224	
GGT1	2678	hgsc.bcm.edu	37	22	25023903	25023903	+	Silent	SNP	C	C	T	rs1041998		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr22:25023903C>T	ENST00000400382.1	+	13	2048	c.1293C>T	c.(1291-1293)aaC>aaT	p.N431N	GGT1_ENST00000401885.1_Silent_p.N87N|GGT1_ENST00000466310.1_3'UTR|GGT1_ENST00000404532.1_Silent_p.N87N|GGT1_ENST00000400383.1_Silent_p.N431N|GGT1_ENST00000404920.1_Silent_p.N87N|GGT1_ENST00000403838.1_Silent_p.N87N|GGT1_ENST00000248923.4_Silent_p.N431N|GGT1_ENST00000406383.2_Silent_p.N431N|GGT1_ENST00000404223.1_Silent_p.N87N|GGT1_ENST00000400380.1_Silent_p.N431N			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1	431					arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|cysteine biosynthetic process (GO:0019344)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione catabolic process (GO:0006751)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|regulation of immune system process (GO:0002682)|regulation of inflammatory response (GO:0050727)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|xenobiotic metabolic process (GO:0006805)|zymogen activation (GO:0031638)	anchored component of external side of plasma membrane (GO:0031362)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			breast(1)|endometrium(2)|kidney(14)|large_intestine(2)|lung(6)|pancreas(1)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	40					Glutathione(DB00143)	GCATCACCAACGAGTTTGGGG	0.627													c|||	1	0.000199681	0.0	0.0014	5008	,	,		10503	0.0		0.0	False		,,,				2504	0.0				p.N431N		Atlas-SNP	.											GGT1,NS,carcinoma,0,1	GGT1	68	1	0			c.C1293T						scavenged	.	C	,,,	1,4405		0,1,2202	72.0	79.0	77.0		1293,1293,1293,1293	0.1	0.0	22	dbSNP_86	77	12,8588		0,12,4288	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GGT1	NM_001032364.2,NM_001032365.2,NM_005265.2,NM_013430.2	,,,	0,13,6490	TT,TC,CC		0.1395,0.0227,0.1	,,,	431/570,431/570,431/570,431/570	25023903	13,12993	2203	4300	6503	SO:0001819	synonymous_variant	2678	exon13			CACCAACGAGTTT	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.1293C>T	22.37:g.25023903C>T		Somatic	586	7	0.0119454		WXS	Illumina HiSeq	Phase_I	540	7	0.012963	NM_013430	Q08247|Q14404|Q8TBS1|Q9UMK1	Silent	SNP	ENST00000400382.1	37	CCDS42992.1																																																																																			.	.	weak		0.627	GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250797.1	NM_013430	
QRSL1	55278	hgsc.bcm.edu	37	6	107100238	107100238	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr6:107100238G>A	ENST00000369046.4	+	6	816	c.712G>A	c.(712-714)Gat>Aat	p.D238N	QRSL1_ENST00000369044.1_Missense_Mutation_p.D238N	NM_018292.4	NP_060762.3			glutaminyl-tRNA synthase (glutamine-hydrolyzing)-like 1											endometrium(2)|kidney(1)|large_intestine(4)|lung(4)	11	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;0.00768)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.248)	Epithelial(6;0.000334)|all cancers(7;0.00157)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0152)	BRCA - Breast invasive adenocarcinoma(108;0.118)|all cancers(137;0.167)|Epithelial(106;0.176)		CAGATGTGTGGATGATGCAGC	0.383																																					p.D238N	NSCLC(192;2127 2142 11668 26277 49545)	Atlas-SNP	.											.	QRSL1	30	.	0			c.G712A						PASS	.						103.0	95.0	98.0					6																	107100238		2203	4300	6503	SO:0001583	missense	55278	exon6			TGTGTGGATGATG	AK001851	CCDS5057.1	6q21	2014-08-04			ENSG00000130348	ENSG00000130348			21020	protein-coding gene	gene with protein product	"""glutamyl-tRNA(Gln) amidotransferase, subunit A"""					11230166, 19805282	Standard	NM_018292		Approved	GatA, FLJ10989, FLJ12189, DKFZP564C1278, FLJ13447	uc003prm.3	Q9H0R6	OTTHUMG00000015301	ENST00000369046.4:c.712G>A	6.37:g.107100238G>A	ENSP00000358042:p.Asp238Asn	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	212	44	0.207547	NM_018292		Missense_Mutation	SNP	ENST00000369046.4	37	CCDS5057.1	.	.	.	.	.	.	.	.	.	.	G	17.48	3.399837	0.62177	.	.	ENSG00000130348	ENST00000369046;ENST00000369044	T;T	0.64260	0.56;-0.09	5.93	5.93	0.95920	.	0.262307	0.42548	D	0.000688	T	0.57227	0.2039	M	0.71581	2.175	0.45172	D	0.998186	B;B	0.21821	0.02;0.061	B;B	0.27608	0.071;0.081	T	0.55068	-0.8198	10	0.46703	T	0.11	-19.3649	20.3495	0.98807	0.0:0.0:1.0:0.0	.	238;238	Q9H0R6;Q9H0R6-2	GATA_HUMAN;.	N	238	ENSP00000358042:D238N;ENSP00000358040:D238N	ENSP00000358040:D238N	D	+	1	0	QRSL1	107206931	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	2.726000	0.47302	2.814000	0.96858	0.591000	0.81541	GAT	.	.	none		0.383	QRSL1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041667.1	NM_018292	
MTCL1	23255	hgsc.bcm.edu	37	18	8824955	8824955	+	Silent	SNP	T	T	C	rs201573119		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr18:8824955T>C	ENST00000306329.11	+	13	4404	c.4404T>C	c.(4402-4404)ccT>ccC	p.P1468P	SOGA2_ENST00000359865.3_Silent_p.P1149P|SOGA2_ENST00000518815.1_Silent_p.P474P|SOGA2_ENST00000517570.1_Silent_p.P1108P|SOGA2_ENST00000400050.3_Silent_p.P1108P|SOGA2_ENST00000306285.7_Silent_p.P474P																							GCACAGAGCCTTTCCCCGACT	0.652																																					p.P1149P		Atlas-SNP	.											CCDC165,NS,carcinoma,+2,1	.	.	1	0			c.T3447C						scavenged	.						82.0	61.0	68.0					18																	8824955		2203	4299	6502	SO:0001819	synonymous_variant	23255	exon15			AGAGCCTTTCCCC																												ENST00000306329.11:c.4404T>C	18.37:g.8824955T>C		Somatic	67	1	0.0149254		WXS	Illumina HiSeq	Phase_I	78	2	0.025641	NM_015210		Silent	SNP	ENST00000306329.11	37																																																																																				T|0.999;A|0.001	.	alt		0.652	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1		
NCOA3	8202	hgsc.bcm.edu	37	20	46265035	46265035	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr20:46265035C>T	ENST00000371998.3	+	12	2096	c.1905C>T	c.(1903-1905)tcC>tcT	p.S635S	NCOA3_ENST00000372004.3_Silent_p.S635S|NCOA3_ENST00000371997.3_Silent_p.S645S|NCOA3_ENST00000341724.6_Silent_p.S645S			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	635	Ser-rich.				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						GGGGTCATTCCTCCTTGACCA	0.473																																					p.S645S		Atlas-SNP	.											.	NCOA3	156	.	0			c.C1935T						PASS	.						79.0	71.0	74.0					20																	46265035		2203	4300	6503	SO:0001819	synonymous_variant	8202	exon12			TCATTCCTCCTTG	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.1905C>T	20.37:g.46265035C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	123	22	0.178862	NM_001174088	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Silent	SNP	ENST00000371998.3	37	CCDS13407.1																																																																																			.	.	none		0.473	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534	
CTSF	8722	hgsc.bcm.edu	37	11	66331416	66331416	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:66331416C>T	ENST00000310325.5	-	13	1552	c.1443G>A	c.(1441-1443)gcG>gcA	p.A481A	ACTN3_ENST00000502692.1_RNA|ACTN3_ENST00000513398.1_RNA|CTSF_ENST00000533168.1_5'Flank	NM_003793.3	NP_003784.2	Q9UBX1	CATF_HUMAN	cathepsin F	481				SDVPFWAIKNSWGTDWGEKGYYYLHRGSGACGVNTMASSAV VD -> EFRCLSCIQPGHRQGWDHSISGPLEGK (in Ref. 9). {ECO:0000305}.	antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|vesicle (GO:0031982)	cysteine-type endopeptidase activity (GO:0004197)	p.A481A(1)		endometrium(1)|large_intestine(7)|lung(8)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	19						AGTCCACCACCGCCGAGCTGG	0.672																																					p.A481A		Atlas-SNP	.											CTSF,caecum,carcinoma,-1,2	CTSF	42	2	1	Substitution - coding silent(1)	large_intestine(1)	c.G1443A						scavenged	.						25.0	28.0	27.0					11																	66331416		2199	4294	6493	SO:0001819	synonymous_variant	8722	exon13			CACCACCGCCGAG	AF071749	CCDS8144.1	11q13.2	2012-02-29			ENSG00000174080	ENSG00000174080		"""Cathepsins"""	2531	protein-coding gene	gene with protein product		603539				9822672, 10318784	Standard	NM_003793		Approved	CATSF, CLN13	uc001oip.3	Q9UBX1	OTTHUMG00000167090	ENST00000310325.5:c.1443G>A	11.37:g.66331416C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	105	2	0.0190476	NM_003793	B2R964|O95240|Q9NSU4|Q9UKQ5	Silent	SNP	ENST00000310325.5	37	CCDS8144.1																																																																																			.	.	none		0.672	CTSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393047.1	NM_003793	
PRAMEF1	65121	hgsc.bcm.edu	37	1	12853441	12853441	+	Missense_Mutation	SNP	C	C	A	rs75270454		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:12853441C>A	ENST00000332296.7	+	2	168	c.65C>A	c.(64-66)gCc>gAc	p.A22D	PRAMEF1_ENST00000400814.3_5'Flank	NM_023013.2	NP_075389.1	O95521	PRAM1_HUMAN	PRAME family member 1	22					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.A22D(2)		cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	35	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		AGAGACCAGGCCTTGTCCATC	0.562																																					p.A22D		Atlas-SNP	.											PRAMEF1,NS,carcinoma,0,2	PRAMEF1	78	2	2	Substitution - Missense(2)	kidney(2)	c.C65A						scavenged	.						71.0	79.0	76.0					1																	12853441		2202	4294	6496	SO:0001583	missense	65121	exon2			ACCAGGCCTTGTC	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.65C>A	1.37:g.12853441C>A	ENSP00000332134:p.Ala22Asp	Somatic	277	5	0.0180505		WXS	Illumina HiSeq	Phase_I	282	9	0.0319149	NM_023013	Q9UQP2	Missense_Mutation	SNP	ENST00000332296.7	37	CCDS148.1	.	.	.	.	.	.	.	.	.	.	.	4.513	0.095223	0.08681	.	.	ENSG00000116721	ENST00000332296	T	0.18016	2.24	1.64	-2.04	0.07343	.	0.350802	0.29537	N	0.011869	T	0.18173	0.0436	M	0.73217	2.22	0.09310	N	1	P	0.48089	0.905	P	0.48400	0.576	T	0.11397	-1.0589	10	0.48119	T	0.1	.	1.0347	0.01546	0.2203:0.4057:0.217:0.157	.	22	O95521	PRAM1_HUMAN	D	22	ENSP00000332134:A22D	ENSP00000332134:A22D	A	+	2	0	PRAMEF1	12776028	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.630000	0.05502	-0.611000	0.05709	-3.517000	0.00032	GCC	A|0.000;C|0.999;T|0.000	0.000	strong		0.562	PRAMEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005458.1	NM_023013	
SLC25A37	51312	hgsc.bcm.edu	37	8	23429088	23429088	+	Missense_Mutation	SNP	C	C	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr8:23429088C>A	ENST00000519973.1	+	4	935	c.737C>A	c.(736-738)gCc>gAc	p.A246D	FP15737_ENST00000399967.3_5'Flank	NM_016612.2	NP_057696.2	Q9NYZ2	MFRN1_HUMAN	solute carrier family 25 (mitochondrial iron transporter), member 37	246					iron ion homeostasis (GO:0055072)|mitochondrial iron ion transport (GO:0048250)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	iron ion transmembrane transporter activity (GO:0005381)			NS(1)|endometrium(3)|large_intestine(2)|lung(8)|urinary_tract(1)	15		Prostate(55;0.114)		Colorectal(74;0.0198)|COAD - Colon adenocarcinoma(73;0.0751)		CTGGCCGGGGCCCTCGCCGCG	0.652																																					p.A246D		Atlas-SNP	.											.	SLC25A37	27	.	0			c.C737A						PASS	.						25.0	29.0	28.0					8																	23429088		1913	4111	6024	SO:0001583	missense	51312	exon4			CCGGGGCCCTCGC	AF495725	CCDS47828.1	8p21.2	2013-05-22	2012-03-29		ENSG00000147454	ENSG00000147454		"""Solute carriers"""	29786	protein-coding gene	gene with protein product	"""mitoferrin"""	610387	"""solute carrier family 25, member 37"""			16511496	Standard	XM_006716352		Approved	MSCP, MFRN, MFRN1	uc003xdo.3	Q9NYZ2	OTTHUMG00000163865	ENST00000519973.1:c.737C>A	8.37:g.23429088C>A	ENSP00000429200:p.Ala246Asp	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	57	32	0.561404	NM_016612	A2RU93|Q53FT7|Q69YJ8|Q969S1|Q9P0J2	Missense_Mutation	SNP	ENST00000519973.1	37	CCDS47828.1	.	.	.	.	.	.	.	.	.	.	C	30	5.055259	0.93793	.	.	ENSG00000147454	ENST00000519973	D	0.81821	-1.54	5.8	5.8	0.92144	Mitochondrial carrier domain (2);	0.046862	0.85682	D	0.000000	D	0.93973	0.8070	H	0.97829	4.085	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.95648	0.8704	10	0.72032	D	0.01	1.0198	18.6148	0.91299	0.0:1.0:0.0:0.0	.	246	Q9NYZ2	MFRN1_HUMAN	D	246	ENSP00000429200:A246D	ENSP00000429200:A246D	A	+	2	0	SLC25A37	23485033	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.473000	0.81007	2.740000	0.93945	0.650000	0.86243	GCC	.	.	none		0.652	SLC25A37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376039.1	NM_016612	
C14orf37	145407	hgsc.bcm.edu	37	14	58598352	58598352	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr14:58598352T>C	ENST00000267485.7	-	4	1903	c.1709A>G	c.(1708-1710)gAa>gGa	p.E570G	C14orf37_ENST00000334342.5_5'UTR	NM_001001872.2	NP_001001872.2	Q86TY3	CN037_HUMAN	chromosome 14 open reading frame 37	570						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						AATGCTGGGTTCCCCCACCAT	0.493																																					p.E570G		Atlas-SNP	.											C14orf37,NS,carcinoma,-1,1	C14orf37	87	1	0			c.A1709G						PASS	.						114.0	107.0	109.0					14																	58598352		2203	4300	6503	SO:0001583	missense	145407	exon4			CTGGGTTCCCCCA		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.1709A>G	14.37:g.58598352T>C	ENSP00000267485:p.Glu570Gly	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	110	40	0.363636	NM_001001872	A8K8Z8|Q6P5Q1|Q86TY1	Missense_Mutation	SNP	ENST00000267485.7	37	CCDS32089.1	.	.	.	.	.	.	.	.	.	.	T	5.939	0.357220	0.11239	.	.	ENSG00000139971	ENST00000267485;ENST00000438670	T	0.18338	2.22	5.78	-2.62	0.06152	.	1.333660	0.04700	N	0.415699	T	0.10252	0.0251	N	0.22421	0.69	0.09310	N	1	B;B;B;B	0.26400	0.039;0.148;0.039;0.039	B;B;B;B	0.24394	0.023;0.053;0.023;0.023	T	0.28038	-1.0056	10	0.32370	T	0.25	0.0768	4.1407	0.10191	0.2759:0.0:0.3626:0.3615	.	608;570;570;570	B4DMS4;Q86TY3-2;A8K990;Q86TY3	.;.;.;CN037_HUMAN	G	570;608	ENSP00000267485:E570G	ENSP00000267485:E570G	E	-	2	0	C14orf37	57668105	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	0.036000	0.13819	-0.865000	0.04073	-0.219000	0.12488	GAA	.	.	none		0.493	C14orf37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412059.1	NM_001001872	
HIST1H2BM	8342	hgsc.bcm.edu	37	6	27783062	27783062	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr6:27783062C>T	ENST00000359465.4	+	1	241	c.241C>T	c.(241-243)Ctg>Ttg	p.L81L	HIST1H2AJ_ENST00000333151.3_5'Flank	NM_003521.2	NP_003512.1	Q99879	H2B1M_HUMAN	histone cluster 1, H2bm	81					chromatin organization (GO:0006325)|nucleosome assembly (GO:0006334)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)	12						AGCGTCACGCCTGGCGCATTA	0.597																																					p.L81L		Atlas-SNP	.											HIST1H2BM,NS,carcinoma,0,2	HIST1H2BM	36	2	0			c.C241T						scavenged	.						109.0	101.0	104.0					6																	27783062		2203	4300	6503	SO:0001819	synonymous_variant	8342	exon1			TCACGCCTGGCGC	Z83738	CCDS4629.1	6p22.1	2011-01-27	2006-10-11	2003-02-28	ENSG00000196374	ENSG00000273703		"""Histones / Replication-dependent"""	4750	protein-coding gene	gene with protein product		602802	"""H2B histone family, member E"", ""histone 1, H2bm"""	H2BFE		9439656, 12408966	Standard	NM_003521		Approved	H2B/e, dJ160A22.3	uc003njo.3	Q99879	OTTHUMG00000014489	ENST00000359465.4:c.241C>T	6.37:g.27783062C>T		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	116	2	0.0172414	NM_003521	Q6NWQ3	Silent	SNP	ENST00000359465.4	37	CCDS4629.1																																																																																			.	.	none		0.597	HIST1H2BM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040157.1	NM_003521	
ZNF611	81856	hgsc.bcm.edu	37	19	53209453	53209453	+	Silent	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:53209453T>C	ENST00000319783.1	-	7	1171	c.855A>G	c.(853-855)aaA>aaG	p.K285K	ZNF611_ENST00000602162.1_Silent_p.K216K|ZNF611_ENST00000595798.1_Silent_p.K216K|ZNF611_ENST00000540744.1_Silent_p.K285K|ZNF611_ENST00000453741.2_Silent_p.K216K|ZNF611_ENST00000543227.1_Silent_p.K285K|ZNF611_ENST00000602046.1_5'Flank	NM_030972.3	NP_112234.3	Q8N823	ZN611_HUMAN	zinc finger protein 611	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|lung(12)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(262;0.0233)|GBM - Glioblastoma multiforme(134;0.04)		ACTTGTAAGGTTTCTCAACAG	0.408																																					p.K285K		Atlas-SNP	.											ZNF611,NS,carcinoma,-1,1	ZNF611	72	1	0			c.A855G						scavenged	.						180.0	171.0	174.0					19																	53209453		2203	4300	6503	SO:0001819	synonymous_variant	81856	exon7			GTAAGGTTTCTCA	AK091389	CCDS12855.1, CCDS54312.1	19q13.42	2013-01-08			ENSG00000213020	ENSG00000213020		"""Zinc fingers, C2H2-type"", ""-"""	28766	protein-coding gene	gene with protein product						12477932	Standard	NM_030972		Approved	MGC5384	uc010ydq.2	Q8N823	OTTHUMG00000154908	ENST00000319783.1:c.855A>G	19.37:g.53209453T>C		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	118	3	0.0254237	NM_030972	B3KRD5|Q69YG9	Silent	SNP	ENST00000319783.1	37	CCDS12855.1																																																																																			.	.	none		0.408	ZNF611-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337612.1	NM_030972	
PRG4	10216	hgsc.bcm.edu	37	1	186276394	186276394	+	Missense_Mutation	SNP	T	T	G	rs201070519	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:186276394T>G	ENST00000445192.2	+	7	1588	c.1543T>G	c.(1543-1545)Tca>Gca	p.S515A	PRG4_ENST00000367486.3_Missense_Mutation_p.S472A|PRG4_ENST00000367483.4_Missense_Mutation_p.S474A|PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367485.4_Missense_Mutation_p.S422A	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	515	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)	p.S515A(2)		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						CAAGGAGCCTTCACCCACCAC	0.647													-|||	7	0.00139776	0.0	0.0	5008	,	,		8157	0.0		0.003	False		,,,				2504	0.0041				p.S515A		Atlas-SNP	.											PRG4,NS,lymphoid_neoplasm,0,3	PRG4	259	3	2	Substitution - Missense(2)	upper_aerodigestive_tract(1)|skin(1)	c.T1543G						scavenged	.																																			SO:0001583	missense	10216	exon7			GAGCCTTCACCCA	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.1543T>G	1.37:g.186276394T>G	ENSP00000399679:p.Ser515Ala	Somatic	149	11	0.0738255		WXS	Illumina HiSeq	Phase_I	158	34	0.21519	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Missense_Mutation	SNP	ENST00000445192.2	37	CCDS1369.1	.	.	.	.	.	.	.	.	.	.	t	3.981	-0.006477	0.07773	.	.	ENSG00000116690	ENST00000367486;ENST00000367482;ENST00000367483;ENST00000367485;ENST00000445192	T;T;T;T	0.03801	3.83;3.92;3.8;3.9	2.44	-1.2	0.09554	.	.	.	.	.	T	0.01320	0.0043	N	0.01168	-0.975	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	0.46652	-0.9176	8	.	.	.	.	1.1497	0.01783	0.1704:0.1614:0.1814:0.4868	.	381;422;515;474	Q92954-4;Q92954-3;Q92954;Q92954-2	.;.;PRG4_HUMAN;.	A	472;381;474;422;515	ENSP00000356456:S472A;ENSP00000356453:S474A;ENSP00000356455:S422A;ENSP00000399679:S515A	.	S	+	1	0	PRG4	184543017	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.096000	0.15147	-0.472000	0.06881	-1.117000	0.02048	TCA	.	.	weak		0.647	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807	
MUC4	4585	hgsc.bcm.edu	37	3	195508903	195508903	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:195508903G>A	ENST00000463781.3	-	2	10007	c.9548C>T	c.(9547-9549)aCg>aTg	p.T3183M	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T3183M|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.T3183I(1)|p.T3183M(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGGAAGAGGCGTGGTGTCACC	0.592																																					p.T3183M		Atlas-SNP	.											MUC4_ENST00000463781,NS,malignant_melanoma,0,2	MUC4	1505	2	2	Substitution - Missense(2)	NS(2)	c.C9548T						scavenged	.						3.0	2.0	2.0					3																	195508903		442	957	1399	SO:0001583	missense	4585	exon2			AGAGGCGTGGTGT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.9548C>T	3.37:g.195508903G>A	ENSP00000417498:p.Thr3183Met	Somatic	144	4	0.0277778		WXS	Illumina HiSeq	Phase_I	149	16	0.107383	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	1.721	-0.496684	0.04291	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.38887	1.11;1.23	.	.	.	.	.	.	.	.	T	0.34395	0.0896	N	0.19112	0.55	0.09310	N	1	D	0.69078	0.997	P	0.55615	0.78	T	0.16247	-1.0409	7	.	.	.	.	4.5608	0.12160	0.0:0.4156:0.5844:0.0	.	3055	E7ESK3	.	M	3183	ENSP00000417498:T3183M;ENSP00000420243:T3183M	.	T	-	2	0	MUC4	196993682	0.001000	0.12720	0.010000	0.14722	0.010000	0.07245	0.267000	0.18552	0.073000	0.16731	0.074000	0.15403	ACG	.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SALL1	6299	hgsc.bcm.edu	37	16	51171056	51171056	+	Silent	SNP	G	G	A	rs189411650	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr16:51171056G>A	ENST00000251020.4	-	3	3975	c.3942C>T	c.(3940-3942)ttC>ttT	p.F1314F	SALL1_ENST00000566102.1_3'UTR|SALL1_ENST00000541611.1_Silent_p.F137F|SALL1_ENST00000440970.1_Silent_p.F1217F	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	1314					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)			TGTCCTCCACGAAGCGGGTGA	0.562													G|||	19	0.00379393	0.0	0.0058	5008	,	,		15436	0.0		0.0	False		,,,				2504	0.0153				p.F1314F	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											SALL1,colon,carcinoma,0,2	SALL1	301	2	0			c.C3942T						scavenged	.						66.0	57.0	60.0					16																	51171056		2198	4300	6498	SO:0001819	synonymous_variant	6299	exon3			CTCCACGAAGCGG	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.3942C>T	16.37:g.51171056G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	122	3	0.0245902	NM_002968	Q99881|Q9NSC3|Q9P1R0	Silent	SNP	ENST00000251020.4	37	CCDS10747.1																																																																																			G|0.999;A|0.001	0.001	strong		0.562	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968	
MUC6	4588	hgsc.bcm.edu	37	11	1017068	1017068	+	Silent	SNP	C	C	T	rs78992004		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:1017068C>T	ENST00000421673.2	-	31	5783	c.5733G>A	c.(5731-5733)acG>acA	p.T1911T		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1911	Approximate repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AAGTTTTGGCCGTGCTAAATG	0.552																																					p.T1911T		Atlas-SNP	.											MUC6,NS,carcinoma,-1,1	MUC6	408	1	0			c.G5733A						scavenged	.																																			SO:0001819	synonymous_variant	4588	exon31			TTTGGCCGTGCTA	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.5733G>A	11.37:g.1017068C>T		Somatic	732	80	0.10929		WXS	Illumina HiSeq	Phase_I	698	77	0.110315	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Silent	SNP	ENST00000421673.2	37	CCDS44513.1																																																																																			C|0.500;T|0.500	0.500	weak		0.552	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
BLVRB	645	hgsc.bcm.edu	37	19	40964385	40964385	+	Silent	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:40964385G>A	ENST00000263368.4	-	2	298	c.147C>T	c.(145-147)caC>caT	p.H49H	BLVRB_ENST00000595483.1_Silent_p.H49H	NM_000713.2	NP_000704.1	P30043	BLVRB_HUMAN	biliverdin reductase B (flavin reductase (NADPH))	49					heme catabolic process (GO:0042167)|porphyrin-containing compound metabolic process (GO:0006778)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	biliverdin reductase activity (GO:0004074)|riboflavin reductase (NADPH) activity (GO:0042602)			large_intestine(3)|lung(3)	6			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)		Riboflavin(DB00140)	CCACTACCACGTGGGCCGGCC	0.637																																					p.H49H		Atlas-SNP	.											.	BLVRB	12	.	0			c.C147T						PASS	.																																			SO:0001819	synonymous_variant	645	exon2			TACCACGTGGGCC	D26308	CCDS33029.1	19q13.1-q13.2	2011-09-14				ENSG00000090013	1.3.1.24, 1.5.1.30	"""Short chain dehydrogenase/reductase superfamily / Atypical members"""	1063	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 43U, member 1"""	600941	"""Flavin reductase"""	FLR		7656592, 19027726	Standard	NM_000713		Approved	SDR43U1	uc002onw.2	P30043		ENST00000263368.4:c.147C>T	19.37:g.40964385G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	92	51	0.554348	NM_000713	A6NKD8|B2R5C6|P32078|P53005|Q32LZ2	Silent	SNP	ENST00000263368.4	37	CCDS33029.1																																																																																			.	.	none		0.637	BLVRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462563.1		
ATP8B1	5205	hgsc.bcm.edu	37	18	55335757	55335757	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr18:55335757C>T	ENST00000283684.4	-	18	2112	c.2113G>A	c.(2113-2115)Gct>Act	p.A705T	RP11-35G9.3_ENST00000591854.1_RNA|RP11-35G9.3_ENST00000592201.1_RNA|ATP8B1_ENST00000536015.1_Missense_Mutation_p.A705T|RP11-35G9.5_ENST00000588925.1_RNA|RP11-35G9.3_ENST00000599199.1_RNA			O43520	AT8B1_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 1	705					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|drug transmembrane transport (GO:0006855)|inner ear receptor cell development (GO:0060119)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|phospholipid translocation (GO:0045332)|regulation of microvillus assembly (GO:0032534)|sensory perception of sound (GO:0007605)|transmembrane transport (GO:0055085)|vestibulocochlear nerve formation (GO:0021650)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|cardiolipin binding (GO:1901612)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(6)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(19)|ovary(3)|prostate(1)	53		Colorectal(73;0.229)				TCTTCAATAGCTGTAGCTCCC	0.358																																					p.A705T		Atlas-SNP	.											ATP8B1,colon,carcinoma,+2,1	ATP8B1	126	1	0			c.G2113A						scavenged	.						102.0	90.0	94.0					18																	55335757		2203	4300	6503	SO:0001583	missense	5205	exon19			CAATAGCTGTAGC	AF038007	CCDS11965.1	18q21	2010-04-28	2010-04-28		ENSG00000081923	ENSG00000081923		"""ATPases / P-type"""	3706	protein-coding gene	gene with protein product		602397	"""ATPase, Class I, type 8B, member 1"", ""ATPase, class I, type 8B, member 1"""	FIC1, BRIC, PFIC1		9500542, 7655458	Standard	NM_005603		Approved	ATPIC, PFIC	uc002lgw.3	O43520	OTTHUMG00000132739	ENST00000283684.4:c.2113G>A	18.37:g.55335757C>T	ENSP00000283684:p.Ala705Thr	Somatic	116	1	0.00862069		WXS	Illumina HiSeq	Phase_I	110	3	0.0272727	NM_005603	Q9BTP8	Missense_Mutation	SNP	ENST00000283684.4	37	CCDS11965.1	.	.	.	.	.	.	.	.	.	.	C	34	5.358141	0.95854	.	.	ENSG00000081923	ENST00000283684;ENST00000536015	T;T	0.73469	-0.75;-0.75	5.89	5.89	0.94794	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.000000	0.85682	D	0.000000	D	0.92652	0.7665	H	0.98849	4.35	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95003	0.8145	10	0.87932	D	0	.	19.8478	0.96722	0.0:1.0:0.0:0.0	.	705	O43520	AT8B1_HUMAN	T	705	ENSP00000283684:A705T;ENSP00000445359:A705T	ENSP00000283684:A705T	A	-	1	0	ATP8B1	53486755	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.754000	0.85163	2.788000	0.95919	0.557000	0.71058	GCT	.	.	none		0.358	ATP8B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256097.1	NM_005603	
ENTPD6	955	hgsc.bcm.edu	37	20	25199209	25199209	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr20:25199209C>T	ENST00000376652.4	+	10	1065	c.902C>T	c.(901-903)tCg>tTg	p.S301L	ENTPD6_ENST00000433259.2_Missense_Mutation_p.S301L|ENTPD6_ENST00000354989.5_Missense_Mutation_p.S284L|ENTPD6_ENST00000360031.2_Missense_Mutation_p.S300L			O75354	ENTP6_HUMAN	ectonucleoside triphosphate diphosphohydrolase 6 (putative)	301					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						GGGCTGATGTCGGCACGCCTG	0.652																																					p.S301L		Atlas-SNP	.											ENTPD6,NS,carcinoma,0,1	ENTPD6	57	1	0			c.C902T						scavenged	.						44.0	35.0	38.0					20																	25199209		2202	4300	6502	SO:0001583	missense	955	exon10			TGATGTCGGCACG	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.902C>T	20.37:g.25199209C>T	ENSP00000365840:p.Ser301Leu	Somatic	152	1	0.00657895		WXS	Illumina HiSeq	Phase_I	167	3	0.0179641	NM_001247	A6NCX6|D3DW49|Q5QPJ2|Q5QPJ5|Q7Z5B5|Q8N3H3|Q8TAS7|Q9UJD1	Missense_Mutation	SNP	ENST00000376652.4	37	CCDS13170.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.3|22.3	4.275057|4.275057	0.80580|0.80580	.|.	.|.	ENSG00000197586|ENSG00000197586	ENST00000433417;ENST00000447877|ENST00000354989;ENST00000360031;ENST00000525986;ENST00000376641;ENST00000376652;ENST00000439162;ENST00000433259;ENST00000425813	.|T;T;T;T;T;T	.|0.12039	.|2.72;2.72;2.72;2.72;2.72;2.72	5.28|5.28	4.34|4.34	0.51931|0.51931	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.37183|0.37183	0.0994|0.0994	M|M	0.78637|0.78637	2.42|2.42	0.58432|0.58432	D|D	0.999999|0.999999	.|D;P;P;P;D;P;P;D;D	.|0.89917	.|0.998;0.95;0.95;0.95;0.976;0.839;0.933;1.0;1.0	.|P;B;P;P;P;B;P;D;D	.|0.85130	.|0.889;0.362;0.459;0.564;0.642;0.289;0.642;0.997;0.997	T|T	0.18085|0.18085	-1.0348|-1.0348	5|10	.|0.56958	.|D	.|0.05	-13.1173|-13.1173	12.5621|12.5621	0.56288|0.56288	0.0:0.9188:0.0:0.0812|0.0:0.9188:0.0:0.0812	.|.	.|83;283;301;301;301;284;300;300;301	.|B4DHS2;B4DDM7;B4DNK6;E7EP89;Q5QPI9;O75354-2;D3DW49;Q5QPJ2;O75354	.|.;.;.;.;.;.;.;.;ENTP6_HUMAN	W|L	222;194|284;300;221;197;301;283;301;253	.|ENSP00000347084:S284L;ENSP00000353131:S300L;ENSP00000365840:S301L;ENSP00000408098:S283L;ENSP00000401895:S301L;ENSP00000390646:S253L	.|ENSP00000347084:S284L	R|S	+|+	1|2	2|0	ENTPD6|ENTPD6	25147209|25147209	1.000000|1.000000	0.71417|0.71417	0.844000|0.844000	0.33320|0.33320	0.840000|0.840000	0.47671|0.47671	5.946000|5.946000	0.70234|0.70234	1.242000|1.242000	0.43836|0.43836	0.462000|0.462000	0.41574|0.41574	CGG|TCG	.	.	none		0.652	ENTPD6-020	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078414.2		
NCOA6	23054	hgsc.bcm.edu	37	20	33345744	33345744	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr20:33345744C>T	ENST00000374796.2	-	8	3377	c.807G>A	c.(805-807)caG>caA	p.Q269Q	NCOA6_ENST00000359003.2_Silent_p.Q269Q			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	269	CREBBP-binding region.|Gln-rich.|NCOA1-binding region.|TBP/GTF2A-binding region.				brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.Q269Q(15)		NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						gctgctgctgctgttgttgtt	0.537																																					p.Q269Q		Atlas-SNP	.											NCOA6,NS,carcinoma,0,18	NCOA6	219	18	15	Substitution - coding silent(15)	lung(5)|prostate(4)|endometrium(3)|central_nervous_system(1)|urinary_tract(1)|kidney(1)	c.G807A						scavenged	.						64.0	52.0	56.0					20																	33345744		2203	4300	6503	SO:0001819	synonymous_variant	23054	exon7			CTGCTGCTGTTGT	AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"""nuclear receptor coactivator RAP250"", ""activating signal cointegrator-2"", ""peroxisome proliferator-activated receptor interacting protein"""	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.807G>A	20.37:g.33345744C>T		Somatic	97	1	0.0103093		WXS	Illumina HiSeq	Phase_I	134	4	0.0298507	NM_014071	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Silent	SNP	ENST00000374796.2	37	CCDS13241.1																																																																																			.	.	none		0.537	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071	
PCDHB4	56131	hgsc.bcm.edu	37	5	140503797	140503797	+	Silent	SNP	C	C	T	rs561916518		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:140503797C>T	ENST00000194152.1	+	1	2217	c.2217C>T	c.(2215-2217)agC>agT	p.S739S		NM_018938.2	NP_061761.1	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4	739					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)			TGGACGTAAGCGGCACCGGGA	0.622													C|||	1	0.000199681	0.0	0.0	5008	,	,		14549	0.0		0.001	False		,,,				2504	0.0				p.S739S		Atlas-SNP	.											.	PCDHB4	177	.	0			c.C2217T						PASS	.						84.0	96.0	92.0					5																	140503797		2203	4300	6503	SO:0001819	synonymous_variant	56131	exon1			CGTAAGCGGCACC	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.2217C>T	5.37:g.140503797C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	81	4	0.0493827	NM_018938	Q4V761	Silent	SNP	ENST00000194152.1	37	CCDS4246.1																																																																																			.	.	none		0.622	PCDHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251812.2	NM_018938	
EBLN1	340900	hgsc.bcm.edu	37	10	22498749	22498749	+	Missense_Mutation	SNP	A	A	T	rs2478476	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr10:22498749A>T	ENST00000422359.2	-	1	201	c.164T>A	c.(163-165)gTc>gAc	p.V55D		NM_001199938.1	NP_001186867.1	P0CF75	EBLN1_HUMAN	endogenous Bornavirus-like nucleoprotein 1	55																	TTTTTCAATGACCTTAACATC	0.418													T|||	5002	0.998802	0.9992	0.9957	5008	,	,		18594	1.0		0.998	False		,,,				2504	1.0				p.V55D		Atlas-SNP	.											.	.	.	.	0			c.T164A						PASS	.																																			SO:0001583	missense	340900	exon1			TCAATGACCTTAA	AA813437	CCDS60498.1	10p12.31	2013-01-30			ENSG00000223601	ENSG00000223601			39430	protein-coding gene	gene with protein product	"""endogenous Borna-like N element 1"""	613249				20054395, 20686665	Standard	NM_001199938		Approved		uc021pob.1	P0CF75	OTTHUMG00000017801	ENST00000422359.2:c.164T>A	10.37:g.22498749A>T	ENSP00000473842:p.Val55Asp	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_001199938	S4R316	Missense_Mutation	SNP	ENST00000422359.2	37																																																																																				A|0.001;T|0.999	0.999	strong		0.418	EBLN1-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047154.3	NM_001199938	
CCDC87	55231	hgsc.bcm.edu	37	11	66359191	66359191	+	Silent	SNP	A	A	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:66359191A>T	ENST00000333861.3	-	1	1363	c.1296T>A	c.(1294-1296)acT>acA	p.T432T	CCS_ENST00000533244.1_5'Flank|CCS_ENST00000310190.4_5'Flank	NM_018219.2	NP_060689.2	Q9NVE4	CCD87_HUMAN	coiled-coil domain containing 87	432					cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)					central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28						TAAGCTTCAAAGTAATGGTCA	0.552																																					p.T432T		Atlas-SNP	.											.	CCDC87	83	.	0			c.T1296A						PASS	.						38.0	43.0	41.0					11																	66359191		2200	4295	6495	SO:0001819	synonymous_variant	55231	exon1			CTTCAAAGTAATG	BC034469	CCDS8145.1	11q13.2	2006-03-15			ENSG00000182791	ENSG00000182791			25579	protein-coding gene	gene with protein product						12477932	Standard	NM_018219		Approved	FLJ10786	uc001oiq.4	Q9NVE4	OTTHUMG00000167237	ENST00000333861.3:c.1296T>A	11.37:g.66359191A>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	75	25	0.333333	NM_018219	Q8NE76	Silent	SNP	ENST00000333861.3	37	CCDS8145.1																																																																																			.	.	none		0.552	CCDC87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393825.1	NM_018219	
REL	5966	hgsc.bcm.edu	37	2	61147230	61147230	+	Missense_Mutation	SNP	T	T	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:61147230T>A	ENST00000295025.8	+	8	1228	c.908T>A	c.(907-909)cTg>cAg	p.L303Q	REL_ENST00000394479.3_Missense_Mutation_p.L303Q	NM_002908.2	NP_002899.1	Q04864	REL_HUMAN	v-rel avian reticuloendotheliosis viral oncogene homolog	303					cytokine production (GO:0001816)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of neuron death (GO:1901215)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|large_intestine(5)|lung(3)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	16	all_hematologic(2;0.0797)	Ovarian(717;0.0728)	LUSC - Lung squamous cell carcinoma(5;6.2e-08)|Lung(5;1.65e-06)|Epithelial(17;0.064)|all cancers(80;0.221)			TTCCAGAAACTGTGCCAGGAT	0.289			A		Hodgkin Lymphoma																																p.L303Q		Atlas-SNP	.		Dom	yes		2	2p13-p12	5966	v-rel reticuloendotheliosis viral oncogene homolog (avian)		L	.	REL	48	.	0			c.T908A						PASS	.						79.0	80.0	80.0					2																	61147230		2203	4300	6503	SO:0001583	missense	5966	exon8			AGAAACTGTGCCA	M11595	CCDS1864.1, CCDS74515.1	2p13-p12	2013-07-09	2013-07-09		ENSG00000162924	ENSG00000162924			9954	protein-coding gene	gene with protein product		164910				1577270	Standard	XM_005264470		Approved	I-Rel, c-Rel	uc002sam.1	Q04864	OTTHUMG00000129418	ENST00000295025.8:c.908T>A	2.37:g.61147230T>A	ENSP00000295025:p.Leu303Gln	Somatic	403	0	0		WXS	Illumina HiSeq	Phase_I	444	163	0.367117	NM_002908	Q17RU2|Q2PNZ7|Q6LDY0	Missense_Mutation	SNP	ENST00000295025.8	37	CCDS1864.1	.	.	.	.	.	.	.	.	.	.	T	16.67	3.188258	0.57909	.	.	ENSG00000162924	ENST00000295025;ENST00000394479	T;T	0.48522	0.81;0.81	5.49	5.49	0.81192	Immunoglobulin E-set (1);	0.423339	0.21659	N	0.071053	T	0.63319	0.2501	L	0.59436	1.845	0.42356	D	0.992391	D;D	0.89917	0.999;1.0	D;D	0.71184	0.956;0.972	T	0.63427	-0.6640	10	0.46703	T	0.11	-42.4869	13.2498	0.60045	0.0:0.0:0.0:1.0	.	303;303	Q17RU2;Q04864	.;REL_HUMAN	Q	303	ENSP00000295025:L303Q;ENSP00000377989:L303Q	ENSP00000295025:L303Q	L	+	2	0	REL	61000734	0.935000	0.31712	0.991000	0.47740	0.502000	0.33828	4.438000	0.59961	2.213000	0.71641	0.397000	0.26171	CTG	.	.	none		0.289	REL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251576.3	NM_002908	
NEUROD1	4760	hgsc.bcm.edu	37	2	182543437	182543437	+	Missense_Mutation	SNP	C	C	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:182543437C>A	ENST00000295108.3	-	2	608	c.151G>T	c.(151-153)Gac>Tac	p.D51Y	CERKL_ENST00000479558.1_Intron|NEUROD1_ENST00000496876.1_Intron	NM_002500.4	NP_002491.2	Q13562	NDF1_HUMAN	neuronal differentiation 1	51					amacrine cell differentiation (GO:0035881)|anterior/posterior pattern specification (GO:0009952)|cellular response to glucose stimulus (GO:0071333)|cerebellum development (GO:0021549)|dentate gyrus development (GO:0021542)|embryonic organ morphogenesis (GO:0048562)|endocrine pancreas development (GO:0031018)|enteroendocrine cell differentiation (GO:0035883)|glucose homeostasis (GO:0042593)|inner ear development (GO:0048839)|insulin secretion (GO:0030073)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neurogenesis (GO:0022008)|nitric oxide mediated signal transduction (GO:0007263)|nucleocytoplasmic transport (GO:0006913)|pancreatic A cell fate commitment (GO:0003326)|pancreatic PP cell fate commitment (GO:0003329)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell differentiation (GO:0045597)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle arrest (GO:0071156)|regulation of insulin secretion (GO:0050796)|regulation of intestinal epithelial structure maintenance (GO:0060730)|response to drug (GO:0042493)|response to glucose (GO:0009749)|signal transduction involved in regulation of gene expression (GO:0023019)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|protein heterodimerization activity (GO:0046982)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.D51Y(1)		endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25			OV - Ovarian serous cystadenocarcinoma(117;0.088)			CTCAGTGAGTCCTCCTCTGCG	0.562																																					p.D51Y		Atlas-SNP	.											NEUROD1,NS,carcinoma,0,1	NEUROD1	67	1	1	Substitution - Missense(1)	lung(1)	c.G151T						PASS	.						133.0	103.0	113.0					2																	182543437		2203	4300	6503	SO:0001583	missense	4760	exon2			GTGAGTCCTCCTC	U50823	CCDS2283.1	2q32	2013-05-21	2012-02-22		ENSG00000162992	ENSG00000162992		"""Basic helix-loop-helix proteins"""	7762	protein-coding gene	gene with protein product	"""beta-cell E-box transactivator 2"", ""neurogenic helix-loop-helix protein NEUROD"""	601724	"""neurogenic differentiation 1"""	NEUROD		7754368, 8786144	Standard	NM_002500		Approved	BETA2, BHF-1, NeuroD, bHLHa3, MODY6	uc002uof.4	Q13562	OTTHUMG00000132583	ENST00000295108.3:c.151G>T	2.37:g.182543437C>A	ENSP00000295108:p.Asp51Tyr	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	187	70	0.374332	NM_002500	B2R9I8|F1T0E1|O00343|Q13340|Q5U095|Q96TH0|Q99455|Q9UEC8	Missense_Mutation	SNP	ENST00000295108.3	37	CCDS2283.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.070590	0.76301	.	.	ENSG00000162992	ENST00000295108	D	0.95588	-3.75	5.9	5.9	0.94986	.	0.281498	0.32503	N	0.006008	D	0.91885	0.7431	L	0.40543	1.245	0.58432	D	0.999998	P	0.49090	0.919	B	0.34779	0.189	D	0.92806	0.6260	10	0.62326	D	0.03	-0.0043	17.7728	0.88497	0.0:1.0:0.0:0.0	.	51	Q13562	NDF1_HUMAN	Y	51	ENSP00000295108:D51Y	ENSP00000295108:D51Y	D	-	1	0	NEUROD1	182251682	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	2.332000	0.43903	2.788000	0.95919	0.650000	0.86243	GAC	.	.	none		0.562	NEUROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255792.2	NM_002500	
GLTSCR1L	23506	hgsc.bcm.edu	37	6	42797411	42797411	+	Missense_Mutation	SNP	A	A	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr6:42797411A>T	ENST00000314073.5	+	6	1516	c.1340A>T	c.(1339-1341)aAc>aTc	p.N447I	GLTSCR1L_ENST00000394168.1_Missense_Mutation_p.N447I			Q6AI39	GSC1L_HUMAN	GLTSCR1-like	447																	TTGAACAGAAACTCTTCCAAC	0.478																																					p.N447I		Atlas-SNP	.											KIAA0240,NS,carcinoma,-1,1	.	.	1	0			c.A1340T						PASS	.						179.0	175.0	177.0					6																	42797411		2203	4300	6503	SO:0001583	missense	23506	exon5			ACAGAAACTCTTC	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.1340A>T	6.37:g.42797411A>T	ENSP00000313933:p.Asn447Ile	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	89	46	0.516854	NM_015349	A1L3W2|Q5TFZ3|Q92514	Missense_Mutation	SNP	ENST00000314073.5	37	CCDS34451.1	.	.	.	.	.	.	.	.	.	.	A	14.07	2.424540	0.43020	.	.	ENSG00000112624	ENST00000394167;ENST00000536004;ENST00000314073;ENST00000394168	T;T	0.48836	0.8;0.8	5.87	0.737	0.18314	.	0.368457	0.28730	N	0.014329	T	0.18635	0.0447	L	0.44542	1.39	0.40580	D	0.981383	B;P;P	0.40834	0.226;0.631;0.73	B;B;B	0.37304	0.176;0.165;0.246	T	0.02391	-1.1166	10	0.41790	T	0.15	-5.3689	6.926	0.24416	0.6928:0.1162:0.191:0.0	.	447;447;447	F5H616;Q6AI39;B7Z2G7	.;K0240_HUMAN;.	I	447	ENSP00000313933:N447I;ENSP00000377723:N447I	ENSP00000313933:N447I	N	+	2	0	KIAA0240	42905389	0.975000	0.34042	0.824000	0.32777	0.974000	0.67602	1.117000	0.31234	0.190000	0.20209	0.533000	0.62120	AAC	.	.	none		0.478	GLTSCR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040562.3	NM_015349	
SDHA	6389	hgsc.bcm.edu	37	5	236617	236617	+	Silent	SNP	G	G	T	rs200223188	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	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	317	4	0.0126183		WXS	Illumina HiSeq	Phase_I	443	6	0.013544	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	
ANKHD1	54882	hgsc.bcm.edu	37	5	139917069	139917069	+	Nonsense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:139917069C>T	ENST00000360839.2	+	31	7277	c.7123C>T	c.(7123-7125)Cga>Tga	p.R2375*	ANKHD1_ENST00000297183.6_Nonsense_Mutation_p.R2375*|ANKHD1-EIF4EBP3_ENST00000532219.1_Nonsense_Mutation_p.R2375*|ANKHD1_ENST00000544120.1_Nonsense_Mutation_p.R699*	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	2375						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)			GAGACTGGCCCGAATTCGGCA	0.552																																					p.R2375X		Atlas-SNP	.											.	ANKHD1	233	.	0			c.C7123T						PASS	.						98.0	92.0	94.0					5																	139917069		2203	4300	6503	SO:0001587	stop_gained	54882	exon31			CTGGCCCGAATTC	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.7123C>T	5.37:g.139917069C>T	ENSP00000354085:p.Arg2375*	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	162	65	0.401235	NM_017747	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Nonsense_Mutation	SNP	ENST00000360839.2	37	CCDS4225.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	39|39	7.365931|7.365931	0.98238|0.98238	.|.	.|.	ENSG00000131503|ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000254996;ENSG00000254996	ENST00000435794;ENST00000432301|ENST00000360839;ENST00000297183;ENST00000253810;ENST00000431508;ENST00000433049;ENST00000544120;ENST00000532219;ENST00000437495	.|.	.|.	.|.	6.08|6.08	5.19|5.19	0.71726|0.71726	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.36991|.	0.0987|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.35748|.	-0.9776|.	3|.	.|0.02654	.|T	.|1	.|.	14.9548|14.9548	0.71104|0.71104	0.2808:0.7192:0.0:0.0|0.2808:0.7192:0.0:0.0	.|.	.|.	.|.	.|.	L|X	865;766|2375;2375;2392;1048;914;699;2375;403	.|.	.|ENSP00000396882:R403X	P|R	+|+	2|1	0|2	ANKHD1|ANKHD1-EIF4EBP3;ANKHD1	139897253|139897253	0.993000|0.993000	0.37304|0.37304	0.999000|0.999000	0.59377|0.59377	0.992000|0.992000	0.81027|0.81027	3.195000|3.195000	0.51013|0.51013	1.523000|1.523000	0.49018|0.49018	0.591000|0.591000	0.81541|0.81541	CCG|CGA	.	.	none		0.552	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747	
TRIM68	55128	hgsc.bcm.edu	37	11	4621978	4621978	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:4621978T>C	ENST00000300747.5	-	7	1275	c.986A>G	c.(985-987)gAc>gGc	p.D329G		NM_018073.6	NP_060543.5	Q6AZZ1	TRI68_HUMAN	tripartite motif containing 68	329	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				protein autoubiquitination (GO:0051865)|regulation of androgen receptor signaling pathway (GO:0060765)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|histone acetyltransferase binding (GO:0035035)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(4)|ovary(1)|urinary_tract(1)	15		Medulloblastoma(188;0.0025)|Breast(177;0.0101)|all_neural(188;0.0227)		Epithelial(150;9.49e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0288)|LUSC - Lung squamous cell carcinoma(625;0.192)		CTGGTTGGTGTCTCCATAGTG	0.512																																					p.D329G		Atlas-SNP	.											TRIM68,NS,carcinoma,-1,1	TRIM68	53	1	0			c.A986G						scavenged	.						86.0	82.0	83.0					11																	4621978		2201	4298	6499	SO:0001583	missense	55128	exon7			TTGGTGTCTCCAT	AF360739	CCDS31356.1	11p15.4	2013-01-09	2011-01-25	2004-11-17		ENSG00000167333		"""RING-type (C3HC4) zinc fingers"", ""Tripartite motif containing / Tripartite motif containing"""	21161	protein-coding gene	gene with protein product		613184	"""ring finger protein 137"", ""tripartite motif-containing 68"""	RNF137		11597395	Standard	NM_018073		Approved	SS-56, FLJ10369	uc001lzf.2	Q6AZZ1		ENST00000300747.5:c.986A>G	11.37:g.4621978T>C	ENSP00000300747:p.Asp329Gly	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	202	3	0.0148515	NM_018073	A6NI19|A8K551|B3KPM5|B4DVK4|Q8WZ70|Q96LE5|Q96PF7|Q9H9C2|Q9NW18	Missense_Mutation	SNP	ENST00000300747.5	37	CCDS31356.1	.	.	.	.	.	.	.	.	.	.	T	13.11	2.139312	0.37728	.	.	ENSG00000167333	ENST00000300747;ENST00000544055;ENST00000526337	T;T	0.09817	2.94;2.94	5.52	2.96	0.34315	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);Butyrophylin-like (1);B30.2/SPRY domain (1);	0.239376	0.29767	N	0.011248	T	0.06050	0.0157	N	0.13352	0.335	0.29898	N	0.824659	B	0.15473	0.013	B	0.20184	0.028	T	0.26326	-1.0106	10	0.21014	T	0.42	.	8.9462	0.35760	0.2957:0.0:0.0:0.7043	.	329	Q6AZZ1	TRI68_HUMAN	G	329;50;106	ENSP00000300747:D329G;ENSP00000434681:D106G	ENSP00000300747:D329G	D	-	2	0	TRIM68	4578554	0.843000	0.29541	1.000000	0.80357	0.965000	0.64279	1.873000	0.39558	0.985000	0.38656	0.459000	0.35465	GAC	.	.	none		0.512	TRIM68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385948.1	NM_018073	
SLC25A17	10478	hgsc.bcm.edu	37	22	41188619	41188619	+	Missense_Mutation	SNP	A	A	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr22:41188619A>C	ENST00000435456.2	-	4	377	c.244T>G	c.(244-246)Tat>Gat	p.Y82D	SLC25A17_ENST00000542412.1_Intron|SLC25A17_ENST00000491545.1_5'UTR|SLC25A17_ENST00000544408.1_Missense_Mutation_p.Y45D	NM_006358.2	NP_006349.1	O43808	PM34_HUMAN	solute carrier family 25 (mitochondrial carrier; peroxisomal membrane protein, 34kDa), member 17	82	Necessary for targeting to peroxisomes and interaction with PEX19.				ADP transport (GO:0015866)|AMP transport (GO:0080121)|ATP transport (GO:0015867)|cellular lipid metabolic process (GO:0044255)|coenzyme A transmembrane transport (GO:0035349)|FAD transmembrane transport (GO:0035350)|fatty acid alpha-oxidation (GO:0001561)|fatty acid beta-oxidation (GO:0006635)|fatty acid transport (GO:0015908)|NAD transport (GO:0043132)|nucleotide transmembrane transport (GO:1901679)|small molecule metabolic process (GO:0044281)	integral component of peroxisomal membrane (GO:0005779)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ADP transmembrane transporter activity (GO:0015217)|AMP transmembrane transporter activity (GO:0080122)|ATP transmembrane transporter activity (GO:0005347)|chaperone binding (GO:0051087)|coenzyme A transmembrane transporter activity (GO:0015228)|FAD transmembrane transporter activity (GO:0015230)|FMN transmembrane transporter activity (GO:0044610)|NAD transporter activity (GO:0051724)			central_nervous_system(1)|large_intestine(4)|lung(2)|skin(1)	8						gtgtagaaatagacaaaattg	0.433																																					p.Y82D		Atlas-SNP	.											.	SLC25A17	25	.	0			c.T244G						PASS	.						75.0	73.0	74.0					22																	41188619		2203	4300	6503	SO:0001583	missense	10478	exon4			AGAAATAGACAAA	Y12860	CCDS14005.1, CCDS74868.1	22q13.2	2013-05-22	2002-08-29		ENSG00000100372	ENSG00000100372		"""Solute carriers"""	10987	protein-coding gene	gene with protein product	"""peroxisomal membrane protein (34kD)"""	606795	"""solute carrier family 25 (mitochondrial carrier; peroxisomal membrane protein, 34kD), member 17"""			9874197	Standard	NM_006358		Approved	PMP34	uc003azc.3	O43808	OTTHUMG00000151139	ENST00000435456.2:c.244T>G	22.37:g.41188619A>C	ENSP00000390722:p.Tyr82Asp	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	161	38	0.236025	NM_006358	A8KA59|Q5TFL0|Q9UGW8|Q9UGY7	Missense_Mutation	SNP	ENST00000435456.2	37	CCDS14005.1	.	.	.	.	.	.	.	.	.	.	A	8.423	0.846912	0.17034	.	.	ENSG00000100372	ENST00000435456;ENST00000544408;ENST00000434185	T;T;T	0.80123	-1.34;-1.34;-1.34	1.83	1.83	0.25207	Mitochondrial carrier domain (2);	0.065605	0.64402	D	0.000006	D	0.89705	0.6792	M	0.93241	3.395	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.83275	0.995;0.996	D	0.88155	0.2853	10	0.72032	D	0.01	-27.4517	5.7627	0.18209	1.0:0.0:0.0:0.0	.	45;82	B4DU97;O43808	.;PM34_HUMAN	D	82;45;65	ENSP00000390722:Y82D;ENSP00000438355:Y45D;ENSP00000404200:Y65D	ENSP00000394539:Y82D	Y	-	1	0	SLC25A17	39518565	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.290000	0.43531	1.108000	0.41662	0.327000	0.21459	TAT	.	.	none		0.433	SLC25A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321487.1	NM_006358	
PRKD1	5587	hgsc.bcm.edu	37	14	30046446	30046446	+	Nonstop_Mutation	SNP	A	A	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr14:30046446A>T	ENST00000331968.5	-	18	2966	c.2737T>A	c.(2737-2739)Tga>Aga	p.*913R	PRKD1_ENST00000415220.2_Nonstop_Mutation_p.*921R	NM_002742.2	NP_002733.2	Q15139	KPCD1_HUMAN	protein kinase D1	0					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular response to oxidative stress (GO:0034599)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|negative regulation of cell death (GO:0060548)|negative regulation of endocytosis (GO:0045806)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein autophosphorylation (GO:0046777)|regulation of integrin-mediated signaling pathway (GO:2001044)|regulation of keratinocyte proliferation (GO:0010837)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|lung(32)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	78	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)		GATGGAACTCAGAGGATGCTG	0.443																																					p.X913R		Atlas-SNP	.											.	PRKD1	316	.	0			c.T2737A						PASS	.						99.0	87.0	91.0					14																	30046446		2203	4300	6503	SO:0001578	stop_lost	5587	exon18			GAACTCAGAGGAT		CCDS9637.1	14q11	2013-01-10	2004-10-28	2004-10-30	ENSG00000184304	ENSG00000184304	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	9407	protein-coding gene	gene with protein product		605435	"""protein kinase C, mu"""	PRKCM		8119958, 10965134	Standard	NM_002742		Approved	PKCM, PKD, PKC-mu	uc001wqh.3	Q15139	OTTHUMG00000140203	ENST00000331968.5:c.2737T>A	14.37:g.30046446A>T		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	205	49	0.239024	NM_002742	A6NL64|B2RAF6	Missense_Mutation	SNP	ENST00000331968.5	37	CCDS9637.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.076302	0.76415	.	.	ENSG00000184304	ENST00000331968;ENST00000415220	.	.	.	6.03	6.03	0.97812	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.5582	0.84512	1.0:0.0:0.0:0.0	.	.	.	.	R	913;921	.	.	X	-	1	0	PRKD1	29116197	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.300000	0.96151	2.308000	0.77769	0.533000	0.62120	TGA	.	.	none		0.443	PRKD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276611.2	NM_002742	
IDNK	414328	hgsc.bcm.edu	37	9	86258428	86258428	+	Silent	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr9:86258428T>C	ENST00000376419.4	+	5	301	c.297T>C	c.(295-297)gaT>gaC	p.D99D	IDNK_ENST00000277124.8_Silent_p.D53D|IDNK_ENST00000405990.3_3'UTR|IDNK_ENST00000376417.4_Missense_Mutation_p.W85R|IDNK_ENST00000454393.1_Silent_p.D142D	NM_001001551.3	NP_001001551.2	Q5T6J7	GNTK_HUMAN	idnK, gluconokinase homolog (E. coli)	99					D-gluconate catabolic process (GO:0046177)		ATP binding (GO:0005524)|gluconokinase activity (GO:0046316)										AAGGAAAAGATGGTGTAGCTC	0.493																																					p.D99D		Atlas-SNP	.											C9orf103,colon,carcinoma,+2,1	.	.	1	0			c.T297C						PASS	.						80.0	80.0	80.0					9																	86258428		2203	4300	6503	SO:0001819	synonymous_variant	414328	exon5			AAAAGATGGTGTA	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.297T>C	9.37:g.86258428T>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	152	31	0.203947	NM_001001551	A5PLN6|Q5T6J6	Silent	SNP	ENST00000376419.4	37	CCDS35048.2	.	.	.	.	.	.	.	.	.	.	T	6.660	0.490211	0.12702	.	.	ENSG00000148057	ENST00000376417	.	.	.	5.53	-7.14	0.01527	.	.	.	.	.	T	0.24547	0.0595	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.39354	-0.9618	5	0.87932	D	0	-7.5855	1.0152	0.01505	0.2267:0.2169:0.3482:0.2082	.	.	.	.	R	85	.	ENSP00000365599:W85R	W	+	1	0	C9orf103	85448248	0.000000	0.05858	0.000000	0.03702	0.121000	0.20230	-0.065000	0.11617	-1.401000	0.02058	-1.262000	0.01453	TGG	.	.	none		0.493	IDNK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052837.2	NM_001001551	
PON3	5446	hgsc.bcm.edu	37	7	95025645	95025645	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr7:95025645C>T	ENST00000265627.5	-	1	28	c.18G>A	c.(16-18)gcG>gcA	p.A6A	PON3_ENST00000475439.1_5'Flank|PON3_ENST00000451904.1_Silent_p.A6A|PON1_ENST00000542556.1_Silent_p.A6A|PON3_ENST00000427422.1_Silent_p.A6A	NM_000940.2	NP_000931.1	Q15166	PON3_HUMAN	paraoxonase 3	6					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)	GCAGGACCAGCGCCACGAGCT	0.672																																					p.A6A		Atlas-SNP	.											PON3,NS,carcinoma,-1,1	PON3	59	1	0			c.G18A						PASS	.						97.0	87.0	91.0					7																	95025645		2203	4300	6503	SO:0001819	synonymous_variant	5446	exon1			GACCAGCGCCACG	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.18G>A	7.37:g.95025645C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	47	9	0.191489	NM_000940	A4D1H8|O75855|O76060|Q6IRU9|Q8IX97|Q9BZH9	Silent	SNP	ENST00000265627.5	37	CCDS5639.1																																																																																			.	.	none		0.672	PON3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333007.1	NM_000940	
CMYA5	202333	hgsc.bcm.edu	37	5	79032516	79032516	+	Missense_Mutation	SNP	G	G	A	rs368525698		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:79032516G>A	ENST00000446378.2	+	2	7959	c.7928G>A	c.(7927-7929)cGt>cAt	p.R2643H		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2643					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)		CTTTCTTGTCGTGATGAAATA	0.408																																					p.R2643H		Atlas-SNP	.											CMYA5_ENST00000446378,caecum,carcinoma,+1,2	CMYA5	643	2	0			c.G7928A						scavenged	.	G	HIS/ARG	2,3622		0,2,1810	50.0	51.0	51.0		7928	-7.2	0.0	5		51	0,8166		0,0,4083	no	missense	CMYA5	NM_153610.3	29	0,2,5893	AA,AG,GG		0.0,0.0552,0.017	benign	2643/4070	79032516	2,11788	1812	4083	5895	SO:0001583	missense	202333	exon2			CTTGTCGTGATGA	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.7928G>A	5.37:g.79032516G>A	ENSP00000394770:p.Arg2643His	Somatic	123	1	0.00813008		WXS	Illumina HiSeq	Phase_I	142	5	0.0352113	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	.	.	.	.	.	.	.	.	.	.	G	9.478	1.097445	0.20552	5.52E-4	0.0	ENSG00000164309	ENST00000446378	T	0.42900	0.96	3.62	-7.25	0.01470	.	.	.	.	.	T	0.16599	0.0399	N	0.11201	0.11	0.09310	N	1	B	0.16396	0.017	B	0.08055	0.003	T	0.23797	-1.0178	9	0.17369	T	0.5	.	6.3433	0.21335	0.5344:0.2466:0.219:0.0	.	2643	Q8N3K9	CMYA5_HUMAN	H	2643	ENSP00000394770:R2643H	ENSP00000394770:R2643H	R	+	2	0	CMYA5	79068272	0.000000	0.05858	0.000000	0.03702	0.318000	0.28184	-1.953000	0.01526	-1.518000	0.01778	-0.515000	0.04445	CGT	.	.	weak		0.408	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
MUC4	4585	hgsc.bcm.edu	37	3	195506387	195506387	+	Missense_Mutation	SNP	G	G	T	rs201542091	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:195506387G>T	ENST00000463781.3	-	2	12523	c.12064C>A	c.(12064-12066)Cct>Act	p.P4022T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P4022T|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.P4022T(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)		GCTGAGGAAGGGCTGGTGACA	0.582													.|||	113	0.0225639	0.0189	0.0159	5008	,	,		11226	0.0089		0.0447	False		,,,				2504	0.0235				p.P4022T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	1	Substitution - Missense(1)	endometrium(1)	c.C12064A						scavenged	.						19.0	15.0	16.0					3																	195506387		649	1304	1953	SO:0001583	missense	4585	exon2			AGGAAGGGCTGGT	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.12064C>A	3.37:g.195506387G>T	ENSP00000417498:p.Pro4022Thr	Somatic	23	6	0.26087		WXS	Illumina HiSeq	Phase_I	37	13	0.351351	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	2.915	-0.224485	0.06061	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29655	1.56;1.56	.	.	.	.	0.000000	0.25517	N	0.030134	T	0.14700	0.0355	N	0.14661	0.345	0.09310	N	1	D	0.55385	0.971	P	0.46026	0.501	T	0.33007	-0.9885	8	.	.	.	.	6.041	0.19734	0.0:0.6792:0.3208:0.0	.	3894	E7ESK3	.	T	4022	ENSP00000417498:P4022T;ENSP00000420243:P4022T	.	P	-	1	0	MUC4	196991166	0.004000	0.15560	0.000000	0.03702	0.004000	0.04260	-2.457000	0.01001	-2.083000	0.00867	-2.366000	0.00237	CCT	.	.	weak		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PRAMEF2	65122	hgsc.bcm.edu	37	1	12921387	12921387	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:12921387C>T	ENST00000240189.2	+	4	1265	c.1178C>T	c.(1177-1179)gCc>gTc	p.A393V		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	393					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.A393V(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)		TCTATTGACGCCCTGAAGGAC	0.552																																					p.A393V		Atlas-SNP	.											PRAMEF2,extremity,malignant_melanoma,0,1	PRAMEF2	85	1	1	Substitution - Missense(1)	skin(1)	c.C1178T						scavenged	.						95.0	98.0	97.0					1																	12921387		2202	4295	6497	SO:0001583	missense	65122	exon4			TTGACGCCCTGAA		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.1178C>T	1.37:g.12921387C>T	ENSP00000240189:p.Ala393Val	Somatic	592	13	0.0219595		WXS	Illumina HiSeq	Phase_I	607	8	0.0131796	NM_023014		Missense_Mutation	SNP	ENST00000240189.2	37	CCDS149.1	.	.	.	.	.	.	.	.	.	.	C	0.005	-2.121961	0.00346	.	.	ENSG00000120952	ENST00000240189	T	0.08720	3.06	0.824	-0.963	0.10330	.	2.409600	0.01594	N	0.021709	T	0.04724	0.0128	N	0.17674	0.51	0.09310	N	1	B	0.29590	0.25	B	0.29942	0.109	T	0.23226	-1.0194	10	0.02654	T	1	.	3.0964	0.06311	0.0:0.3592:0.0:0.6408	.	393	O60811	PRAM2_HUMAN	V	393	ENSP00000240189:A393V	ENSP00000240189:A393V	A	+	2	0	PRAMEF2	12843974	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.039000	0.03550	-0.277000	0.09193	0.173000	0.16961	GCC	.	.	none		0.552	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
FLG2	388698	hgsc.bcm.edu	37	1	152325795	152325795	+	Silent	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:152325795T>C	ENST00000388718.5	-	3	4539	c.4467A>G	c.(4465-4467)agA>agG	p.R1489R	FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	1489					establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TACTGGACCCTCTCTGTGTGG	0.522																																					p.R1489R		Atlas-SNP	.											FLG2,colon,carcinoma,-1,1	FLG2	431	1	0			c.A4467G						scavenged	.						363.0	346.0	352.0					1																	152325795		2203	4300	6503	SO:0001819	synonymous_variant	388698	exon3			GGACCCTCTCTGT	AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"""EF-hand domain containing"""	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.4467A>G	1.37:g.152325795T>C		Somatic	288	0	0		WXS	Illumina HiSeq	Phase_I	289	3	0.0103806	NM_001014342	Q9H4U1	Silent	SNP	ENST00000388718.5	37	CCDS30861.1																																																																																			.	.	none		0.522	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342	
TBX18	9096	hgsc.bcm.edu	37	6	85466570	85466570	+	Nonsense_Mutation	SNP	G	G	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr6:85466570G>T	ENST00000369663.5	-	4	954	c.617C>A	c.(616-618)tCg>tAg	p.S206*	TBX18_ENST00000606521.1_5'UTR|TBX18_ENST00000606784.1_Nonsense_Mutation_p.S48*	NM_001080508.1	NP_001073977.1	O95935	TBX18_HUMAN	T-box 18	206					anterior/posterior axis specification (GO:0009948)|cochlea morphogenesis (GO:0090103)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060829)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation involved in ureter development (GO:2000729)|sensory perception of sound (GO:0007605)|sinoatrial node development (GO:0003163)|smooth muscle cell differentiation (GO:0051145)|somitogenesis (GO:0001756)|ureter development (GO:0072189)	nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.S206L(1)		NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(9)|liver(1)|lung(31)|ovary(2)|pancreas(3)|prostate(6)|skin(3)	61		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)		BRCA - Breast invasive adenocarcinoma(108;0.0267)		CATCCATTTCGAACTGTGGTA	0.488																																					p.S206X		Atlas-SNP	.											TBX18,colon,carcinoma,+1,4	TBX18	131	4	1	Substitution - Missense(1)	large_intestine(1)	c.C617A						scavenged	.						109.0	86.0	94.0					6																	85466570		2203	4300	6503	SO:0001587	stop_gained	9096	exon4			CATTTCGAACTGT	AJ010278	CCDS34495.1	6q14.1-q15	2012-12-19			ENSG00000112837	ENSG00000112837		"""T-boxes"""	11595	protein-coding gene	gene with protein product		604613				9888994, 16688725, 23242162	Standard	NM_001080508		Approved		uc003pkl.2	O95935	OTTHUMG00000015129	ENST00000369663.5:c.617C>A	6.37:g.85466570G>T	ENSP00000358677:p.Ser206*	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	150	3	0.02	NM_001080508	A2RU13|Q7Z6U4|Q9UJI6	Nonsense_Mutation	SNP	ENST00000369663.5	37	CCDS34495.1	.	.	.	.	.	.	.	.	.	.	G	38	6.666933	0.97747	.	.	ENSG00000112837	ENST00000416980;ENST00000369663	.	.	.	6.06	6.06	0.98353	.	0.095323	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.6208	0.99490	0.0:0.0:1.0:0.0	.	.	.	.	X	121;206	.	ENSP00000358677:S206X	S	-	2	0	TBX18	85523289	1.000000	0.71417	0.998000	0.56505	0.043000	0.13939	9.869000	0.99810	2.882000	0.98803	0.655000	0.94253	TCG	.	.	none		0.488	TBX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041378.2	NM_001080508	
POTEC	388468	hgsc.bcm.edu	37	18	14513764	14513764	+	Missense_Mutation	SNP	C	C	T	rs201788045		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr18:14513764C>T	ENST00000358970.5	-	10	1429	c.1430G>A	c.(1429-1431)cGg>cAg	p.R477Q		NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	477								p.R477Q(12)		NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						AAGTTGTTTCCGGGTATCATT	0.358																																					p.R477Q		Atlas-SNP	.											POTEC,NS,carcinoma,0,17	POTEC	129	17	12	Substitution - Missense(12)	endometrium(4)|kidney(3)|urinary_tract(2)|prostate(2)|soft_tissue(1)	c.G1430A						scavenged	.						13.0	9.0	10.0					18																	14513764		683	1543	2226	SO:0001583	missense	388468	exon10			TGTTTCCGGGTAT	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.1430G>A	18.37:g.14513764C>T	ENSP00000351856:p.Arg477Gln	Somatic	421	1	0.0023753		WXS	Illumina HiSeq	Phase_I	428	9	0.021028	NM_001137671		Missense_Mutation	SNP	ENST00000358970.5	37	CCDS45835.1	492	0.22527472527472528	61	0.12398373983739837	82	0.2265193370165746	187	0.3269230769230769	162	0.21372031662269128	c	0.001	-3.539655	0.00009	.	.	ENSG00000183206	ENST00000358970	T	0.20881	2.04	1.34	0.0657	0.14358	.	.	.	.	.	T	0.00012	0.0000	N	0.00116	-2.08	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42430	-0.9452	9	0.06757	T	0.87	.	3.4153	0.07373	0.0:0.2473:0.0:0.7527	.	477	B2RU33	POTEC_HUMAN	Q	477	ENSP00000351856:R477Q	ENSP00000351856:R477Q	R	-	2	0	POTEC	14503764	0.885000	0.30320	0.063000	0.19743	0.005000	0.04900	1.581000	0.36558	0.005000	0.14708	-1.615000	0.00797	CGG	.	.	weak		0.358	POTEC-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371179.1	XM_496269	
GRHPR	9380	hgsc.bcm.edu	37	9	37432011	37432011	+	Silent	SNP	C	C	T	rs549318773		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr9:37432011C>T	ENST00000318158.6	+	8	826	c.741C>T	c.(739-741)gaC>gaT	p.D247D	GRHPR_ENST00000607784.1_Silent_p.D247D	NM_012203.1	NP_036335.1	Q9UBQ7	GRHPR_HUMAN	glyoxylate reductase/hydroxypyruvate reductase	247					cellular nitrogen compound metabolic process (GO:0034641)|dicarboxylic acid metabolic process (GO:0043648)|excretion (GO:0007588)|glyoxylate metabolic process (GO:0046487)|metabolic process (GO:0008152)|oxidation-reduction process (GO:0055114)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|peroxisomal matrix (GO:0005782)	carboxylic acid binding (GO:0031406)|glycerate dehydrogenase activity (GO:0008465)|glyoxylate reductase (NADP) activity (GO:0030267)|hydroxypyruvate reductase activity (GO:0016618)|NAD binding (GO:0051287)|NADPH binding (GO:0070402)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12				GBM - Glioblastoma multiforme(29;0.00687)		CCAGGGGCGACGTCGTAAACC	0.562													C|||	1	0.000199681	0.0	0.0	5008	,	,		19216	0.0		0.0	False		,,,				2504	0.001				p.D247D		Atlas-SNP	.											GRHPR,rectum,carcinoma,+2,3	GRHPR	35	3	0			c.C741T						scavenged	.						164.0	126.0	139.0					9																	37432011		2203	4300	6503	SO:0001819	synonymous_variant	9380	exon8			GGGCGACGTCGTA	AF134895	CCDS6609.1	9q12	2012-07-13			ENSG00000137106	ENSG00000137106	1.1.1.79, 1.1.1.81		4570	protein-coding gene	gene with protein product	"""primary hyperoxaluria type 2"""	604296		GLXR		10524214, 10484776	Standard	XM_005251631		Approved	PH2	uc003zzu.1	Q9UBQ7	OTTHUMG00000019914	ENST00000318158.6:c.741C>T	9.37:g.37432011C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	136	2	0.0147059	NM_012203	Q5T945|Q9H3E9|Q9H636|Q9UKX1	Silent	SNP	ENST00000318158.6	37	CCDS6609.1																																																																																			.	.	none		0.562	GRHPR-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052442.1	NM_012203	
TEP1	7011	hgsc.bcm.edu	37	14	20848107	20848107	+	Silent	SNP	C	C	T	rs563568149		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr14:20848107C>T	ENST00000262715.5	-	35	5149	c.5109G>A	c.(5107-5109)ttG>ttA	p.L1703L	TEP1_ENST00000556935.1_Silent_p.L1595L|TEP1_ENST00000545983.1_Silent_p.L41L	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1703					RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		TTCTCAGGTCCAACAGGTAAA	0.532													C|||	1	0.000199681	0.0	0.0	5008	,	,		20605	0.001		0.0	False		,,,				2504	0.0				p.L1703L		Atlas-SNP	.											TEP1,NS,carcinoma,0,1	TEP1	224	1	0			c.G5109A						scavenged	.						71.0	70.0	70.0					14																	20848107		2203	4300	6503	SO:0001819	synonymous_variant	7011	exon35			CAGGTCCAACAGG		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"""WD repeat domain containing"""	11726	protein-coding gene	gene with protein product	"""TROVE domain family, member 1"""	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.5109G>A	14.37:g.20848107C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	106	2	0.0188679	NM_007110	A0AUV9	Silent	SNP	ENST00000262715.5	37	CCDS9548.1																																																																																			.	.	none		0.532	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
HERC2	8924	hgsc.bcm.edu	37	15	28483809	28483809	+	Silent	SNP	G	G	A	rs149204675	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr15:28483809G>A	ENST00000261609.7	-	24	3795	c.3687C>T	c.(3685-3687)gaC>gaT	p.D1229D		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)		ACACCTTCCCGTCAATCACAG	0.373													G|||	26	0.00519169	0.0129	0.0	5008	,	,		17942	0.0		0.004	False		,,,				2504	0.0051				p.D1229D		Atlas-SNP	.											HERC2,NS,carcinoma,0,1	HERC2	501	1	0			c.C3687T						scavenged	.						73.0	68.0	70.0					15																	28483809		2203	4300	6503	SO:0001819	synonymous_variant	8924	exon24			CTTCCCGTCAATC	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.3687C>T	15.37:g.28483809G>A		Somatic	463	5	0.0107991		WXS	Illumina HiSeq	Phase_I	435	5	0.0114943	NM_004667		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																			G|0.998;A|0.002	0.002	strong		0.373	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
CHRM2	1129	hgsc.bcm.edu	37	7	136700095	136700095	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr7:136700095C>T	ENST00000445907.2	+	3	1011	c.483C>T	c.(481-483)ttC>ttT	p.F161F	hsa-mir-490_ENST00000597642.1_RNA|hsa-mir-490_ENST00000592183.1_RNA|hsa-mir-490_ENST00000425981.2_RNA|CHRM2_ENST00000320658.5_Silent_p.F161F|CHRM2_ENST00000401861.1_Silent_p.F161F|CHRM2_ENST00000397608.3_Silent_p.F161F|hsa-mir-490_ENST00000598184.1_RNA|CHRM2_ENST00000402486.3_Silent_p.F161F|CHRM2_ENST00000453373.1_Silent_p.F161F|hsa-mir-490_ENST00000439694.1_RNA|hsa-mir-490_ENST00000586239.1_RNA|hsa-mir-490_ENST00000593789.1_RNA	NM_001006627.1|NM_001006629.1	NP_001006628.1|NP_001006630.1	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2	161					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|nervous system development (GO:0007399)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|regulation of heart contraction (GO:0008016)|response to virus (GO:0009615)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled acetylcholine receptor activity (GO:0016907)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(13)|liver(1)|lung(29)|ovary(4)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	68					Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Bethanechol(DB01019)|Brompheniramine(DB00835)|Carbachol(DB00411)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Dimetindene(DB08801)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxacurium chloride(DB01135)|Doxepin(DB01142)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Gallamine Triethiodide(DB00483)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Rocuronium(DB00728)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	CCATTCTCTTCTGGCAGTTCA	0.512																																					p.F161F		Atlas-SNP	.											CHRM2,lower_third,carcinoma,+1,1	CHRM2	167	1	0			c.C483T						scavenged	.						93.0	91.0	92.0					7																	136700095		2203	4299	6502	SO:0001819	synonymous_variant	1129	exon3			TCTCTTCTGGCAG		CCDS5843.1	7q35-q36	2014-09-17			ENSG00000181072	ENSG00000181072		"""Cholinergic receptors"", ""GPCR / Class A : Cholinergic receptors, muscarinic"""	1951	protein-coding gene	gene with protein product	"""acetylcholine receptor, muscarinic 2"""	118493					Standard	NM_000739		Approved		uc003vtl.1	P08172	OTTHUMG00000155658	ENST00000445907.2:c.483C>T	7.37:g.136700095C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	131	2	0.0152672	NM_001006632	Q4VBK6|Q9P1X9	Silent	SNP	ENST00000445907.2	37	CCDS5843.1																																																																																			.	.	none		0.512	CHRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341010.1		
EIF3D	8664	hgsc.bcm.edu	37	22	36907798	36907798	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr22:36907798C>T	ENST00000216190.8	-	14	1755	c.1385G>A	c.(1384-1386)cGc>cAc	p.R462H	EIF3D_ENST00000478547.1_5'Flank|EIF3D_ENST00000541106.1_Missense_Mutation_p.R413H|EIF3D_ENST00000405442.1_Missense_Mutation_p.R462H	NM_003753.3	NP_003744.1			eukaryotic translation initiation factor 3, subunit D											cervix(1)|endometrium(2)|large_intestine(6)|lung(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	15						GATGACGTGGCGTGAGGAGTC	0.532											OREG0026522	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R462H		Atlas-SNP	.											.	EIF3D	37	.	0			c.G1385A						PASS	.						98.0	72.0	81.0					22																	36907798		2203	4300	6503	SO:0001583	missense	8664	exon14			ACGTGGCGTGAGG	U54558	CCDS13930.1	22q13.1	2007-07-27	2007-07-27	2007-07-27	ENSG00000100353	ENSG00000100353			3278	protein-coding gene	gene with protein product		603915	"""eukaryotic translation initiation factor 3, subunit 7 zeta, 66/67kDa"""	EIF3S7		9341143	Standard	NM_003753		Approved	eIF3-p66, eIF3-zeta, eIF3d	uc003apr.3	O15371	OTTHUMG00000150599	ENST00000216190.8:c.1385G>A	22.37:g.36907798C>T	ENSP00000216190:p.Arg462His	Somatic	180	0	0	866	WXS	Illumina HiSeq	Phase_I	194	90	0.463918	NM_003753		Missense_Mutation	SNP	ENST00000216190.8	37	CCDS13930.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.166071	0.78339	.	.	ENSG00000100353	ENST00000216190;ENST00000397177;ENST00000541106;ENST00000405442;ENST00000426531;ENST00000458572	.	.	.	6.07	5.04	0.67666	.	0.044401	0.85682	D	0.000000	T	0.47673	0.1458	L	0.39326	1.205	0.80722	D	1	B;P	0.38565	0.162;0.637	B;B	0.31547	0.017;0.132	T	0.45323	-0.9269	9	0.34782	T	0.22	-13.3282	17.384	0.87411	0.0:0.8752:0.1248:0.0	.	413;462	B4DVY1;O15371	.;EIF3D_HUMAN	H	462;447;413;462;115;149	.	ENSP00000216190:R462H	R	-	2	0	EIF3D	35237744	1.000000	0.71417	0.986000	0.45419	0.995000	0.86356	7.129000	0.77225	1.554000	0.49487	0.655000	0.94253	CGC	.	.	none		0.532	EIF3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319026.1		
LILRB1	10859	hgsc.bcm.edu	37	19	55148105	55148105	+	Splice_Site	SNP	T	T	A	rs201250339	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:55148105T>A	ENST00000396331.1	+	15	2163		c.e15+2		AC009892.10_ENST00000456337.1_Intron|LILRB1_ENST00000396332.4_Splice_Site|LILRB1_ENST00000448689.1_Splice_Site|LILRB1_ENST00000462628.1_Splice_Site|LILRB1_ENST00000396321.2_Splice_Site|LILRB1_ENST00000427581.2_Splice_Site|LILRB1_ENST00000324602.7_Splice_Site|LILRB1_ENST00000396315.1_Splice_Site|LILRB1_ENST00000434867.2_Splice_Site|LILRB1_ENST00000396327.3_Splice_Site|LILRB1_ENST00000396317.1_Splice_Site|LILRB1_ENST00000418536.2_Splice_Site	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 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)		GACACTGAGGTGAGTCCTTTC	0.622										HNSCC(37;0.09)																											.		Atlas-SNP	.											LILRB1,NS,carcinoma,0,1	LILRB1	140	1	0			c.1806+2T>A						scavenged	.						81.0	69.0	73.0					19																	55148105		2202	4297	6499	SO:0001630	splice_region_variant	10859	exon15			CTGAGGTGAGTCC	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.1806+2T>A	19.37:g.55148105T>A		Somatic	278	6	0.0215827		WXS	Illumina HiSeq	Phase_I	350	18	0.0514286	NM_006669	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Splice_Site	SNP	ENST00000396331.1	37	CCDS42617.1	.	.	.	.	.	.	.	.	.	.	T	2.107	-0.404766	0.04832	.	.	ENSG00000104972	ENST00000396321;ENST00000418536;ENST00000396331;ENST00000396327;ENST00000324602;ENST00000434867;ENST00000396332;ENST00000427581;ENST00000396317;ENST00000396315	.	.	.	1.59	0.53	0.17102	.	.	.	.	.	.	.	.	.	.	.	0.19945	N	0.999945	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.3096	0.10964	0.0:0.2015:0.0:0.7985	.	.	.	.	.	-1	.	.	.	+	.	.	LILRB1	59839917	.	.	0.003000	0.11579	0.012000	0.07955	.	.	0.005000	0.14708	-1.140000	0.01884	.	T|0.983;A|0.016	0.016	strong		0.622	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4		Intron
IL4R	3566	hgsc.bcm.edu	37	16	27373599	27373599	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr16:27373599T>C	ENST00000395762.2	+	11	1185	c.926T>C	c.(925-927)cTc>cCc	p.L309P	IL4R_ENST00000380922.3_Missense_Mutation_p.L294P|IL4R_ENST00000170630.2_Missense_Mutation_p.L309P|IL4R_ENST00000565915.1_3'UTR|IL4R_ENST00000543915.2_Missense_Mutation_p.L309P	NM_000418.3	NP_000409.1	P24394	IL4RA_HUMAN	interleukin 4 receptor	309					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						CTTACCAAGCTCTTGCCCTGT	0.468																																					p.L309P		Atlas-SNP	.											.	IL4R	70	.	0			c.T926C						PASS	.						84.0	93.0	90.0					16																	27373599		2197	4300	6497	SO:0001583	missense	3566	exon11			CCAAGCTCTTGCC	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.926T>C	16.37:g.27373599T>C	ENSP00000379111:p.Leu309Pro	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	129	21	0.162791	NM_000418	B4E076|B9EKU8|H3BSY5|Q96P01|Q9H181|Q9H182|Q9H183|Q9H184|Q9H185|Q9H186|Q9H187|Q9H188	Missense_Mutation	SNP	ENST00000395762.2	37	CCDS10629.1	.	.	.	.	.	.	.	.	.	.	T	18.59	3.657837	0.67586	.	.	ENSG00000077238	ENST00000395762;ENST00000543915;ENST00000380922;ENST00000170630	T;T;T;T	0.16196	2.36;2.36;2.36;2.36	4.8	4.8	0.61643	.	0.430475	0.18627	N	0.135694	T	0.37019	0.0988	M	0.62723	1.935	0.48087	D	0.999589	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.78314	0.991;0.991;0.991	T	0.08289	-1.0729	10	0.62326	D	0.03	-23.6721	10.7721	0.46330	0.0:0.0:0.0:1.0	.	294;309;309	B4E076;B9EGC0;P24394	.;.;IL4RA_HUMAN	P	309;309;294;309	ENSP00000379111:L309P;ENSP00000441667:L309P;ENSP00000370309:L294P;ENSP00000170630:L309P	ENSP00000170630:L309P	L	+	2	0	IL4R	27281100	1.000000	0.71417	0.980000	0.43619	0.957000	0.61999	3.498000	0.53302	1.801000	0.52704	0.533000	0.62120	CTC	.	.	none		0.468	IL4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214104.4		
STK35	140901	hgsc.bcm.edu	37	20	2083900	2083900	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr20:2083900G>A	ENST00000381482.3	+	2	1052	c.781G>A	c.(781-783)Gtc>Atc	p.V261I	STK35_ENST00000400064.3_Missense_Mutation_p.V89I|STK35_ENST00000246032.3_Missense_Mutation_p.V128I			Q8TDR2	STK35_HUMAN	serine/threonine kinase 35	261	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			large_intestine(2)|liver(2)|lung(6)|ovary(1)|prostate(2)	13						CCACCAGAACGTCGTGCAGTT	0.637																																					p.V261I		Atlas-SNP	.											STK35,NS,carcinoma,-2,1	STK35	31	1	0			c.G781A						scavenged	.						30.0	27.0	28.0					20																	2083900		2203	4300	6503	SO:0001583	missense	140901	exon2			CAGAACGTCGTGC	AL359916	CCDS13024.1, CCDS13024.2	20p13	2008-07-02			ENSG00000125834	ENSG00000125834			16254	protein-coding gene	gene with protein product	"""CLP-36 interacting kinase"""	609370				11973348	Standard	NM_080836		Approved	bA550O8.2, CLIK1	uc002wfw.4	Q8TDR2	OTTHUMG00000031688	ENST00000381482.3:c.781G>A	20.37:g.2083900G>A	ENSP00000370891:p.Val261Ile	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	92	2	0.0217391	NM_080836	B2RBM3|C7ENV8|Q2NKW6|Q5T3R1|Q5T3R2|Q96AB4|Q9BZ06	Missense_Mutation	SNP	ENST00000381482.3	37	CCDS13024.2	.	.	.	.	.	.	.	.	.	.	G	11.68	1.710984	0.30322	.	.	ENSG00000125834	ENST00000381482;ENST00000246032;ENST00000400064	D;D;T	0.91295	-2.82;-2.82;1.46	4.25	2.3	0.28687	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.075453	0.51477	N	0.000085	T	0.75649	0.3878	N	0.10645	0.015	0.31947	N	0.610125	B;B	0.25719	0.132;0.056	B;B	0.24006	0.023;0.05	T	0.68191	-0.5474	10	0.10377	T	0.69	-10.5804	8.1089	0.30903	0.2064:0.0:0.7936:0.0	.	89;261	B4DYV9;Q8TDR2	.;STK35_HUMAN	I	261;128;89	ENSP00000370891:V261I;ENSP00000246032:V128I;ENSP00000382937:V89I	ENSP00000246032:V128I	V	+	1	0	STK35	2031900	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.487000	0.81328	0.719000	0.32188	-0.136000	0.14681	GTC	.	.	none		0.637	STK35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077574.3	NM_080836	
TTPAL	79183	hgsc.bcm.edu	37	20	43113093	43113093	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr20:43113093G>A	ENST00000372904.3	+	4	705	c.562G>A	c.(562-564)Gac>Aac	p.D188N	TTPAL_ENST00000372906.2_Intron|TTPAL_ENST00000262605.4_Missense_Mutation_p.D188N	NM_024331.4	NP_077307.2	Q9BTX7	TTPAL_HUMAN	tocopherol (alpha) transfer protein-like	188	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.					intracellular (GO:0005622)|membrane (GO:0016020)	transporter activity (GO:0005215)	p.D188N(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|ovary(2)|skin(5)	18						AATTCTTGCAGACTACAAAGG	0.413																																					p.D188N		Atlas-SNP	.											TTPAL,trunk,malignant_melanoma,0,1	TTPAL	31	1	1	Substitution - Missense(1)	skin(1)	c.G562A						scavenged	.						122.0	111.0	115.0					20																	43113093		2203	4300	6503	SO:0001583	missense	79183	exon3			CTTGCAGACTACA	BC003071	CCDS13332.2	20q13.12	2008-06-23	2008-06-23	2008-06-23	ENSG00000124120	ENSG00000124120			16114	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 121"""	C20orf121			Standard	NM_024331		Approved	dJ179M20.3	uc002xmd.2	Q9BTX7	OTTHUMG00000032536	ENST00000372904.3:c.562G>A	20.37:g.43113093G>A	ENSP00000361995:p.Asp188Asn	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	144	2	0.0138889	NM_001039199	E1P5X3|Q5QPC1|Q9H1G2|Q9NQG8	Missense_Mutation	SNP	ENST00000372904.3	37	CCDS13332.2	.	.	.	.	.	.	.	.	.	.	G	34	5.403595	0.96051	.	.	ENSG00000124120	ENST00000262605;ENST00000372904	D;D	0.95788	-3.81;-3.81	6.05	6.05	0.98169	Cellular retinaldehyde-binding/triple function, C-terminal (5);	0.000000	0.85682	D	0.000000	D	0.97882	0.9304	M	0.82056	2.57	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97512	1.0067	10	0.54805	T	0.06	-43.975	20.6013	0.99457	0.0:0.0:1.0:0.0	.	188	Q9BTX7	TTPAL_HUMAN	N	188	ENSP00000262605:D188N;ENSP00000361995:D188N	ENSP00000262605:D188N	D	+	1	0	TTPAL	42546507	1.000000	0.71417	0.993000	0.49108	0.990000	0.78478	9.845000	0.99498	2.878000	0.98634	0.650000	0.86243	GAC	.	.	none		0.413	TTPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106886.2	NM_024331	
SPTA1	6708	hgsc.bcm.edu	37	1	158592861	158592861	+	Missense_Mutation	SNP	G	G	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:158592861G>T	ENST00000368147.4	-	43	6212	c.6032C>A	c.(6031-6033)gCc>gAc	p.A2011D		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	2011					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)	p.A2011V(6)		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)					CAGCAGAGCGGCATAACGCTC	0.483																																					p.A2011D		Atlas-SNP	.											SPTA1,NS,carcinoma,+1,9	SPTA1	720	9	6	Substitution - Missense(6)	lung(4)|urinary_tract(1)|prostate(1)	c.C6032A						scavenged	.						267.0	267.0	267.0					1																	158592861		1943	4143	6086	SO:0001583	missense	6708	exon43			AGAGCGGCATAAC	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.6032C>A	1.37:g.158592861G>T	ENSP00000357129:p.Ala2011Asp	Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	241	3	0.0124481	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	G	5.573	0.290558	0.10567	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.48836	0.8;0.8	4.78	0.669	0.17918	.	.	.	.	.	T	0.11239	0.0274	L	0.39245	1.2	0.33091	D	0.537999	B	0.17852	0.024	B	0.21151	0.033	T	0.25293	-1.0136	9	0.02654	T	1	.	5.4632	0.16627	0.1562:0.0:0.5633:0.2805	.	2011	P02549	SPTA1_HUMAN	D	2011;2008	ENSP00000357130:A2011D;ENSP00000357129:A2008D	ENSP00000357129:A2008D	A	-	2	0	SPTA1	156859485	1.000000	0.71417	0.002000	0.10522	0.000000	0.00434	4.149000	0.58091	-0.029000	0.13827	-0.140000	0.14226	GCC	.	.	none		0.483	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
ZNF101	94039	hgsc.bcm.edu	37	19	19790525	19790525	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:19790525C>T	ENST00000592502.1	+	4	837	c.727C>T	c.(727-729)Cat>Tat	p.H243Y	ZNF101_ENST00000444249.2_3'UTR|ZNF101_ENST00000415784.2_Missense_Mutation_p.H123Y			Q8IZC7	ZN101_HUMAN	zinc finger protein 101	243					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(4)|ovary(2)|prostate(1)	17						ATTTCAAATTCATGTTAGAAC	0.358																																					p.H243Y		Atlas-SNP	.											.	ZNF101	43	.	0			c.C727T						PASS	.						31.0	32.0	32.0					19																	19790525		2203	4300	6503	SO:0001583	missense	94039	exon4			CAAATTCATGTTA	AK097169	CCDS32971.1	19p13.11	2013-01-08	2004-02-10		ENSG00000181896	ENSG00000181896		"""Zinc fingers, C2H2-type"", ""-"""	12881	protein-coding gene	gene with protein product		603983	"""zinc finger protein 101 (Y2)"""			11441184	Standard	XM_005260165		Approved	HZF12, DKFZp570I0164	uc002nni.2	Q8IZC7	OTTHUMG00000167736	ENST00000592502.1:c.727C>T	19.37:g.19790525C>T	ENSP00000468049:p.His243Tyr	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	54	13	0.240741	NM_033204	C9JU83|Q0VDG9	Missense_Mutation	SNP	ENST00000592502.1	37	CCDS32971.1	.	.	.	.	.	.	.	.	.	.	C	19.96	3.923897	0.73213	.	.	ENSG00000181896	ENST00000318110;ENST00000415440;ENST00000415784	D;D	0.86769	-2.17;-2.17	0.235	0.235	0.15431	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.93569	0.7947	M	0.93763	3.455	0.30664	N	0.754114	D	0.89917	1.0	D	0.91635	0.999	D	0.87769	0.2604	8	.	.	.	.	6.2532	0.20859	0.0:0.9997:0.0:3.0E-4	.	243	Q8IZC7	ZN101_HUMAN	Y	243;243;123	ENSP00000319716:H243Y;ENSP00000400952:H123Y	.	H	+	1	0	ZNF101	19651525	0.996000	0.38824	0.884000	0.34674	0.883000	0.51084	5.267000	0.65530	0.308000	0.22923	0.313000	0.20887	CAT	.	.	none		0.358	ZNF101-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460559.1	NM_033204	
FAM186A	121006	hgsc.bcm.edu	37	12	50745677	50745677	+	Silent	SNP	T	T	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:50745677T>A	ENST00000327337.5	-	4	4937	c.4938A>T	c.(4936-4938)gcA>gcT	p.A1646A	FAM186A_ENST00000543111.1_Silent_p.A1646A|FAM186A_ENST00000543096.1_5'Flank	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	1646																	GGACTCCCAGTGCCTGGGCCT	0.607																																					p.A1646A	NSCLC(138;1796 1887 12511 19463 37884)	Atlas-SNP	.											FAM186A_ENST00000327337,rectum,carcinoma,0,4	FAM186A	181	4	0			c.A4938T						scavenged	.						30.0	30.0	30.0					12																	50745677		692	1591	2283	SO:0001819	synonymous_variant	121006	exon4			TCCCAGTGCCTGG		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.4938A>T	12.37:g.50745677T>A		Somatic	108	5	0.0462963		WXS	Illumina HiSeq	Phase_I	128	3	0.0234375	NM_001145475		Silent	SNP	ENST00000327337.5	37	CCDS44878.1																																																																																			.	.	none		0.607	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
MYH6	4624	hgsc.bcm.edu	37	14	23865523	23865523	+	Missense_Mutation	SNP	C	C	T	rs535438755		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr14:23865523C>T	ENST00000356287.3	-	19	2428	c.2399G>A	c.(2398-2400)cGc>cAc	p.R800H	MYH6_ENST00000405093.3_Missense_Mutation_p.R800H			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	800	IQ. {ECO:0000255|PROSITE- ProRule:PRU00116}.				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)		GAACTCAATGCGCATGAGCTG	0.577													C|||	1	0.000199681	0.0	0.0	5008	,	,		18438	0.0		0.0	False		,,,				2504	0.001				p.R800H		Atlas-SNP	.											MYH6,NS,carcinoma,-1,1	MYH6	274	1	0			c.G2399A						PASS	.						101.0	89.0	93.0					14																	23865523		2203	4300	6503	SO:0001583	missense	4624	exon20			TCAATGCGCATGA	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.2399G>A	14.37:g.23865523C>T	ENSP00000348634:p.Arg800His	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	136	63	0.463235	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Missense_Mutation	SNP	ENST00000356287.3	37	CCDS9600.1	.	.	.	.	.	.	.	.	.	.	c	20.4	3.991779	0.74703	.	.	ENSG00000197616	ENST00000405093;ENST00000356287	T;T	0.77098	-1.07;-1.07	4.78	4.78	0.61160	.	.	.	.	.	D	0.91915	0.7440	H	0.96365	3.81	0.58432	D	0.999999	D	0.89917	1.0	D	0.72075	0.976	D	0.94612	0.7805	9	0.87932	D	0	.	18.1704	0.89743	0.0:1.0:0.0:0.0	.	800	P13533	MYH6_HUMAN	H	800	ENSP00000386041:R800H;ENSP00000348634:R800H	ENSP00000348634:R800H	R	-	2	0	MYH6	22935363	1.000000	0.71417	1.000000	0.80357	0.200000	0.23975	7.522000	0.81844	2.382000	0.81193	0.650000	0.86243	CGC	.	.	none		0.577	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3		
ANKRD36	375248	hgsc.bcm.edu	37	2	97869931	97869931	+	Missense_Mutation	SNP	A	A	T	rs76309140		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:97869931A>T	ENST00000461153.2	+	50	3236	c.2992A>T	c.(2992-2994)Aca>Tca	p.T998S	ANKRD36_ENST00000420699.2_Missense_Mutation_p.T998S			A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	998								p.T998S(13)		endometrium(9)|kidney(5)|liver(1)|lung(3)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23						CATTCAGGCTACAAGTGATGA	0.289																																					p.T998S		Atlas-SNP	.											ANKRD36_ENST00000420699,NS,carcinoma,0,14	ANKRD36	170	14	13	Substitution - Missense(13)	kidney(6)|endometrium(4)|prostate(3)	c.A2992T						scavenged	.						37.0	44.0	42.0					2																	97869931		692	1587	2279	SO:0001583	missense	375248	exon50			CAGGCTACAAGTG	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.2992A>T	2.37:g.97869931A>T	ENSP00000419530:p.Thr998Ser	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	35	4	0.114286	NM_001164315	B4E3I8|Q6UX02|Q86X62|Q9HCD1	Missense_Mutation	SNP	ENST00000461153.2	37	CCDS54379.1	.	.	.	.	.	.	.	.	.	.	.	3.819	-0.038219	0.07497	.	.	ENSG00000135976	ENST00000461153;ENST00000420699;ENST00000461694	T;T	0.32753	1.44;1.44	0.63	-0.824	0.10812	.	.	.	.	.	T	0.14056	0.0340	L	0.27053	0.805	0.09310	N	1	P	0.40476	0.718	B	0.28849	0.095	T	0.12837	-1.0532	8	0.38643	T	0.18	.	.	.	.	.	998	A6QL64	AN36A_HUMAN	S	998;998;360	ENSP00000419530:T998S;ENSP00000391950:T998S	ENSP00000391950:T998S	T	+	1	0	ANKRD36	97233658	0.019000	0.18553	0.011000	0.14972	0.022000	0.10575	-0.850000	0.04317	-0.324000	0.08589	0.147000	0.16070	ACA	.	.	weak		0.289	ANKRD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339154.5		
XIRP2	129446	hgsc.bcm.edu	37	2	168107691	168107691	+	Missense_Mutation	SNP	G	G	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:168107691G>T	ENST00000409195.1	+	9	9878	c.9789G>T	c.(9787-9789)agG>agT	p.R3263S	XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.R3263S|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.R3041S|XIRP2_ENST00000409043.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	3088					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						AGGAAATCAGGAAAGTGGAGA	0.423																																					p.R3263S		Atlas-SNP	.											.	XIRP2	914	.	0			c.G9789T						PASS	.						70.0	66.0	67.0					2																	168107691		1908	4138	6046	SO:0001583	missense	129446	exon9			AATCAGGAAAGTG	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.9789G>T	2.37:g.168107691G>T	ENSP00000386840:p.Arg3263Ser	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	108	10	0.0925926	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	G	8.433	0.849012	0.17034	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273;ENST00000413534	T;T;T	0.02656	4.21;4.21;4.21	5.61	4.73	0.59995	.	0.251797	0.42053	D	0.000767	T	0.04003	0.0112	L	0.56769	1.78	0.34058	D	0.656942	P;P;P	0.46142	0.651;0.763;0.873	B;B;B	0.39660	0.084;0.173;0.306	T	0.40961	-0.9535	10	0.39692	T	0.17	-11.0608	8.8487	0.35186	0.17:0.0:0.83:0.0	.	3088;3088;3041	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	S	3263;3263;3041;677	ENSP00000386840:R3263S;ENSP00000295237:R3263S;ENSP00000387255:R3041S	ENSP00000295237:R3263S	R	+	3	2	XIRP2	167815937	0.962000	0.33011	0.852000	0.33557	0.171000	0.22731	1.442000	0.35046	1.504000	0.48704	0.460000	0.39030	AGG	.	.	none		0.423	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
PCDHB10	56126	hgsc.bcm.edu	37	5	140573649	140573649	+	Silent	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:140573649G>A	ENST00000239446.4	+	1	1708	c.1524G>A	c.(1522-1524)gcG>gcA	p.A508A		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	508	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(30)|ovary(4)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	76			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCATCAACGCGGACAACGGCC	0.692																																					p.A508A		Atlas-SNP	.											PCDHB10,NS,carcinoma,+1,3	PCDHB10	177	3	0			c.G1524A						scavenged	.						104.0	121.0	115.0					5																	140573649		2203	4298	6501	SO:0001819	synonymous_variant	56126	exon1			CAACGCGGACAAC	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.1524G>A	5.37:g.140573649G>A		Somatic	334	3	0.00898204		WXS	Illumina HiSeq	Phase_I	200	3	0.015	NM_018930	Q96T99	Silent	SNP	ENST00000239446.4	37	CCDS4252.1																																																																																			G|0.344;A|0.656	0.656	strong		0.692	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930	
CDC42BPG	55561	hgsc.bcm.edu	37	11	64594201	64594201	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:64594201C>T	ENST00000342711.5	-	35	4454	c.4455G>A	c.(4453-4455)gaG>gaA	p.E1485E		NM_017525.2	NP_059995.2			CDC42 binding protein kinase gamma (DMPK-like)											central_nervous_system(1)|lung(3)	4						GCCGCAACGCCTCGGAGAAGC	0.711																																					p.E1485E		Atlas-SNP	.											.	CDC42BPG	101	.	0			c.G4455A						PASS	.						11.0	15.0	14.0					11																	64594201		2184	4250	6434	SO:0001819	synonymous_variant	55561	exon35			CAACGCCTCGGAG	AY648038	CCDS31601.1	11q13	2013-01-10			ENSG00000171219	ENSG00000171219		"""Pleckstrin homology (PH) domain containing"""	29829	protein-coding gene	gene with protein product		613991				9341881, 15194684	Standard	NM_017525		Approved	HSMDPKIN, MRCKgamma, DMPK2, kappa-200	uc001obs.4	Q6DT37	OTTHUMG00000045365	ENST00000342711.5:c.4455G>A	11.37:g.64594201C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	16	10	0.625	NM_017525		Silent	SNP	ENST00000342711.5	37	CCDS31601.1																																																																																			.	.	none		0.711	CDC42BPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105352.4	XM_290516	
NRXN1	9378	hgsc.bcm.edu	37	2	50724589	50724589	+	Silent	SNP	A	A	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:50724589A>G	ENST00000406316.2	-	14	4237	c.2761T>C	c.(2761-2763)Ttg>Ctg	p.L921L	NRXN1_ENST00000401710.1_5'Flank|NRXN1_ENST00000402717.3_Silent_p.L913L|NRXN1_ENST00000405472.3_Silent_p.L913L|NRXN1_ENST00000404971.1_Silent_p.L961L|NRXN1_ENST00000406859.3_Silent_p.L921L|NRXN1_ENST00000401669.2_Silent_p.L921L|NRXN1_ENST00000331040.5_5'UTR	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	921	Laminin G-like 5. {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)			TAGGCTTGCAAGGTAGCTAAG	0.398																																					p.L961L		Atlas-SNP	.											NRXN1_ENST00000536085,right_upper_lobe,carcinoma,+1,3	NRXN1	1118	3	0			c.T2881C						scavenged	.						134.0	123.0	126.0					2																	50724589		1931	4162	6093	SO:0001819	synonymous_variant	9378	exon15			CTTGCAAGGTAGC	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.2761T>C	2.37:g.50724589A>G		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	110	2	0.0181818	NM_001135659	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Silent	SNP	ENST00000406316.2	37	CCDS54360.1																																																																																			.	.	none		0.398	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2		
FAM161A	84140	hgsc.bcm.edu	37	2	62081028	62081028	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:62081028T>C	ENST00000405894.3	-	1	250	c.149A>G	c.(148-150)gAg>gGg	p.E50G	FAM161A_ENST00000404929.1_Missense_Mutation_p.E50G	NM_032180.2	NP_115556.2	Q3B820	F161A_HUMAN	family with sequence similarity 161, member A	50	Poly-Glu.				cilium assembly (GO:0042384)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|photoreceptor connecting cilium (GO:0032391)				breast(1)|endometrium(5)|large_intestine(8)|lung(4)|ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TTTCTCCTCCTCTTCGTCCTC	0.657																																					p.E50G		Atlas-SNP	.											FAM161A_ENST00000405894,NS,carcinoma,-1,1	FAM161A	200	1	0			c.A149G						scavenged	.						48.0	48.0	48.0					2																	62081028		1568	3582	5150	SO:0001583	missense	84140	exon1			TCCTCCTCTTCGT		CCDS42687.2, CCDS56120.1	2p15	2011-03-15			ENSG00000170264	ENSG00000170264			25808	protein-coding gene	gene with protein product		613596	"""retinitis pigmentosa 28 (autosomal recessive)"""	RP28		10507729, 20705278, 20705279	Standard	NM_032180		Approved	FLJ13305	uc002sbm.4	Q3B820	OTTHUMG00000152165	ENST00000405894.3:c.149A>G	2.37:g.62081028T>C	ENSP00000385893:p.Glu50Gly	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	174	2	0.0114943	NM_032180	B4DJV7|Q9H8R2	Missense_Mutation	SNP	ENST00000405894.3	37	CCDS42687.2	.	.	.	.	.	.	.	.	.	.	T	12.30	1.896197	0.33442	.	.	ENSG00000170264	ENST00000404929;ENST00000405894	T;T	0.66638	-0.22;-0.22	4.36	4.36	0.52297	.	.	.	.	.	T	0.53769	0.1817	N	0.14661	0.345	0.09310	N	1	P;P	0.40731	0.608;0.728	B;B	0.43623	0.244;0.425	T	0.50550	-0.8815	9	0.87932	D	0	.	10.2378	0.43294	0.0:0.0:0.0:1.0	.	50;50	Q3B820;Q3B820-3	F161A_HUMAN;.	G	50	ENSP00000385158:E50G;ENSP00000385893:E50G	ENSP00000303170:E50G	E	-	2	0	FAM161A	61934532	0.000000	0.05858	0.005000	0.12908	0.004000	0.04260	-0.216000	0.09266	2.192000	0.70111	0.533000	0.62120	GAG	.	.	none		0.657	FAM161A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325537.2	NM_032180	
ECM1	1893	hgsc.bcm.edu	37	1	150484192	150484192	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:150484192G>A	ENST00000369047.4	+	7	1093	c.968G>A	c.(967-969)cGc>cAc	p.R323H	ECM1_ENST00000369049.4_Missense_Mutation_p.R350H|ECM1_ENST00000346569.6_Intron|ECM1_ENST00000470432.1_3'UTR	NM_004425.3	NP_004416.2	Q16610	ECM1_HUMAN	extracellular matrix protein 1	323	2 X approximate repeats.				angiogenesis (GO:0001525)|biomineral tissue development (GO:0031214)|inflammatory response (GO:0006954)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of peptidase activity (GO:0010466)|ossification (GO:0001503)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of T cell migration (GO:2000404)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of type 2 immune response (GO:0002828)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	enzyme binding (GO:0019899)|laminin binding (GO:0043236)|protease binding (GO:0002020)|protein C-terminus binding (GO:0008022)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|urinary_tract(1)	22	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.29e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			TCTGTGCCACGCAACCTGCCA	0.592																																					p.R350H	Melanoma(156;1696 2560 11093 19685)	Atlas-SNP	.											ECM1_ENST00000369049,NS,carcinoma,+1,2	ECM1	96	2	0			c.G1049A						scavenged	.						53.0	49.0	51.0					1																	150484192		2203	4300	6503	SO:0001583	missense	1893	exon7			TGCCACGCAACCT	U68186	CCDS953.1, CCDS954.1, CCDS55632.1	1q21	2008-02-05			ENSG00000143369	ENSG00000143369			3153	protein-coding gene	gene with protein product		602201				9367673, 9501329	Standard	NM_004425		Approved		uc001eus.3	Q16610	OTTHUMG00000012806	ENST00000369047.4:c.968G>A	1.37:g.150484192G>A	ENSP00000358043:p.Arg323His	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	146	2	0.0136986	NM_001202858	A8K8S0|B4DW49|B4DY60|O43266|Q5T5G4|Q5T5G5|Q5T5G6|Q8IZ60	Missense_Mutation	SNP	ENST00000369047.4	37	CCDS953.1	.	.	.	.	.	.	.	.	.	.	G	17.80	3.477246	0.63849	.	.	ENSG00000143369	ENST00000369049;ENST00000369047	T;T	0.79940	-1.32;-1.32	4.19	3.27	0.37495	.	0.400394	0.21009	N	0.081706	T	0.81517	0.4839	L	0.60455	1.87	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.998	T	0.82339	-0.0506	10	0.72032	D	0.01	-20.086	7.9404	0.29955	0.1133:0.0:0.8867:0.0	.	350;323;323	Q16610-4;C8CHS3;Q16610	.;.;ECM1_HUMAN	H	350;323	ENSP00000358045:R350H;ENSP00000358043:R323H	ENSP00000358043:R323H	R	+	2	0	ECM1	148750816	0.109000	0.22037	0.998000	0.56505	0.926000	0.56050	0.523000	0.22925	1.116000	0.41820	0.555000	0.69702	CGC	.	.	none		0.592	ECM1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035832.2	NM_004425	
CHD4	1108	hgsc.bcm.edu	37	12	6710854	6710854	+	Nonsense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:6710854G>A	ENST00000357008.2	-	5	680	c.517C>T	c.(517-519)Cga>Tga	p.R173*	CHD4_ENST00000544040.1_Nonsense_Mutation_p.R166*|CHD4_ENST00000544484.1_Nonsense_Mutation_p.R170*|CHD4_ENST00000309577.6_Nonsense_Mutation_p.R173*	NM_001273.2	NP_001264.2	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	173					ATP-dependent chromatin remodeling (GO:0043044)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spindle assembly (GO:0051225)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|RNA polymerase II repressing transcription factor binding (GO:0001103)|zinc ion binding (GO:0008270)			central_nervous_system(2)	2						GTGAGGGTTCGATAATCCTCC	0.488																																					p.R173X	Colon(32;586 792 4568 16848 45314)	Atlas-SNP	.											CHD4_ENST00000357008,NS,malignant_melanoma,0,3	CHD4	539	3	0			c.C517T						scavenged	.						274.0	278.0	277.0					12																	6710854		2203	4300	6503	SO:0001587	stop_gained	1108	exon5			GGGTTCGATAATC	X86691	CCDS8552.1	12p13	2013-01-28				ENSG00000111642		"""Zinc fingers, PHD-type"""	1919	protein-coding gene	gene with protein product		603277				7575689, 8843877	Standard	XM_006718958		Approved	Mi-2b, Mi2-BETA	uc001qpo.3	Q14839		ENST00000357008.2:c.517C>T	12.37:g.6710854G>A	ENSP00000349508:p.Arg173*	Somatic	174	1	0.00574713		WXS	Illumina HiSeq	Phase_I	221	75	0.339367	NM_001273	Q8IXZ5	Nonsense_Mutation	SNP	ENST00000357008.2	37	CCDS8552.1	.	.	.	.	.	.	.	.	.	.	G	37	6.145184	0.97324	.	.	ENSG00000111642	ENST00000544484;ENST00000544040;ENST00000309577;ENST00000357008;ENST00000537464;ENST00000545942	.	.	.	5.87	5.87	0.94306	.	0.228496	0.32081	N	0.006603	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10377	T	0.69	-0.807	16.49	0.84198	0.0:0.0:0.8686:0.1314	.	.	.	.	X	170;166;173;173;147;173	.	ENSP00000312419:R173X	R	-	1	2	CHD4	6581115	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	7.382000	0.79729	2.774000	0.95407	0.650000	0.86243	CGA	.	.	none		0.488	CHD4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001273	
LAMA5	3911	hgsc.bcm.edu	37	20	60892438	60892438	+	Missense_Mutation	SNP	C	C	T	rs373181217		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr20:60892438C>T	ENST00000252999.3	-	55	7540	c.7474G>A	c.(7474-7476)Gca>Aca	p.A2492T		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	2492	Domain II and I.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			AGCTGCTGTGCGTGGGCCTCG	0.701																																					p.A2492T		Atlas-SNP	.											.	LAMA5	268	.	0			c.G7474A						PASS	.		THR/ALA	1,4311		0,1,2155	13.0	16.0	15.0		7474	3.5	0.8	20		15	1,8509		0,1,4254	no	missense	LAMA5	NM_005560.3	58	0,2,6409	TT,TC,CC		0.0118,0.0232,0.0156	probably-damaging	2492/3696	60892438	2,12820	2156	4255	6411	SO:0001583	missense	3911	exon55			GCTGTGCGTGGGC	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.7474G>A	20.37:g.60892438C>T	ENSP00000252999:p.Ala2492Thr	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	25	9	0.36	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	.	.	.	.	.	.	.	.	.	.	c	25.3	4.629064	0.87560	2.32E-4	1.18E-4	ENSG00000130702	ENST00000252999	T	0.39592	1.07	3.54	3.54	0.40534	.	0.000000	0.85682	U	0.000000	T	0.64349	0.2590	M	0.77486	2.375	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.71227	-0.4655	10	0.72032	D	0.01	.	14.7386	0.69437	0.0:1.0:0.0:0.0	.	2492	O15230	LAMA5_HUMAN	T	2492	ENSP00000252999:A2492T	ENSP00000252999:A2492T	A	-	1	0	LAMA5	60325833	1.000000	0.71417	0.833000	0.33012	0.717000	0.41224	7.039000	0.76544	1.522000	0.49001	0.436000	0.28706	GCA	.	.	weak		0.701	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
ZBTB21	49854	hgsc.bcm.edu	37	21	43411305	43411305	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr21:43411305G>A	ENST00000310826.5	-	3	3083	c.2900C>T	c.(2899-2901)tCg>tTg	p.S967L	ZBTB21_ENST00000465968.1_5'Flank|ZBTB21_ENST00000398505.3_Missense_Mutation_p.S766L|ZBTB21_ENST00000398499.1_Missense_Mutation_p.S967L|ZBTB21_ENST00000398511.3_Missense_Mutation_p.S967L	NM_001098402.1	NP_001091872.1	Q9ULJ3	ZBT21_HUMAN	zinc finger and BTB domain containing 21	967					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyl-CpG binding (GO:0008327)										CTTATGTGCCGATTCCTCTGA	0.517																																					p.S967L		Atlas-SNP	.											ZNF295,NS,lymphoid_neoplasm,0,1	.	.	1	0			c.C2900T						scavenged	.						89.0	89.0	89.0					21																	43411305		2203	4300	6503	SO:0001583	missense	49854	exon3			TGTGCCGATTCCT	AB033053	CCDS13678.1, CCDS42934.1	21q22.3	2013-01-09	2013-01-09	2013-01-09	ENSG00000173276	ENSG00000173276		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	13083	protein-coding gene	gene with protein product			"""zinc finger protein 295"""	ZNF295			Standard	NM_020727		Approved	KIAA1227	uc002yzy.4	Q9ULJ3	OTTHUMG00000086789	ENST00000310826.5:c.2900C>T	21.37:g.43411305G>A	ENSP00000308759:p.Ser967Leu	Somatic	265	1	0.00377358		WXS	Illumina HiSeq	Phase_I	414	6	0.0144928	NM_001098402	Q5R2W1|Q5R2W2|Q6P4R0	Missense_Mutation	SNP	ENST00000310826.5	37	CCDS13678.1	.	.	.	.	.	.	.	.	.	.	G	10.40	1.339361	0.24339	.	.	ENSG00000173276	ENST00000398505;ENST00000310826;ENST00000398499;ENST00000398511	T;T;T;T	0.08282	3.41;3.11;3.11;3.11	5.26	4.38	0.52667	.	0.631136	0.15354	N	0.266811	T	0.05593	0.0147	N	0.14661	0.345	0.09310	N	1	P;B	0.35192	0.489;0.177	B;B	0.27380	0.079;0.008	T	0.30707	-0.9969	10	0.49607	T	0.09	-1.4281	13.8002	0.63194	0.0738:0.0:0.9262:0.0	.	766;967	Q9ULJ3-2;Q9ULJ3	.;ZN295_HUMAN	L	766;967;967;967	ENSP00000381517:S766L;ENSP00000308759:S967L;ENSP00000381512:S967L;ENSP00000381523:S967L	ENSP00000308759:S967L	S	-	2	0	ZNF295	42284374	0.940000	0.31905	0.005000	0.12908	0.412000	0.31113	5.241000	0.65384	1.240000	0.43803	0.655000	0.94253	TCG	.	.	none		0.517	ZBTB21-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195308.1	NM_020727	
CCDC146	57639	hgsc.bcm.edu	37	7	76908080	76908080	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr7:76908080C>T	ENST00000285871.4	+	12	1579	c.1452C>T	c.(1450-1452)acC>acT	p.T484T	CCDC146_ENST00000431197.1_Silent_p.T198T|CCDC146_ENST00000415740.2_3'UTR	NM_020879.2	NP_065930.2	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146	484								p.T484T(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)				AAAAATACACCAACATTGTTA	0.299																																					p.T484T		Atlas-SNP	.											CCDC146,NS,carcinoma,0,1	CCDC146	87	1	1	Substitution - coding silent(1)	kidney(1)	c.C1452T						scavenged	.						66.0	63.0	64.0					7																	76908080		2202	4298	6500	SO:0001819	synonymous_variant	57639	exon12			ATACACCAACATT	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.1452C>T	7.37:g.76908080C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	107	2	0.0186916	NM_020879	A8K8X6|Q9P223	Silent	SNP	ENST00000285871.4	37	CCDS34671.1																																																																																			.	.	none		0.299	CCDC146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341449.1	NM_020879	
RAB11FIP4	84440	hgsc.bcm.edu	37	17	29850575	29850575	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr17:29850575C>T	ENST00000325874.8	+	8	1204	c.975C>T	c.(973-975)acC>acT	p.T325T	RAB11FIP4_ENST00000394744.2_Silent_p.T223T	NM_032932.3	NP_116321.2	Q86YS3	RFIP4_HUMAN	RAB11 family interacting protein 4 (class II)	325	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)				ATGGCAGCACCGAAGACCTGT	0.607																																					p.T325T		Atlas-SNP	.											RAB11FIP4,caecum,carcinoma,0,1	RAB11FIP4	65	1	0			c.C975T						scavenged	.						158.0	145.0	150.0					17																	29850575		2203	4300	6503	SO:0001819	synonymous_variant	84440	exon8			CAGCACCGAAGAC	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.975C>T	17.37:g.29850575C>T		Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	268	6	0.0223881	NM_032932	Q52LI1|Q8N829|Q8NDT7|Q969D8	Silent	SNP	ENST00000325874.8	37	CCDS11267.1																																																																																			.	.	none		0.607	RAB11FIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256195.2	NM_032932	
PDZD7	79955	hgsc.bcm.edu	37	10	102778029	102778029	+	Missense_Mutation	SNP	T	T	G	rs555444131	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr10:102778029T>G	ENST00000370215.3	-	9	1574	c.1349A>C	c.(1348-1350)gAg>gCg	p.E450A		NM_024895.4	NP_079171.1	Q9H5P4	PDZD7_HUMAN	PDZ domain containing 7	450						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)		CCCCGACTTCTCCTTCTTCCG	0.667																																					p.E450A		Atlas-SNP	.											.	PDZD7	101	.	0			c.A1349C						PASS	.						42.0	42.0	42.0					10																	102778029		2203	4300	6503	SO:0001583	missense	79955	exon9			GACTTCTCCTTCT	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.1349A>C	10.37:g.102778029T>G	ENSP00000359234:p.Glu450Ala	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	110	45	0.409091	NM_001195263	D5FJ77|Q8N321	Missense_Mutation	SNP	ENST00000370215.3	37	CCDS31269.1	.	.	.	.	.	.	.	.	.	.	T	15.48	2.844861	0.51164	.	.	ENSG00000186862	ENST00000393462;ENST00000370215	T	0.14266	2.52	3.98	2.75	0.32379	.	1.878030	0.03231	N	0.179010	T	0.14184	0.0343	L	0.34521	1.04	0.33421	D	0.579826	B;B	0.30406	0.278;0.122	B;B	0.30572	0.057;0.117	T	0.23547	-1.0185	10	0.62326	D	0.03	.	8.9983	0.36066	0.0:0.0:0.1856:0.8144	.	450;450	Q9H5P4;Q9H5P4-2	PDZD7_HUMAN;.	A	450	ENSP00000359234:E450A	ENSP00000359234:E450A	E	-	2	0	PDZD7	102768019	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	3.560000	0.53763	1.661000	0.50771	0.418000	0.28097	GAG	.	.	none		0.667	PDZD7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049883.1	NM_024895	
TRPS1	7227	hgsc.bcm.edu	37	8	116599566	116599566	+	Missense_Mutation	SNP	C	C	T	rs200408178		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr8:116599566C>T	ENST00000220888.5	-	4	2482	c.2323G>A	c.(2323-2325)Ggg>Agg	p.G775R	TRPS1_ENST00000395715.3_Missense_Mutation_p.G788R|TRPS1_ENST00000520276.1_Missense_Mutation_p.G779R|TRPS1_ENST00000519076.1_Missense_Mutation_p.G529R|TRPS1_ENST00000519674.1_Missense_Mutation_p.G775R			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	775	Mediates interaction with GLI3.				chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			TCTTTGAGCCCGTCCTTCTCT	0.507									Langer-Giedion syndrome				C|||	1	0.000199681	0.0	0.0014	5008	,	,		19874	0.0		0.0	False		,,,				2504	0.0				p.G788R		Atlas-SNP	.											TRPS1_ENST00000395715,right_upper_lobe,carcinoma,+1,2	TRPS1	516	2	0			c.G2362A						scavenged	.						290.0	298.0	296.0					8																	116599566		1952	4141	6093	SO:0001583	missense	7227	exon5	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	TGAGCCCGTCCTT	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447		"""GATA zinc finger domain containing"", ""Zinc fingers, C2H2-type"""	12340	protein-coding gene	gene with protein product		604386				8530105, 10615131, 10647898	Standard	NM_001282903		Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000220888.5:c.2323G>A	8.37:g.116599566C>T	ENSP00000220888:p.Gly775Arg	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	113	2	0.0176991	NM_014112	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Missense_Mutation	SNP	ENST00000220888.5	37		1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	8.916	0.959915	0.18507	.	.	ENSG00000104447	ENST00000395715;ENST00000220888;ENST00000519076;ENST00000520276;ENST00000519674	D;D;D;D;T	0.98249	-4.82;-4.79;-4.78;-4.79;0.99	5.76	3.98	0.46160	.	0.351400	0.30419	N	0.009675	D	0.94258	0.8156	N	0.24115	0.695	0.29039	N	0.885228	B;B;B	0.27351	0.176;0.11;0.176	B;B;B	0.15870	0.014;0.006;0.014	D	0.90361	0.4373	10	0.72032	D	0.01	.	9.4407	0.38666	0.0:0.7859:0.0:0.2141	.	779;775;788	Q9UHF7-3;Q9UHF7;Q9UHF7-2	.;TRPS1_HUMAN;.	R	788;775;529;779;775	ENSP00000379065:G788R;ENSP00000220888:G775R;ENSP00000428910:G529R;ENSP00000428680:G779R;ENSP00000429174:G775R	ENSP00000220888:G775R	G	-	1	0	TRPS1	116668741	0.979000	0.34478	0.687000	0.30102	0.572000	0.35998	3.117000	0.50407	0.790000	0.33803	0.655000	0.94253	GGG	C|1.000;T|0.000	0.000	strong		0.507	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112	
ZSCAN32	54925	hgsc.bcm.edu	37	16	3434848	3434848	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr16:3434848T>C	ENST00000396852.4	-	6	1152	c.845A>G	c.(844-846)cAg>cGg	p.Q282R	ZSCAN32_ENST00000304926.3_Missense_Mutation_p.Q70R|ZSCAN32_ENST00000574940.1_Missense_Mutation_p.Q282R|ZSCAN32_ENST00000573830.1_5'UTR|ZSCAN32_ENST00000422427.2_Missense_Mutation_p.Q70R|ZSCAN32_ENST00000396846.3_Missense_Mutation_p.Q282R|ZSCAN32_ENST00000439568.2_5'UTR	NM_001284527.1|NM_001284529.1	NP_001271456.1|NP_001271458.1	Q9NX65	ZSC32_HUMAN	zinc finger and SCAN domain containing 32	282	KRAB.				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)										CTGGCTGTTCTGCTGACAGGT	0.532																																					p.Q70R		Atlas-SNP	.											.	.	.	.	0			c.A209G						PASS	.						104.0	110.0	108.0					16																	3434848		2197	4300	6497	SO:0001583	missense	54925	exon5			CTGTTCTGCTGAC	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.845A>G	16.37:g.3434848T>C	ENSP00000380061:p.Gln282Arg	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	128	31	0.242188	NM_017810	B4DWL5|C9JB03|Q6WMU8|Q7Z6G2|Q8NFX8|Q9BU74	Missense_Mutation	SNP	ENST00000396852.4	37		.	.	.	.	.	.	.	.	.	.	T	0.032	-1.329858	0.01298	.	.	ENSG00000140987	ENST00000304926;ENST00000396852;ENST00000396846;ENST00000422427	T;T;T;T	0.36699	1.24;1.24;1.24;1.24	3.68	-0.497	0.12023	.	1.118750	0.07237	U	0.863657	T	0.09379	0.0231	N	0.00517	-1.405	0.09310	N	1	B;B;B	0.21606	0.002;0.058;0.058	B;B;B	0.22880	0.005;0.042;0.025	T	0.30119	-0.9989	10	0.02654	T	1	.	7.606	0.28103	0.0:0.1686:0.0:0.8314	.	70;70;282	B4DR24;Q9NX65;Q6WMU8	.;ZN434_HUMAN;.	R	70;282;282;70	ENSP00000302502:Q70R;ENSP00000380061:Q282R;ENSP00000380057:Q282R;ENSP00000407312:Q70R	ENSP00000302502:Q70R	Q	-	2	0	ZNF434	3374849	0.000000	0.05858	0.000000	0.03702	0.073000	0.16967	-0.014000	0.12656	-0.454000	0.07066	-0.912000	0.02778	CAG	.	.	none		0.532	ZSCAN32-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000251509.2	NM_017810	
NAP1L3	4675	hgsc.bcm.edu	37	X	92928107	92928107	+	Missense_Mutation	SNP	C	C	A	rs62635803		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:92928107C>A	ENST00000373079.3	-	1	460	c.197G>T	c.(196-198)gGc>gTc	p.G66V	NAP1L3_ENST00000475430.2_Missense_Mutation_p.G59V|FAM133A_ENST00000322139.4_5'Flank|FAM133A_ENST00000332647.4_5'Flank|FAM133A_ENST00000355813.5_5'Flank|FAM133A_ENST00000538690.1_5'Flank	NM_004538.5	NP_004529.2	Q99457	NP1L3_HUMAN	nucleosome assembly protein 1-like 3	66	Ser-rich.				nucleosome assembly (GO:0006334)	nucleus (GO:0005634)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	34						gctagtgctgccgctgctgct	0.612													C|||	27	0.00715232	0.0204	0.0	3775	,	,		7467	0.0		0.0	False		,,,				2504	0.0				p.G66V		Atlas-SNP	.											.	NAP1L3	81	.	0			c.G197T						PASS	.	C	VAL/GLY	81,3313		1,68,11,1394,457	8.0	9.0	9.0		197	0.9	0.1	X	dbSNP_129	9	0,5910		0,0,0,2185,1540	yes	missense	NAP1L3	NM_004538.5	109	1,68,11,3579,1997	AA,AC,A,CC,C		0.0,2.3866,0.8706	probably-damaging	66/507	92928107	81,9223	1931	3725	5656	SO:0001583	missense	4675	exon1			GTGCTGCCGCTGC		CCDS14465.1	Xq21.3-q22	2008-08-01			ENSG00000186310	ENSG00000186310			7639	protein-coding gene	gene with protein product		300117				8976385	Standard	NM_004538		Approved	MB20, NPL3, MGC26312	uc004efq.3	Q99457	OTTHUMG00000021974	ENST00000373079.3:c.197G>T	X.37:g.92928107C>A	ENSP00000362171:p.Gly66Val	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	68	14	0.205882	NM_004538	B2RCM0|O60788	Missense_Mutation	SNP	ENST00000373079.3	37	CCDS14465.1	12	0.007233273056057866	9	0.01859504132231405	0	0.0	0	0.0	0	0.0	C	3.961	-0.010248	0.07727	0.023866	0.0	ENSG00000186310	ENST00000373079;ENST00000543136	T	0.29142	1.58	0.913	0.913	0.19354	.	0.385153	0.26231	N	0.025574	T	0.06234	0.0161	N	0.14661	0.345	0.32519	N	0.536487	B	0.30482	0.281	B	0.22753	0.041	T	0.26155	-1.0111	9	0.12766	T	0.61	.	.	.	.	.	66	Q99457	NP1L3_HUMAN	V	66;59	ENSP00000362171:G66V	ENSP00000362171:G66V	G	-	2	0	NAP1L3	92814763	0.001000	0.12720	0.051000	0.19133	0.018000	0.09664	0.098000	0.15189	0.718000	0.32166	0.292000	0.19580	GGC	C|0.992;A|0.008	0.008	strong		0.612	NAP1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057449.1	NM_004538	
SAP130	79595	hgsc.bcm.edu	37	2	128758026	128758026	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:128758026C>T	ENST00000259235.3	-	8	1079	c.950G>A	c.(949-951)aGg>aAg	p.R317K	SAP130_ENST00000357702.5_Missense_Mutation_p.R317K|SAP130_ENST00000259234.6_Missense_Mutation_p.R291K	NM_024545.3	NP_078821.2	Q9H0E3	SP130_HUMAN	Sin3A-associated protein, 130kDa	317					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|STAGA complex (GO:0030914)	transcription coactivator activity (GO:0003713)			NS(4)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(2)	45	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0771)		CAAGGTTGGCCTACTGAAAAG	0.428																																					p.R317K		Atlas-SNP	.											.	SAP130	169	.	0			c.G950A						PASS	.						155.0	135.0	141.0					2																	128758026		2203	4300	6503	SO:0001583	missense	79595	exon8			GTTGGCCTACTGA	BC017453	CCDS2153.1, CCDS54397.1	2q14.3	2008-02-05	2006-02-02		ENSG00000136715	ENSG00000136715			29813	protein-coding gene	gene with protein product		609697	"""sin3A-associated protein, 130kDa"""			11230166, 12724404	Standard	NM_001145928		Approved	FLJ12761	uc010fmd.2	Q9H0E3	OTTHUMG00000131571	ENST00000259235.3:c.950G>A	2.37:g.128758026C>T	ENSP00000259235:p.Arg317Lys	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	86	20	0.232558	NM_001145928	B7ZLM3|C9K0X9|Q4ZFV4|Q53T46|Q8WVW4|Q9H9G8	Missense_Mutation	SNP	ENST00000259235.3	37	CCDS2153.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.543573	0.86022	.	.	ENSG00000136715	ENST00000357702;ENST00000259235;ENST00000259234	.	.	.	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	T	0.65523	0.2699	L	0.29908	0.895	0.80722	D	1	D;D	0.67145	0.996;0.99	D;D	0.76071	0.987;0.979	T	0.57911	-0.7729	9	0.16896	T	0.51	-20.9485	19.5036	0.95105	0.0:1.0:0.0:0.0	.	317;317	B7ZLM3;Q9H0E3	.;SP130_HUMAN	K	317;317;291	.	ENSP00000259234:R291K	R	-	2	0	SAP130	128474496	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.105000	0.77031	2.672000	0.90937	0.650000	0.86243	AGG	.	.	none		0.428	SAP130-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254436.3	NM_024545	
TNFAIP8	25816	hgsc.bcm.edu	37	5	118728686	118728686	+	Silent	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:118728686G>A	ENST00000503646.1	+	3	895	c.207G>A	c.(205-207)gaG>gaA	p.E69E	TNFAIP8_ENST00000504771.2_Silent_p.E69E|TNFAIP8_ENST00000415806.2_3'UTR|TNFAIP8_ENST00000274456.6_Silent_p.E59E|TNFAIP8_ENST00000513374.1_Silent_p.E81E|TNFAIP8_ENST00000504642.1_Silent_p.E71E			O95379	TFIP8_HUMAN	tumor necrosis factor, alpha-induced protein 8	69					defense response to Gram-positive bacterium (GO:0050830)|interleukin-1 beta production (GO:0032611)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)	cytoplasm (GO:0005737)	cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)			ovary(1)	1		all_cancers(142;0.0317)|Prostate(80;0.111)|Breast(839;0.231)		Epithelial(69;4.63e-83)|OV - Ovarian serous cystadenocarcinoma(64;1.39e-82)|all cancers(49;4.88e-75)|GBM - Glioblastoma multiforme(465;0.00338)|BRCA - Breast invasive adenocarcinoma(61;0.0148)|COAD - Colon adenocarcinoma(49;0.0829)		AGGAGGCAGAGAAGATCATCA	0.428																																					p.E69E		Atlas-SNP	.											.	TNFAIP8	12	.	0			c.G207A						PASS	.						70.0	67.0	68.0					5																	118728686		2021	4191	6212	SO:0001819	synonymous_variant	25816	exon2			GGCAGAGAAGATC	AF070671	CCDS47257.1, CCDS47258.1, CCDS68933.1	5q23.1	2008-02-05			ENSG00000145779	ENSG00000145779			17260	protein-coding gene	gene with protein product		612111				10233894, 10644768	Standard	NM_001286813		Approved	GG2-1, MDC-3.13, SCC-S2	uc003ksi.3	O95379	OTTHUMG00000162949	ENST00000503646.1:c.207G>A	5.37:g.118728686G>A		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	170	54	0.317647	NM_014350	B3KMH1|B3KMI2|B7Z713|Q9P1Q1|Q9UER5|Q9UP47	Silent	SNP	ENST00000503646.1	37	CCDS47258.1																																																																																			.	.	none		0.428	TNFAIP8-002	PUTATIVE	alternative_5_UTR|basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000371134.2	NM_014350	
MYPN	84665	hgsc.bcm.edu	37	10	69959256	69959256	+	Silent	SNP	C	C	T	rs144488384	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr10:69959256C>T	ENST00000358913.5	+	17	3905	c.3417C>T	c.(3415-3417)cgC>cgT	p.R1139R	MYPN_ENST00000354393.2_Silent_p.R864R|MYPN_ENST00000540630.1_Silent_p.R1139R	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	1139	Ig-like 4.|Interaction with ACTN.				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)	p.R1139R(1)		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						TCACTCAGCGCGACGCAGGGA	0.547																																					p.R1139R		Atlas-SNP	.											MYPN,NS,carcinoma,0,1	MYPN	189	1	1	Substitution - coding silent(1)	endometrium(1)	c.C3417T						scavenged	.	C		1,4405	2.1+/-5.4	0,1,2202	126.0	104.0	111.0		3417	-10.8	0.0	10	dbSNP_134	111	0,8600		0,0,4300	no	coding-synonymous	MYPN	NM_032578.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		1139/1321	69959256	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	84665	exon17			TCAGCGCGACGCA	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.3417C>T	10.37:g.69959256C>T		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	245	3	0.0122449	NM_032578	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Silent	SNP	ENST00000358913.5	37	CCDS7275.1																																																																																			C|1.000;T|0.000	0.000	weak		0.547	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578	
LRRC15	131578	hgsc.bcm.edu	37	3	194080325	194080325	+	Missense_Mutation	SNP	C	C	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:194080325C>G	ENST00000347624.3	-	2	1533	c.1448G>C	c.(1447-1449)aGt>aCt	p.S483T	LRRC15_ENST00000428839.1_Missense_Mutation_p.S489T|LRRC15_ENST00000439944.2_Missense_Mutation_p.S489T	NM_130830.4	NP_570843.2	Q8TF66	LRC15_HUMAN	leucine rich repeat containing 15	483					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)		TTCTGGGTAACTAGGCACCTC	0.532																																					p.S489T		Atlas-SNP	.											.	LRRC15	137	.	0			c.G1466C						PASS	.						162.0	151.0	155.0					3																	194080325		2203	4300	6503	SO:0001583	missense	131578	exon3			GGGTAACTAGGCA	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.1448G>C	3.37:g.194080325C>G	ENSP00000306276:p.Ser483Thr	Somatic	291	0	0		WXS	Illumina HiSeq	Phase_I	242	55	0.227273	NM_001135057	Q495Q6|Q7RTN7	Missense_Mutation	SNP	ENST00000347624.3	37	CCDS3306.1	.	.	.	.	.	.	.	.	.	.	C	0.557	-0.846990	0.02651	.	.	ENSG00000172061	ENST00000347624;ENST00000439944;ENST00000428839	T;T;T	0.56941	0.43;0.45;0.45	5.24	-0.0103	0.13997	.	1.652070	0.03016	N	0.150004	T	0.37544	0.1007	N	0.19112	0.55	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.0;0.002	T	0.17592	-1.0364	10	0.13470	T	0.59	.	10.0974	0.42484	0.253:0.3793:0.3677:0.0	.	483;489	Q8TF66;Q8TF66-2	LRC15_HUMAN;.	T	483;489;489	ENSP00000306276:S483T;ENSP00000389128:S489T;ENSP00000413707:S489T	ENSP00000306276:S483T	S	-	2	0	LRRC15	195561620	0.000000	0.05858	0.003000	0.11579	0.006000	0.05464	-0.283000	0.08433	-0.217000	0.10033	-0.309000	0.09137	AGT	.	.	none		0.532	LRRC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342858.2		
ZYG11B	79699	hgsc.bcm.edu	37	1	53237431	53237431	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:53237431C>T	ENST00000294353.6	+	3	1081	c.936C>T	c.(934-936)ggC>ggT	p.G312G	ZYG11B_ENST00000443756.2_Silent_p.G312G|ZYG11B_ENST00000545132.1_Silent_p.G312G	NM_024646.2	NP_078922.1	Q9C0D3	ZY11B_HUMAN	zyg-11 family member B, cell cycle regulator	312										breast(1)|endometrium(1)|kidney(6)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	30						TCCTCACAGGCGAAGGACATT	0.373																																					p.G312G		Atlas-SNP	.											ZYG11B,NS,carcinoma,0,1	ZYG11B	61	1	0			c.C936T						scavenged	.						81.0	80.0	80.0					1																	53237431		2203	4295	6498	SO:0001819	synonymous_variant	79699	exon3			CACAGGCGAAGGA	AB051517	CCDS30717.1	1p32.3	2013-01-17	2012-12-10	2005-07-11	ENSG00000162378	ENSG00000162378		"""ZYG11 cell cycle regulator family"""	25820	protein-coding gene	gene with protein product			"""zyg-11 homolog (C. elegans)"", ""zyg-11 homolog B (C. elegans)"""	ZYG11		11214970	Standard	NM_024646		Approved	FLJ13456	uc001cuj.3	Q9C0D3	OTTHUMG00000008938	ENST00000294353.6:c.936C>T	1.37:g.53237431C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	157	2	0.0127389	NM_024646	Q8N2X3|Q9H8L8	Silent	SNP	ENST00000294353.6	37	CCDS30717.1																																																																																			.	.	none		0.373	ZYG11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024749.1	NM_024646	
ITPKB	3707	hgsc.bcm.edu	37	1	226924388	226924388	+	Missense_Mutation	SNP	C	C	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:226924388C>G	ENST00000272117.3	-	1	771	c.772G>C	c.(772-774)Gag>Cag	p.E258Q	ITPKB_ENST00000366784.1_Missense_Mutation_p.E258Q|ITPKB_ENST00000429204.1_Missense_Mutation_p.E258Q			P27987	IP3KB_HUMAN	inositol-trisphosphate 3-kinase B	258					cell surface receptor signaling pathway (GO:0007166)|inositol phosphate metabolic process (GO:0043647)|MAPK cascade (GO:0000165)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of Ras protein signal transduction (GO:0046579)|positive thymic T cell selection (GO:0045059)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(1)	30		Prostate(94;0.0773)				ATACCCTTCTCCATCCTTACA	0.597																																					p.E258Q	Colon(84;110 1851 5306 33547)	Atlas-SNP	.											.	ITPKB	158	.	0			c.G772C						PASS	.						49.0	48.0	49.0					1																	226924388		2203	4300	6503	SO:0001583	missense	3707	exon2			CCTTCTCCATCCT	AJ242780	CCDS1555.1	1q42.12	2011-04-28	2011-04-28		ENSG00000143772	ENSG00000143772	2.7.1.127		6179	protein-coding gene	gene with protein product		147522	"""inositol 1,4,5-trisphosphate 3-kinase B"""			1654894, 1330886	Standard	NM_002221		Approved	IP3KB, IP3-3KB	uc010pvo.2	P27987	OTTHUMG00000037582	ENST00000272117.3:c.772G>C	1.37:g.226924388C>G	ENSP00000272117:p.Glu258Gln	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	134	62	0.462687	NM_002221	Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47	Missense_Mutation	SNP	ENST00000272117.3	37	CCDS1555.1	.	.	.	.	.	.	.	.	.	.	C	16.57	3.159960	0.57368	.	.	ENSG00000143772	ENST00000272117;ENST00000429204;ENST00000366784	T;T;T	0.35973	1.32;1.32;1.28	4.6	3.68	0.42216	.	0.263808	0.27064	N	0.021114	T	0.23014	0.0556	N	0.24115	0.695	0.27144	N	0.961579	P	0.50443	0.935	B	0.42245	0.381	T	0.06588	-1.0818	10	0.21014	T	0.42	-16.2733	10.3145	0.43729	0.0:0.905:0.0:0.095	.	258	P27987	IP3KB_HUMAN	Q	258	ENSP00000272117:E258Q;ENSP00000411152:E258Q;ENSP00000355748:E258Q	ENSP00000272117:E258Q	E	-	1	0	ITPKB	224991011	0.888000	0.30383	0.751000	0.31187	0.218000	0.24690	1.098000	0.31000	1.137000	0.42214	0.561000	0.74099	GAG	.	.	none		0.597	ITPKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091632.1	NM_002221	
TIAM2	26230	hgsc.bcm.edu	37	6	155577707	155577707	+	Missense_Mutation	SNP	G	G	A	rs116807909	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr6:155577707G>A	ENST00000461783.3	+	29	5831	c.4558G>A	c.(4558-4560)Gag>Aag	p.E1520K	TIAM2_ENST00000360366.4_Missense_Mutation_p.E1544K|TIAM2_ENST00000529824.2_Missense_Mutation_p.E1549K|RP11-477D19.2_ENST00000435295.1_RNA|TIAM2_ENST00000528391.2_Missense_Mutation_p.E864K|TIAM2_ENST00000456877.2_Missense_Mutation_p.E832K|TIAM2_ENST00000275246.7_Missense_Mutation_p.E445K|TIAM2_ENST00000367174.2_Missense_Mutation_p.E896K|TIAM2_ENST00000318981.5_Missense_Mutation_p.E1520K|TIAM2_ENST00000456144.1_Missense_Mutation_p.E1549K			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	1520					apoptotic signaling pathway (GO:0097190)|cellular lipid metabolic process (GO:0044255)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(20)|lung(21)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	65		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		GGACTCTGACGAGGGCAGCTT	0.597													G|||	3	0.000599042	0.0023	0.0	5008	,	,		17970	0.0		0.0	False		,,,				2504	0.0				p.E1520K		Atlas-SNP	.											.	TIAM2	161	.	0			c.G4558A						PASS	.	G	LYS/GLU,LYS/GLU,	11,4395	17.9+/-39.9	0,11,2192	35.0	38.0	37.0		1333,4558,	5.9	1.0	6	dbSNP_132	37	0,8598		0,0,4299	yes	missense,missense,utr-3	TIAM2,TFB1M	NM_001010927.2,NM_012454.3,NM_016020.3	56,56,	0,11,6491	AA,AG,GG		0.0,0.2497,0.0846	benign,benign,	445/627,1520/1702,	155577707	11,12993	2203	4299	6502	SO:0001583	missense	26230	exon26			TCTGACGAGGGCA		CCDS34558.1, CCDS34559.1	6q25	2013-01-10			ENSG00000146426	ENSG00000146426		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11806	protein-coding gene	gene with protein product		604709				10512681	Standard	NM_012454		Approved	STEF	uc003qqe.3	Q8IVF5	OTTHUMG00000015880	ENST00000461783.3:c.4558G>A	6.37:g.155577707G>A	ENSP00000437188:p.Glu1520Lys	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	183	85	0.464481	NM_012454	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Missense_Mutation	SNP	ENST00000461783.3	37	CCDS34558.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	18.40	3.615581	0.66672	0.002497	0.0	ENSG00000146426	ENST00000461783;ENST00000528928;ENST00000456144;ENST00000318981;ENST00000367174;ENST00000360366;ENST00000529824;ENST00000456877;ENST00000528391;ENST00000275246	T;T;T;T;T;T;T;T;T	0.08546	3.56;3.5;3.56;3.39;3.56;3.5;3.38;3.38;3.08	5.86	5.86	0.93980	.	0.351137	0.32357	N	0.006205	T	0.04497	0.0123	L	0.59436	1.845	0.37039	D	0.897031	P;P;P;P	0.52061	0.95;0.937;0.854;0.896	B;B;B;B	0.38296	0.154;0.27;0.27;0.139	T	0.43147	-0.9409	10	0.10377	T	0.69	.	18.3756	0.90435	0.0:0.0:1.0:0.0	.	864;1549;1544;1520	E9PKT1;Q8IVF5-2;Q8IVF5-5;Q8IVF5	.;.;.;TIAM2_HUMAN	K	1520;1766;1549;1520;896;1544;1549;832;864;445	ENSP00000437188:E1520K;ENSP00000407746:E1549K;ENSP00000327315:E1520K;ENSP00000356142:E896K;ENSP00000353528:E1544K;ENSP00000433348:E1549K;ENSP00000407183:E832K;ENSP00000435335:E864K;ENSP00000275246:E445K	ENSP00000275246:E445K	E	+	1	0	TIAM2	155619399	1.000000	0.71417	0.994000	0.49952	0.865000	0.49528	6.868000	0.75516	2.780000	0.95670	0.585000	0.79938	GAG	G|0.998;A|0.002	0.002	strong		0.597	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454	
CELA3B	23436	hgsc.bcm.edu	37	1	22304901	22304901	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:22304901G>A	ENST00000337107.6	+	2	102	c.83G>A	c.(82-84)cGc>cAc	p.R28H	RN7SL421P_ENST00000582599.1_RNA	NM_007352.2	NP_031378.1	P08861	CEL3B_HUMAN	chymotrypsin-like elastase family, member 3B	28					cholesterol metabolic process (GO:0008203)|proteolysis (GO:0006508)		peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			breast(2)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	8						CCTTCCAGCCGCGTTGTCAAT	0.612																																					p.R28H		Atlas-SNP	.											.	CELA3B	24	.	0			c.G83A						PASS	.						166.0	103.0	124.0					1																	22304901		2203	4300	6503	SO:0001583	missense	23436	exon2			CCAGCCGCGTTGT	M18692	CCDS219.1	1p36.12	2009-05-05	2009-05-05	2009-05-05	ENSG00000219073	ENSG00000219073	3.4.21.70		15945	protein-coding gene	gene with protein product	"""proteinase E"", ""elastase 1"", ""cholesterol-binding pancreatic protease"", ""pancreatic endopeptidase E"""		"""elastase 3B, pancreatic"""	ELA3B		2826474, 2460440	Standard	NM_007352		Approved	CBPP	uc001bfk.3	P08861	OTTHUMG00000002758	ENST00000337107.6:c.83G>A	1.37:g.22304901G>A	ENSP00000338369:p.Arg28His	Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	239	45	0.188285	NM_007352	B2RE44|P11423|Q5VU28|Q5VU29|Q5VU30	Missense_Mutation	SNP	ENST00000337107.6	37	CCDS219.1	.	.	.	.	.	.	.	.	.	.	G	37	6.058413	0.97246	.	.	ENSG00000219073	ENST00000337107;ENST00000374666	T;T	0.23552	1.9;1.9	5.1	5.1	0.69264	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (1);	0.000000	0.85682	D	0.000000	T	0.53158	0.1779	M	0.78049	2.395	0.36974	D	0.893974	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.984	T	0.64588	-0.6372	10	0.87932	D	0	-47.2794	16.0019	0.80301	0.0:0.0:1.0:0.0	.	28;28	B1AQ52;P08861	.;CEL3B_HUMAN	H	28;44	ENSP00000338369:R28H;ENSP00000363798:R44H	ENSP00000338369:R28H	R	+	2	0	CELA3B	22177488	0.998000	0.40836	0.262000	0.24481	0.821000	0.46438	8.940000	0.92958	2.375000	0.81037	0.650000	0.86243	CGC	.	.	none		0.612	CELA3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007797.1	NM_007352	
CCDC64	92558	hgsc.bcm.edu	37	12	120518805	120518805	+	Missense_Mutation	SNP	G	G	A	rs373363052		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:120518805G>A	ENST00000397558.2	+	7	1423	c.1423G>A	c.(1423-1425)Gac>Aac	p.D475N	CCDC64_ENST00000446727.2_Missense_Mutation_p.D146N|CCDC64_ENST00000257583.4_Missense_Mutation_p.D172N	NM_207311.2	NP_997194.2	Q6ZP65	BICR1_HUMAN	coiled-coil domain containing 64	475					Golgi to secretory granule transport (GO:0055107)|neuron projection development (GO:0031175)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	dynactin binding (GO:0034452)|Rab GTPase binding (GO:0017137)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(2)|lung(4)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	22	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CAGGGACCGCGACGAGGCCAT	0.438																																					p.D475N		Atlas-SNP	.											.	CCDC64	40	.	0			c.G1423A						PASS	.	G	ASN/ASP	0,4044		0,0,2022	70.0	79.0	76.0		1423	5.3	1.0	12		76	1,8361		0,1,4180	no	missense	CCDC64	NM_207311.2	23	0,1,6202	AA,AG,GG		0.012,0.0,0.0081	probably-damaging	475/574	120518805	1,12405	2022	4181	6203	SO:0001583	missense	92558	exon7			GACCGCGACGAGG	U88834, AK129960	CCDS41845.1	12q24.23	2006-01-24				ENSG00000135127			28095	protein-coding gene	gene with protein product							Standard	NM_207311		Approved	FLJ26450	uc001txl.1	Q6ZP65	OTTHUMG00000169311	ENST00000397558.2:c.1423G>A	12.37:g.120518805G>A	ENSP00000380690:p.Asp475Asn	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	29	9	0.310345	NM_207311	A8MUC8|B4DWL0|B5MDJ0|O95000	Missense_Mutation	SNP	ENST00000397558.2	37	CCDS41845.1	.	.	.	.	.	.	.	.	.	.	G	35	5.417810	0.96092	0.0	1.2E-4	ENSG00000135127	ENST00000397558;ENST00000446727;ENST00000548673;ENST00000257583	T;T;T	0.04862	3.56;3.6;3.54	5.32	5.32	0.75619	.	529.136000	0.00166	N	0.000000	T	0.35038	0.0918	M	0.76170	2.325	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.998	T	0.00699	-1.1604	10	0.87932	D	0	-12.8386	18.9942	0.92806	0.0:0.0:1.0:0.0	.	172;146;475	B4DWL0;B4DNE7;Q6ZP65	.;.;BICR1_HUMAN	N	475;146;193;172	ENSP00000380690:D475N;ENSP00000399658:D146N;ENSP00000447477:D193N	ENSP00000257583:D172N	D	+	1	0	CCDC64	119003188	1.000000	0.71417	0.955000	0.39395	0.944000	0.59088	9.731000	0.98807	2.492000	0.84095	0.561000	0.74099	GAC	.	.	weak		0.438	CCDC64-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000403390.2	NM_207311	
CYB5B	80777	hgsc.bcm.edu	37	16	69496394	69496394	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr16:69496394T>C	ENST00000512062.1	+	5	583	c.412T>C	c.(412-414)Tac>Cac	p.Y138H	RP11-140H17.1_ENST00000567834.1_RNA|CYB5B_ENST00000515314.1_Missense_Mutation_p.L118P|CYB5B_ENST00000307892.8_Missense_Mutation_p.Y142H|CYB5B_ENST00000561792.1_Missense_Mutation_p.L127P			O43169	CYB5B_HUMAN	cytochrome b5 type B (outer mitochondrial membrane)	138					oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)	heme binding (GO:0020037)|metal ion binding (GO:0046872)			endometrium(3)|kidney(3)|lung(2)	8		Ovarian(137;0.101)				CCTGTACCGCTACTACACATC	0.463																																					p.Y142H		Atlas-SNP	.											CYB5B,NS,carcinoma,-1,1	CYB5B	12	1	0			c.T424C						scavenged	.						120.0	113.0	115.0					16																	69496394		1867	4102	5969	SO:0001583	missense	80777	exon5			TACCGCTACTACA		CCDS10880.2	16q22.1	2006-02-02			ENSG00000103018	ENSG00000103018			24374	protein-coding gene	gene with protein product		611964				11867265, 14733950	Standard	NM_030579		Approved	CYB5-M	uc002exg.1	O43169	OTTHUMG00000133020	ENST00000512062.1:c.412T>C	16.37:g.69496394T>C	ENSP00000423679:p.Tyr138His	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	149	2	0.0134228	NM_030579	A8K6B1|Q96CC3|Q9BT35	Missense_Mutation	SNP	ENST00000512062.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.25|13.25	2.180392|2.180392	0.38511|0.38511	.|.	.|.	ENSG00000103018|ENSG00000103018	ENST00000515314|ENST00000512062;ENST00000307892	D|T;T	0.84589|0.11821	-1.87|2.74;2.74	5.89|5.89	3.62|3.62	0.41486|0.41486	.|Aquaporin-like (1);	.|0.224693	.|0.47852	.|N	.|0.000212	T|T	0.11410|0.11410	0.0278|0.0278	L|L	0.49455|0.49455	1.56|1.56	0.32579|0.32579	N|N	0.528701|0.528701	P|B	0.42039|0.06786	0.769|0.001	B|B	0.39840|0.08055	0.311|0.003	T|T	0.16719|0.16719	-1.0393|-1.0393	9|10	0.72032|0.22109	D|T	0.01|0.4	-0.3787|-0.3787	6.397|6.397	0.21618|0.21618	0.0:0.2105:0.0:0.7895|0.0:0.2105:0.0:0.7895	.|.	118|138	D6RFH4|O43169	.|CYB5B_HUMAN	P|H	118|138;142	ENSP00000421492:L118P|ENSP00000423679:Y138H;ENSP00000308430:Y142H	ENSP00000421492:L118P|ENSP00000308430:Y142H	L|Y	+|+	2|1	0|0	CYB5B|CYB5B	68053895|68053895	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.829000|0.829000	0.46940|0.46940	1.641000|1.641000	0.37197|0.37197	0.489000|0.489000	0.27749|0.27749	0.482000|0.482000	0.46254|0.46254	CTA|TAC	.	.	none		0.463	CYB5B-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000256606.2	NM_030579	
NSRP1	84081	hgsc.bcm.edu	37	17	28511766	28511766	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr17:28511766G>A	ENST00000247026.5	+	7	814	c.751G>A	c.(751-753)Gat>Aat	p.D251N	NSRP1_ENST00000540900.3_3'UTR	NM_001261467.1|NM_032141.3	NP_001248396.1|NP_115517.1	Q9H0G5	NSRP1_HUMAN	nuclear speckle splicing regulatory protein 1	251					developmental process (GO:0032502)|mRNA processing (GO:0006397)|nucleocytoplasmic transport (GO:0006913)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	14						CAGTGACTTCGATGCTAAGAG	0.418																																					p.D251N		Atlas-SNP	.											NSRP1,lower_third,carcinoma,0,1	NSRP1	49	1	0			c.G751A						scavenged	.						76.0	71.0	73.0					17																	28511766		2203	4300	6503	SO:0001583	missense	84081	exon7			GACTTCGATGCTA	AL136806	CCDS11255.1, CCDS74025.1	17q11.2	2011-05-24	2011-05-24	2011-05-24	ENSG00000126653	ENSG00000126653			25305	protein-coding gene	gene with protein product			"""coiled-coil domain containing 55"""	CCDC55		11230166	Standard	NM_032141		Approved	DKFZP434K1421, NSrp70	uc002heu.4	Q9H0G5	OTTHUMG00000132754	ENST00000247026.5:c.751G>A	17.37:g.28511766G>A	ENSP00000247026:p.Asp251Asn	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	207	3	0.0144928	NM_032141	Q6FI71	Missense_Mutation	SNP	ENST00000247026.5	37	CCDS11255.1	.	.	.	.	.	.	.	.	.	.	G	16.54	3.151233	0.57151	.	.	ENSG00000126653	ENST00000247026;ENST00000540900;ENST00000394826	T	0.48836	0.8	5.97	5.97	0.96955	.	0.399046	0.29280	N	0.012608	T	0.41903	0.1179	L	0.56769	1.78	0.80722	D	1	P	0.36483	0.555	B	0.23716	0.048	T	0.30238	-0.9985	10	0.25106	T	0.35	-7.5625	17.5657	0.87919	0.0:0.0:1.0:0.0	.	251	Q9H0G5	NSRP1_HUMAN	N	251;182;197	ENSP00000247026:D251N	ENSP00000247026:D251N	D	+	1	0	NSRP1	25535892	1.000000	0.71417	0.998000	0.56505	0.958000	0.62258	3.131000	0.50515	2.828000	0.97474	0.650000	0.86243	GAT	.	.	none		0.418	NSRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256121.2	NM_032141	
KCNK1	3775	hgsc.bcm.edu	37	1	233802348	233802348	+	Silent	SNP	C	C	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:233802348C>G	ENST00000366621.3	+	2	531	c.363C>G	c.(361-363)ggC>ggG	p.G121G	KCNK1_ENST00000366620.1_Silent_p.G5G|KCNK1_ENST00000472190.1_3'UTR	NM_002245.3	NP_002236.1	O00180	KCNK1_HUMAN	potassium channel, subfamily K, member 1	121					potassium ion transport (GO:0006813)|response to nicotine (GO:0035094)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endosome (GO:0005768)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(4)|skin(1)	11		all_cancers(173;0.00217)|all_epithelial(177;0.121)|Prostate(94;0.122)|Acute lymphoblastic leukemia(190;0.175)			Ibutilide(DB00308)|Quinidine barbiturate(DB01346)|Quinidine(DB00908)	CAGGTTATGGCCACACCGTGC	0.502																																					p.G121G		Atlas-SNP	.											KCNK1,colon,carcinoma,+1,1	KCNK1	36	1	0			c.C363G						PASS	.						166.0	119.0	135.0					1																	233802348		2203	4300	6503	SO:0001819	synonymous_variant	3775	exon2			TTATGGCCACACC	U33632	CCDS1599.1	1q42-q43	2012-03-07			ENSG00000135750	ENSG00000135750		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6272	protein-coding gene	gene with protein product		601745				8661042, 16382106	Standard	NM_002245		Approved	K2p1.1, DPK, TWIK-1	uc010pxo.1	O00180	OTTHUMG00000037923	ENST00000366621.3:c.363C>G	1.37:g.233802348C>G		Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	230	108	0.469565	NM_002245	Q13307|Q5T5E8	Silent	SNP	ENST00000366621.3	37	CCDS1599.1																																																																																			.	.	none		0.502	KCNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092565.1	NM_002245	
MAML3	55534	hgsc.bcm.edu	37	4	140811099	140811099	+	Splice_Site	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr4:140811099C>T	ENST00000398940.1	-	1	107	c.108G>A	c.(106-108)caG>caA	p.Q36Q	MAML3_ENST00000509479.2_Silent_p.Q497Q|MAML3_ENST00000327122.5_Silent_p.Q341Q					mastermind-like 3 (Drosophila)									p.Q497Q(2)		breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					gctgctgctgctgctgctgct	0.542																																					p.Q497Q		Atlas-SNP	.											MAML3_ENST00000509479,caecum,carcinoma,0,12	MAML3	192	12	2	Substitution - coding silent(2)	prostate(2)	c.G1491A						scavenged	.						13.0	19.0	17.0					4																	140811099		2117	4226	6343	SO:0001630	splice_region_variant	55534	exon2			CTGCTGCTGCTGC	AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"""mastermind (drosophila)-like 3"""	608991	"""trinucleotide repeat containing 3"""	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000398940.1:c.108+1G>A	4.37:g.140811099C>T		Somatic	86	2	0.0232558		WXS	Illumina HiSeq	Phase_I	94	4	0.0425532	NM_018717		Silent	SNP	ENST00000398940.1	37																																																																																				.	.	none		0.542	MAML3-202	KNOWN	basic	protein_coding	protein_coding			Silent
PRKD1	5587	hgsc.bcm.edu	37	14	30046591	30046591	+	Silent	SNP	A	A	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr14:30046591A>G	ENST00000331968.5	-	18	2821	c.2592T>C	c.(2590-2592)agT>agC	p.S864S	PRKD1_ENST00000415220.2_Silent_p.S872S	NM_002742.2	NP_002733.2	Q15139	KPCD1_HUMAN	protein kinase D1	864					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular response to oxidative stress (GO:0034599)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|negative regulation of cell death (GO:0060548)|negative regulation of endocytosis (GO:0045806)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein autophosphorylation (GO:0046777)|regulation of integrin-mediated signaling pathway (GO:2001044)|regulation of keratinocyte proliferation (GO:0010837)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|lung(32)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	78	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)		TCAGGTCATCACTTTCATGGG	0.498																																					p.S864S		Atlas-SNP	.											.	PRKD1	316	.	0			c.T2592C						PASS	.						145.0	128.0	134.0					14																	30046591		2203	4300	6503	SO:0001819	synonymous_variant	5587	exon18			GTCATCACTTTCA		CCDS9637.1	14q11	2013-01-10	2004-10-28	2004-10-30	ENSG00000184304	ENSG00000184304	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	9407	protein-coding gene	gene with protein product		605435	"""protein kinase C, mu"""	PRKCM		8119958, 10965134	Standard	NM_002742		Approved	PKCM, PKD, PKC-mu	uc001wqh.3	Q15139	OTTHUMG00000140203	ENST00000331968.5:c.2592T>C	14.37:g.30046591A>G		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	189	37	0.195767	NM_002742	A6NL64|B2RAF6	Silent	SNP	ENST00000331968.5	37	CCDS9637.1																																																																																			.	.	none		0.498	PRKD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276611.2	NM_002742	
AFF1	4299	hgsc.bcm.edu	37	4	88026962	88026962	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr4:88026962C>T	ENST00000307808.6	+	9	1740	c.1320C>T	c.(1318-1320)acC>acT	p.T440T	AFF1_ENST00000544085.1_Silent_p.T78T|AFF1_ENST00000395146.4_Silent_p.T447T	NM_005935.2	NP_005926.1	P51825	AFF1_HUMAN	AF4/FMR2 family, member 1	440					positive regulation of transcription, DNA-templated (GO:0045893)	transcription elongation factor complex (GO:0008023)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|large_intestine(2)	3		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)		ATGCCTAGACCCCAGAGAAGC	0.428																																					p.T447T		Atlas-SNP	.											AFF1_ENST00000395146,NS,carcinoma,+1,1	AFF1	102	1	0			c.C1341T						scavenged	.						225.0	215.0	218.0					4																	88026962		2203	4300	6503	SO:0001819	synonymous_variant	4299	exon10			CTAGACCCCAGAG	L22179	CCDS3616.1, CCDS54775.1	4q21.3	2009-08-04	2005-06-27	2005-06-27	ENSG00000172493	ENSG00000172493			7135	protein-coding gene	gene with protein product		159557	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 2"", ""pre-B-cell monocytic leukemia partner 1"""	PBM1, MLLT2		7689231, 1423625, 8353274	Standard	NM_005935		Approved	AF-4, AF4	uc011ccz.2	P51825	OTTHUMG00000130603	ENST00000307808.6:c.1320C>T	4.37:g.88026962C>T		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	185	2	0.0108108	NM_001166693	B4DTU1|E9PBM3	Silent	SNP	ENST00000307808.6	37	CCDS3616.1																																																																																			.	.	none		0.428	AFF1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253053.3	NM_005935	
ZNF816	125893	hgsc.bcm.edu	37	19	53456125	53456125	+	Silent	SNP	G	G	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:53456125G>C	ENST00000357666.4	-	4	369	c.69C>G	c.(67-69)cgC>cgG	p.R23R	ZNF816_ENST00000391786.2_Intron|ZNF816_ENST00000444460.2_Silent_p.R23R|ZNF816_ENST00000434371.2_Silent_p.R23R|ZNF321P_ENST00000391777.3_Silent_p.R23R|ZNF816_ENST00000270457.4_Silent_p.R23R|ZNF816_ENST00000438970.2_Silent_p.R23R|ZNF816_ENST00000535506.1_Silent_p.R23R	NM_001031665.2	NP_001026835.1	Q0VGE8	ZN816_HUMAN	zinc finger protein 816	23					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						TGAAAGTCAAGCGTCCCTAAA	0.408																																					p.R23R		Atlas-SNP	.											.	ZNF816	73	.	0			c.C69G						PASS	.						85.0	93.0	90.0					19																	53456125		2203	4300	6503	SO:0001819	synonymous_variant	125893	exon3			AGTCAAGCGTCCC	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.69C>G	19.37:g.53456125G>C		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	49	14	0.285714	NM_001202457	A8K7H5|Q3KR39|Q659B3	Silent	SNP	ENST00000357666.4	37	CCDS33096.1	.	.	.	.	.	.	.	.	.	.	g	1.272	-0.612855	0.03690	.	.	ENSG00000180257	ENST00000332302	T	0.42513	0.97	1.84	0.498	0.16908	.	.	.	.	.	T	0.42245	0.1194	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.39482	-0.9612	6	0.72032	D	0.01	.	8.3219	0.32134	0.0:0.3546:0.6454:0.0	.	.	.	.	V	59	ENSP00000333199:L59V	ENSP00000333199:L59V	L	-	1	0	ZNF816	58147937	0.000000	0.05858	0.011000	0.14972	0.541000	0.35023	-0.031000	0.12287	0.003000	0.14656	0.305000	0.20034	CTT	.	.	none		0.408	ZNF816-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396132.1	NM_001031665	
SKP1	6500	hgsc.bcm.edu	37	5	133494195	133494195	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:133494195C>T	ENST00000353411.6	-	5	590	c.407G>A	c.(406-408)cGc>cAc	p.R136H	SKP1_ENST00000522552.1_Missense_Mutation_p.R136H|SKP1_ENST00000522855.1_Missense_Mutation_p.R136H|SKP1_ENST00000521216.1_Missense_Mutation_p.R136H|SKP1_ENST00000517625.1_Missense_Mutation_p.R136H	NM_170679.2	NP_733779.1	P63208	SKP1_HUMAN	S-phase kinase-associated protein 1	136	Interaction with the F-box domain of F- box proteins. {ECO:0000250}.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|histone H2A monoubiquitination (GO:0035518)|mitotic cell cycle (GO:0000278)|Notch signaling pathway (GO:0007219)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|viral process (GO:0016032)	Cul7-RING ubiquitin ligase complex (GO:0031467)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|SCF ubiquitin ligase complex (GO:0019005)	ubiquitin-protein transferase activity (GO:0004842)			large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GAAGGTCTTGCGAATCTCCTC	0.408																																					p.R136H		Atlas-SNP	.											SKP1,colon,carcinoma,-1,1	SKP1	10	1	0			c.G407A						scavenged	.						156.0	152.0	153.0					5																	133494195		2203	4300	6503	SO:0001583	missense	6500	exon5			GTCTTGCGAATCT	U33760	CCDS4171.1, CCDS4172.1	5q31	2011-11-18	2007-11-13	2007-11-13	ENSG00000113558	ENSG00000113558			10899	protein-coding gene	gene with protein product		601434	"""S-phase kinase-associated protein 1A (p19A)"""	SKP1A		7553852, 8646875	Standard	NM_006930		Approved	EMC19, OCP2, TCEB1L, MGC34403, OCP-II, p19A	uc003kzc.4	P63208	OTTHUMG00000129117	ENST00000353411.6:c.407G>A	5.37:g.133494195C>T	ENSP00000231487:p.Arg136His	Somatic	145	1	0.00689655		WXS	Illumina HiSeq	Phase_I	132	45	0.340909	NM_170679	D3DQ97|D3DQ98|P34991|Q8TAY2	Missense_Mutation	SNP	ENST00000353411.6	37	CCDS4171.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.405507	0.83230	.	.	ENSG00000113558	ENST00000353411;ENST00000522552;ENST00000521216;ENST00000517625;ENST00000522855;ENST00000328392;ENST00000519321	T;T;T;T;T;T;T	0.59364	0.34;0.29;0.27;0.34;0.34;0.29;0.27	5.06	5.06	0.68205	SKP1 component, dimerisation (2);BTB/POZ fold (1);	0.000000	0.85682	U	0.000000	T	0.75968	0.3922	H	0.95151	3.63	0.80722	D	1	B;B;D	0.59357	0.072;0.048;0.985	B;B;P	0.47528	0.038;0.005;0.549	D	0.85050	0.0928	10	0.66056	D	0.02	-0.7947	18.7998	0.92011	0.0:1.0:0.0:0.0	.	136;136;136	E5RJR5;P63208-2;P63208	.;.;SKP1_HUMAN	H	136	ENSP00000231487:R136H;ENSP00000429472:R136H;ENSP00000431067:R136H;ENSP00000429961:R136H;ENSP00000429686:R136H;ENSP00000331708:R136H;ENSP00000429415:R136H	ENSP00000331708:R136H	R	-	2	0	SKP1	133522094	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	7.214000	0.77958	2.522000	0.85027	0.563000	0.77884	CGC	.	.	none		0.408	SKP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251162.2	NM_170679	
ZBTB17	7709	hgsc.bcm.edu	37	1	16274938	16274938	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:16274938C>T	ENST00000375743.4	-	3	285	c.53G>A	c.(52-54)cGg>cAg	p.R18Q	ZBTB17_ENST00000537142.1_Intron|ZBTB17_ENST00000448462.2_Missense_Mutation_p.R18Q|ZBTB17_ENST00000375733.2_Missense_Mutation_p.R18Q|ZBTB17_ENST00000479282.1_5'UTR	NM_003443.2	NP_003434.2	Q13105	ZBT17_HUMAN	zinc finger and BTB domain containing 17	18	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|ectoderm development (GO:0007398)|endoplasmic reticulum unfolded protein response (GO:0030968)|gastrulation with mouth forming second (GO:0001702)|negative regulation of cell cycle (GO:0045786)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(4)|large_intestine(1)|lung(4)|ovary(2)|prostate(2)	15		Colorectal(325;0.000257)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|Colorectal(212;4.12e-07)|COAD - Colon adenocarcinoma(227;2.43e-05)|BRCA - Breast invasive adenocarcinoma(304;9.97e-05)|Kidney(64;0.000182)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0649)		CCCCAGCTGCCGCTGCTGGTT	0.557																																					p.R18Q		Atlas-SNP	.											ZBTB17,NS,carcinoma,0,1	ZBTB17	45	1	0			c.G53A						scavenged	.						57.0	57.0	57.0					1																	16274938		2203	4300	6503	SO:0001583	missense	7709	exon3			AGCTGCCGCTGCT	U20647	CCDS165.1, CCDS55576.1, CCDS72712.1	1p36.13	2013-01-08	2004-07-16	2004-07-16	ENSG00000116809	ENSG00000116809		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	12936	protein-coding gene	gene with protein product		604084	"""zinc finger protein 151 (pHZ-67)"", ""zinc finger protein 60"""	ZNF151, ZNF60			Standard	NM_003443		Approved	MIZ1, pHZ-67	uc001axl.4	Q13105	OTTHUMG00000009377	ENST00000375743.4:c.53G>A	1.37:g.16274938C>T	ENSP00000364895:p.Arg18Gln	Somatic	140	1	0.00714286		WXS	Illumina HiSeq	Phase_I	134	3	0.0223881	NM_003443	A0AV07|B4DXB4|B7ZLQ9|F5H411|Q15932|Q5JYB2|Q9NUC9	Missense_Mutation	SNP	ENST00000375743.4	37	CCDS165.1	.	.	.	.	.	.	.	.	.	.	C	36	5.939461	0.97128	.	.	ENSG00000116809	ENST00000375743;ENST00000375733;ENST00000444654;ENST00000448462	T;T;T	0.73152	1.75;1.75;-0.72	5.3	5.3	0.74995	BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.64402	D	0.000001	D	0.88202	0.6373	M	0.92555	3.32	0.42812	D	0.993965	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.999;0.993;0.998;0.993;1.0;0.995	D	0.90932	0.4791	10	0.87932	D	0	.	18.3218	0.90241	0.0:1.0:0.0:0.0	.	18;18;18;18;18;18	B4DGV6;E7EPQ4;Q13105-2;B4DSM7;B2RCP2;Q13105	.;.;.;.;.;ZBT17_HUMAN	Q	18	ENSP00000364895:R18Q;ENSP00000364885:R18Q;ENSP00000391002:R18Q	ENSP00000364885:R18Q	R	-	2	0	ZBTB17	16147525	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.666000	0.83877	2.649000	0.89929	0.561000	0.74099	CGG	.	.	none		0.557	ZBTB17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025998.1	NM_003443	
LAP3	51056	hgsc.bcm.edu	37	4	17606285	17606285	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr4:17606285T>C	ENST00000226299.4	+	11	1529	c.1255T>C	c.(1255-1257)Ttc>Ctc	p.F419L	AC006160.5_ENST00000511010.1_RNA|LAP3_ENST00000606142.1_Missense_Mutation_p.F388L|LAP3_ENST00000503467.1_3'UTR	NM_015907.2	NP_056991.2	P28838	AMPL_HUMAN	leucine aminopeptidase 3	419					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)			endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|urinary_tract(1)	20						GAACAAACTCTTCGAGGTAGG	0.418																																					p.F419L		Atlas-SNP	.											.	LAP3	50	.	0			c.T1255C						PASS	.						107.0	101.0	103.0					4																	17606285		2203	4300	6503	SO:0001583	missense	51056	exon11			AAACTCTTCGAGG	AF061738	CCDS3422.1	4p15.33	2012-07-25	2003-09-12		ENSG00000002549	ENSG00000002549	3.4.11.1		18449	protein-coding gene	gene with protein product		170250	"""peptidase S"""	PEPS		6350155, 689684	Standard	NM_015907		Approved	LAPEP, LAP	uc003gph.1	P28838	OTTHUMG00000048214	ENST00000226299.4:c.1255T>C	4.37:g.17606285T>C	ENSP00000226299:p.Phe419Leu	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	107	39	0.364486	NM_015907	B3KMQ3|Q6IAM6|Q6P0L6|Q9UQE3	Missense_Mutation	SNP	ENST00000226299.4	37	CCDS3422.1	.	.	.	.	.	.	.	.	.	.	T	9.660	1.143920	0.21205	.	.	ENSG00000002549	ENST00000226299;ENST00000513105	T;T	0.39229	1.09;1.14	5.84	3.41	0.39046	Peptidase M17, leucyl aminopeptidase, C-terminal (1);	0.261443	0.44097	N	0.000492	T	0.12689	0.0308	N	0.00707	-1.245	0.29001	N	0.887486	B	0.27416	0.178	B	0.30495	0.116	T	0.31052	-0.9957	10	0.09338	T	0.73	-2.9227	8.5381	0.33375	0.0:0.2084:0.0:0.7916	.	419	P28838	AMPL_HUMAN	L	419;189	ENSP00000226299:F419L;ENSP00000424724:F189L	ENSP00000226299:F419L	F	+	1	0	LAP3	17215383	1.000000	0.71417	0.216000	0.23742	0.270000	0.26580	5.560000	0.67332	0.473000	0.27368	-0.290000	0.09829	TTC	.	.	none		0.418	LAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250365.1		
NLRX1	79671	hgsc.bcm.edu	37	11	119045894	119045894	+	Missense_Mutation	SNP	C	C	T	rs574477974		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:119045894C>T	ENST00000409109.1	+	6	2169	c.1582C>T	c.(1582-1584)Cgt>Tgt	p.R528C	NLRX1_ENST00000525863.1_Missense_Mutation_p.R528C|NLRX1_ENST00000292199.2_Missense_Mutation_p.R528C|NLRX1_ENST00000409991.1_Missense_Mutation_p.R528C|NLRX1_ENST00000409265.4_Missense_Mutation_p.R528C	NM_001282144.1	NP_001269073.1	Q86UT6	NLRX1_HUMAN	NLR family member X1	528	Required for interaction with MAVS.				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)		GCTCGTGGGCCGTGTTGGGGA	0.607													C|||	1	0.000199681	0.0	0.0	5008	,	,		18271	0.0		0.0	False		,,,				2504	0.001				p.R528C		Atlas-SNP	.											.	NLRX1	128	.	0			c.C1582T						PASS	.						145.0	132.0	136.0					11																	119045894		2200	4295	6495	SO:0001583	missense	79671	exon6			GTGGGCCGTGTTG	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.1582C>T	11.37:g.119045894C>T	ENSP00000387334:p.Arg528Cys	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	125	5	0.04	NM_024618	A8K6Q1|B3KPK2|B3KTA2|Q7RTR3|Q96D51|Q9H724	Missense_Mutation	SNP	ENST00000409109.1	37	CCDS8416.1	.	.	.	.	.	.	.	.	.	.	C	11.65	1.703299	0.30232	.	.	ENSG00000160703	ENST00000409991;ENST00000292199;ENST00000409265;ENST00000409109;ENST00000525863	T;T;T;T;T	0.73047	-0.6;-0.6;-0.71;-0.6;-0.71	5.62	4.7	0.59300	.	0.188113	0.38217	N	0.001762	T	0.53610	0.1807	N	0.19112	0.55	0.42859	D	0.994101	B;B	0.19706	0.038;0.005	B;B	0.12156	0.007;0.002	T	0.53851	-0.8380	10	0.87932	D	0	.	8.1864	0.31341	0.2513:0.6692:0.0:0.0795	.	528;528	Q86UT6-2;Q86UT6	.;NLRX1_HUMAN	C	528	ENSP00000386851:R528C;ENSP00000292199:R528C;ENSP00000386858:R528C;ENSP00000387334:R528C;ENSP00000433442:R528C	ENSP00000292199:R528C	R	+	1	0	NLRX1	118551104	1.000000	0.71417	0.993000	0.49108	0.759000	0.43091	4.547000	0.60712	1.346000	0.45694	0.561000	0.74099	CGT	.	.	none		0.607	NLRX1-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335403.1	NM_170722	
PPP1R42	286187	hgsc.bcm.edu	37	8	67922976	67922976	+	Missense_Mutation	SNP	C	C	T	rs200466525	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr8:67922976C>T	ENST00000324682.5	-	5	670	c.526G>A	c.(526-528)Gtt>Att	p.V176I	PPP1R42_ENST00000522909.1_Missense_Mutation_p.V176I|PPP1R42_ENST00000517834.1_5'Flank	NM_001013626.2	NP_001013648.1	Q7Z4L9	PPR42_HUMAN	protein phosphatase 1, regulatory subunit 42	176					regulation of phosphatase activity (GO:0010921)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|manchette (GO:0002177)|microtubule cytoskeleton (GO:0015630)|microtubule organizing center (GO:0005815)	actin binding (GO:0003779)|dynein binding (GO:0045502)|tubulin binding (GO:0015631)										TGGTTGTCAACGGCTATGAGC	0.284													C|||	2	0.000399361	0.0008	0.0014	5008	,	,		16546	0.0		0.0	False		,,,				2504	0.0				p.V176I		Atlas-SNP	.											.	PPP1R42	2	.	0			c.G526A						PASS	.						75.0	74.0	75.0					8																	67922976		2203	4297	6500	SO:0001583	missense	286187	exon5			TGTCAACGGCTAT	BC055413	CCDS34902.1	8q13.1-q13.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000178125	ENSG00000178125		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	33732	protein-coding gene	gene with protein product	"""testis leucine-rich repeat"""		"""leucine rich repeat containing 67"""	LRRC67			Standard	NM_001013626		Approved	dtr, TLLR	uc003xxc.3	Q7Z4L9	OTTHUMG00000164745	ENST00000324682.5:c.526G>A	8.37:g.67922976C>T	ENSP00000315035:p.Val176Ile	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	63	20	0.31746	NM_001013626		Missense_Mutation	SNP	ENST00000324682.5	37	CCDS34902.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	14.75	2.629273	0.46944	.	.	ENSG00000178125	ENST00000522909;ENST00000421742;ENST00000324682	T;T	0.37058	2.25;1.22	5.83	4.06	0.47325	.	0.157823	0.56097	N	0.000040	T	0.20170	0.0485	N	0.04746	-0.17	0.27969	N	0.936469	B	0.23442	0.085	B	0.25987	0.065	T	0.13764	-1.0497	10	0.37606	T	0.19	-4.3848	12.6376	0.56692	0.0:0.8663:0.0:0.1337	.	176	Q7Z4L9-2	.	I	176	ENSP00000429721:V176I;ENSP00000315035:V176I	ENSP00000315035:V176I	V	-	1	0	LRRC67	68085530	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	3.529000	0.53532	0.838000	0.34948	-0.194000	0.12790	GTT	C|1.000;T|0.000	0.000	strong		0.284	PPP1R42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380034.2	NM_001013626	
CEP170	9859	hgsc.bcm.edu	37	1	243328077	243328077	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:243328077T>C	ENST00000366542.1	-	13	3236	c.3185A>G	c.(3184-3186)gAg>gGg	p.E1062G	RP11-261C10.4_ENST00000422938.1_RNA|RP11-261C10.4_ENST00000437499.1_RNA|CEP170_ENST00000490813.1_5'Flank|CEP170_ENST00000366543.1_Missense_Mutation_p.E964G|CEP170_ENST00000366544.1_Missense_Mutation_p.E964G	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	1062	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)			ATGTACATGCTCATCAGCTGA	0.423																																					p.E1062G		Atlas-SNP	.											CEP170_ENST00000366543,NS,carcinoma,+1,2	CEP170	153	2	0			c.A3185G						scavenged	.						33.0	30.0	31.0					1																	243328077		1813	4041	5854	SO:0001583	missense	9859	exon13			ACATGCTCATCAG	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.3185A>G	1.37:g.243328077T>C	ENSP00000355500:p.Glu1062Gly	Somatic	312	1	0.00320513		WXS	Illumina HiSeq	Phase_I	368	5	0.013587	NM_014812	O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	Missense_Mutation	SNP	ENST00000366542.1	37	CCDS44339.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.88|11.88	1.770320|1.770320	0.31320|0.31320	.|.	.|.	ENSG00000143702|ENSG00000143702	ENST00000366542;ENST00000366544;ENST00000366543;ENST00000532008|ENST00000336415	T;T;T|.	0.49720|.	0.8;0.78;0.77|.	5.15|5.15	5.15|5.15	0.70609|0.70609	.|.	0.124834|.	0.64402|.	D|.	0.000010|.	T|T	0.51261|0.51261	0.1664|0.1664	N|N	0.22421|0.22421	0.69|0.69	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.76494|.	0.991;0.996;0.996;0.999|.	D;D;D;D|.	0.77557|.	0.921;0.986;0.986;0.99|.	T|T	0.48317|0.48317	-0.9046|-0.9046	9|5	.|.	.|.	.|.	-15.5611|-15.5611	14.1711|14.1711	0.65510|0.65510	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1025;964;964;1062|.	B1ARM6;Q5SW79-3;Q5SW79-2;Q5SW79|.	.;.;.;CE170_HUMAN|.	G|G	1062;964;964;23|1026	ENSP00000355500:E1062G;ENSP00000355502:E964G;ENSP00000355501:E964G|.	.|.	E|S	-|-	2|1	0|0	CEP170|CEP170	241394700|241394700	1.000000|1.000000	0.71417|0.71417	0.984000|0.984000	0.44739|0.44739	0.985000|0.985000	0.73830|0.73830	7.446000|7.446000	0.80609|0.80609	1.937000|1.937000	0.56155|0.56155	0.454000|0.454000	0.30748|0.30748	GAG|AGC	.	.	none		0.423	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096178.2	NM_014812	
RPL3	6122	hgsc.bcm.edu	37	22	39714450	39714450	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr22:39714450C>T	ENST00000216146.4	-	2	324	c.151G>A	c.(151-153)Gct>Act	p.A51T	SNORD43_ENST00000583861.1_RNA|RPL3_ENST00000465618.1_5'UTR|RPL3_ENST00000401609.1_5'UTR	NM_000967.3|NM_001033853.1	NP_000958.1|NP_001029025.1	P39023	RL3_HUMAN	ribosomal protein L3	51					cellular protein metabolic process (GO:0044267)|cellular response to interleukin-4 (GO:0071353)|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)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			breast(1)|kidney(4)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	12	Melanoma(58;0.04)				Homoharringtonine(DB04865)	GTCATGCCAGCCTTGTATCCC	0.577																																					p.A51T		Atlas-SNP	.											.	RPL3	29	.	0			c.G151A						PASS	.						77.0	72.0	74.0					22																	39714450		2203	4300	6503	SO:0001583	missense	6122	exon2			TGCCAGCCTTGTA	AB007166	CCDS13988.1	22q13	2011-04-06			ENSG00000100316	ENSG00000100316		"""L ribosomal proteins"""	10332	protein-coding gene	gene with protein product		604163				2891103, 9582194	Standard	NM_000967		Approved	L3	uc003axi.3	P39023	OTTHUMG00000151079	ENST00000216146.4:c.151G>A	22.37:g.39714450C>T	ENSP00000346001:p.Ala51Thr	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	90	21	0.233333	NM_001033853	B2RDV9|Q15548|Q5I0G0	Missense_Mutation	SNP	ENST00000216146.4	37	CCDS13988.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	35|35	5.552848|5.552848	0.96501|0.96501	.|.	.|.	ENSG00000100316|ENSG00000100316	ENST00000216146;ENST00000453303|ENST00000427905	T;T|.	0.25749|.	1.78;1.78|.	4.68|4.68	4.68|4.68	0.58851|0.58851	Translation elongation/initiation factor/Ribosomal, beta-barrel (1);|.	0.051981|.	0.85682|.	D|.	0.000000|.	D|D	0.90280|0.90280	0.6960|0.6960	H|H	0.98111|0.98111	4.15|4.15	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;1.0|.	D|D	0.94293|0.94293	0.7530|0.7530	10|5	0.87932|.	D|.	0|.	.|.	17.6103|17.6103	0.88050|0.88050	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	51;51|.	P39023;B3KS36|.	RL3_HUMAN;.|.	T|D	51;78|82	ENSP00000346001:A51T;ENSP00000415198:A78T|.	ENSP00000346001:A51T|.	A|G	-|-	1|2	0|0	RPL3|RPL3	38044396|38044396	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	4.464000|4.464000	0.60134|0.60134	2.150000|2.150000	0.67090|0.67090	0.455000|0.455000	0.32223|0.32223	GCT|GGC	.	.	none		0.577	RPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321196.1	NM_000967	
MUC2	4583	hgsc.bcm.edu	37	11	1092929	1092929	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:1092929C>T	ENST00000441003.2	+	30	4775	c.4748C>T	c.(4747-4749)tCg>tTg	p.S1583L	MUC2_ENST00000359061.5_Missense_Mutation_p.S1584L|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_5'Flank	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	accccaacatcgacacccatc	0.632																																					p.S1583L		Atlas-SNP	.											MUC2_ENST00000441003,rectum,carcinoma,+1,4	MUC2	614	4	0			c.C4748T						scavenged	.						78.0	115.0	102.0					11																	1092929		1918	3556	5474	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.4748C>T	11.37:g.1092929C>T	ENSP00000415183:p.Ser1583Leu	Somatic	111	1	0.00900901		WXS	Illumina HiSeq	Phase_I	105	9	0.0857143	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	4.659	0.122508	0.08931	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.13538	2.58;3.12	1.75	-1.21	0.09524	.	3.022220	0.02729	U	0.114829	T	0.09202	0.0227	.	.	.	0.09310	N	1	B	0.22541	0.071	B	0.10450	0.005	T	0.31336	-0.9947	9	0.29301	T	0.29	.	6.8082	0.23788	0.6899:0.3101:0.0:0.0	.	1583	E7EUV1	.	L	1583;1584	ENSP00000415183:S1583L;ENSP00000351956:S1584L	ENSP00000351956:S1584L	S	+	2	0	MUC2	1082929	0.156000	0.22821	0.002000	0.10522	0.037000	0.13140	2.746000	0.47467	0.075000	0.16796	0.121000	0.15741	TCG	.	.	none		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
APOBEC3A	200315	hgsc.bcm.edu	37	22	39357649	39357649	+	Silent	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr22:39357649G>A	ENST00000402255.1	+	4	636	c.432G>A	c.(430-432)cgG>cgA	p.R144R	APOBEC3A_ENST00000249116.2_Silent_p.R144R			P31941	ABC3A_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3A	144					cellular response to xenobiotic stimulus (GO:0071466)|clearance of foreign intracellular DNA by conversion of DNA cytidine to uridine (GO:0044356)|cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|DNA demethylation (GO:0080111)|innate immune response (GO:0045087)|negative regulation of transposition (GO:0010529)|negative regulation of viral genome replication (GO:0045071)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cytidine deaminase activity (GO:0004126)|deoxycytidine deaminase activity (GO:0047844)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(2)|ovary(1)|skin(1)	5	Melanoma(58;0.04)					AAATGCTGCGGGATGCTGGGG	0.557																																					p.R144R		Atlas-SNP	.											APOBEC3A,lower_third,carcinoma,+2,1	APOBEC3A	20	1	0			c.G432A						scavenged	.						25.0	36.0	33.0					22																	39357649		1998	3968	5966	SO:0001819	synonymous_variant	200315	exon3			GCTGCGGGATGCT	U03891	CCDS13981.1	22q13.1-q13.2	2014-01-28			ENSG00000128383	ENSG00000128383		"""Apolipoprotein B mRNA editing enzymes"""	17343	protein-coding gene	gene with protein product	"""phorbolin I"""	607109				11863358, 10469298	Standard	NM_145699		Approved	ARP3, PHRBN		P31941	OTTHUMG00000151004	ENST00000402255.1:c.432G>A	22.37:g.39357649G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	120	2	0.0166667	NM_145699	A0AVM1|Q12807|Q5JZ93|Q9UH18	Silent	SNP	ENST00000402255.1	37	CCDS13981.1																																																																																			.	.	none		0.557	APOBEC3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320915.2	NM_145699	
MYH2	4620	hgsc.bcm.edu	37	17	10428646	10428646	+	Silent	SNP	C	C	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr17:10428646C>A	ENST00000245503.5	-	33	4941	c.4557G>T	c.(4555-4557)acG>acT	p.T1519T	RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|MYH2_ENST00000532183.2_Intron|CTC-297N7.11_ENST00000587182.2_RNA|MYH2_ENST00000397183.2_Silent_p.T1519T	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	1519					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|plasma membrane repair (GO:0001778)|response to activity (GO:0014823)	A band (GO:0031672)|actomyosin contractile ring (GO:0005826)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|protein complex (GO:0043234)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.T1519T(1)		NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(99)|ovary(6)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(4)	176						CAATCTGTTCCGTGAGGTCAG	0.388																																					p.T1519T		Atlas-SNP	.											MYH2,NS,carcinoma,0,2	MYH2	390	2	1	Substitution - coding silent(1)	kidney(1)	c.G4557T						scavenged	.						100.0	88.0	92.0					17																	10428646		2203	4300	6503	SO:0001819	synonymous_variant	4620	exon33			CTGTTCCGTGAGG		CCDS11156.1	17p13.1	2014-02-04	2006-09-29		ENSG00000125414	ENSG00000125414		"""Myosins / Myosin superfamily : Class II"""	7572	protein-coding gene	gene with protein product		160740	"""myosin, heavy polypeptide 2, skeletal muscle, adult"", ""inclusion body myopathy 3, autosomal dominant"""	IBM3		7545970, 11889243	Standard	NM_001100112		Approved	MYH2A, MYHSA2, MyHC-IIa, MYHas8, MyHC-2A	uc010coi.3	Q9UKX2	OTTHUMG00000130363	ENST00000245503.5:c.4557G>T	17.37:g.10428646C>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	125	2	0.016	NM_017534	A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Silent	SNP	ENST00000245503.5	37	CCDS11156.1																																																																																			.	.	none		0.388	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3	NM_017534	
SOCS1	8651	hgsc.bcm.edu	37	16	11349329	11349329	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr16:11349329C>T	ENST00000332029.2	-	2	157	c.7G>A	c.(7-9)Gca>Aca	p.A3T	RMI2_ENST00000572173.1_Intron	NM_003745.1	NP_003736.1	O15524	SOCS1_HUMAN	suppressor of cytokine signaling 1	3					cellular response to amino acid stimulus (GO:0071230)|cytokine-mediated signaling pathway (GO:0019221)|fat cell differentiation (GO:0045444)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of protein phosphorylation (GO:0001932)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)	insulin-like growth factor receptor binding (GO:0005159)|kinase inhibitor activity (GO:0019210)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)	p.0?(1)|p.A3T(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(66)|lung(3)	71						TGGTTGTGTGCTACCATCCTA	0.697			"""F, O"""		"""Hodgkin Lymphoma, PMBL"""																																p.A3T	Colon(177;456 3548 27231)	Atlas-SNP	.		Rec	yes		16	16p13.13	8651	suppressor of cytokine signaling 1		L	SOCS1,NS,lymphoid_neoplasm,0,2	SOCS1	84	2	2	Substitution - Missense(1)|Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(2)	c.G7A						scavenged	.						6.0	7.0	6.0					16																	11349329		1898	3954	5852	SO:0001583	missense	8651	exon2			TGTGTGCTACCAT	U88326	CCDS10546.1	16p13.13	2013-02-14			ENSG00000185338	ENSG00000185338		"""Suppressors of cytokine signaling"", ""SH2 domain containing"""	19383	protein-coding gene	gene with protein product		603597				7796808, 9266833	Standard	NM_003745		Approved	SOCS-1, SSI-1, JAB, TIP3, Cish1	uc002dar.1	O15524	OTTHUMG00000129792	ENST00000332029.2:c.7G>A	16.37:g.11349329C>T	ENSP00000329418:p.Ala3Thr	Somatic	16	2	0.125		WXS	Illumina HiSeq	Phase_I	12	8	0.666667	NM_003745	O15097|Q9NSA7	Missense_Mutation	SNP	ENST00000332029.2	37	CCDS10546.1	.	.	.	.	.	.	.	.	.	.	C	19.78	3.891903	0.72524	.	.	ENSG00000185338	ENST00000332029	T	0.27104	1.69	3.27	3.27	0.37495	.	0.182614	0.47455	D	0.000237	T	0.15825	0.0381	N	0.08118	0	0.44871	D	0.997889	D	0.55385	0.971	P	0.44772	0.46	T	0.09530	-1.0670	10	0.46703	T	0.11	-4.6538	13.6611	0.62368	0.0:1.0:0.0:0.0	.	3	O15524	SOCS1_HUMAN	T	3	ENSP00000329418:A3T	ENSP00000329418:A3T	A	-	1	0	SOCS1	11256830	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.316000	0.65815	1.668000	0.50843	0.491000	0.48974	GCA	.	.	none		0.697	SOCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252018.1		
FBXL6	26233	hgsc.bcm.edu	37	8	145579962	145579962	+	Missense_Mutation	SNP	C	C	T	rs77494279	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr8:145579962C>T	ENST00000331890.5	-	7	1287	c.1223G>A	c.(1222-1224)cGg>cAg	p.R408Q	FBXL6_ENST00000455319.2_Missense_Mutation_p.R402Q|FBXL6_ENST00000526524.1_5'UTR|SLC52A2_ENST00000527078.1_5'Flank|TMEM249_ENST00000531225.1_5'Flank|SLC52A2_ENST00000530047.1_5'Flank|SLC52A2_ENST00000402965.1_5'Flank|SLC52A2_ENST00000329994.2_5'Flank|SLC52A2_ENST00000540505.1_5'Flank|TMEM249_ENST00000398633.3_5'Flank|SLC52A2_ENST00000526752.1_5'Flank|SLC52A2_ENST00000532887.1_5'Flank	NM_012162.2	NP_036294.2	Q8N531	FBXL6_HUMAN	F-box and leucine-rich repeat protein 6	408					protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)		ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|lung(3)|ovary(1)	5	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;4.43e-40)|Epithelial(56;1.48e-39)|all cancers(56;1.49e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0441)|Colorectal(110;0.055)			CTGCTGACCCCGACATGGCAG	0.642																																					p.R408Q		Atlas-SNP	.											FBXL6,colon,carcinoma,0,1	FBXL6	26	1	0			c.G1223A						scavenged	.						37.0	38.0	37.0					8																	145579962		2199	4296	6495	SO:0001583	missense	26233	exon7			TGACCCCGACATG	AF174592	CCDS6422.1, CCDS47942.1	8q24.3	2011-06-09			ENSG00000182325	ENSG00000182325		"""F-boxes / Leucine-rich repeats"""	13603	protein-coding gene	gene with protein product		609076				10531035, 10531037	Standard	NM_012162		Approved	FBL6	uc003zcb.3	Q8N531	OTTHUMG00000165169	ENST00000331890.5:c.1223G>A	8.37:g.145579962C>T	ENSP00000330098:p.Arg408Gln	Somatic	62	2	0.0322581		WXS	Illumina HiSeq	Phase_I	75	8	0.106667	NM_012162	Q53G43|Q9H5W9|Q9UKC7	Missense_Mutation	SNP	ENST00000331890.5	37	CCDS6422.1	.	.	.	.	.	.	.	.	.	.	C	2.320	-0.355930	0.05138	.	.	ENSG00000182325	ENST00000455319;ENST00000331890	T;T	0.23147	5.54;1.92	4.72	2.42	0.29668	.	0.526222	0.16851	N	0.196922	T	0.11410	0.0278	N	0.15975	0.35	0.23559	N	0.99742	B;B	0.06786	0.001;0.001	B;B	0.01281	0.0;0.0	T	0.29610	-1.0006	10	0.16420	T	0.52	-1.2663	4.1831	0.10385	0.0:0.125:0.2883:0.5867	.	408;402	Q8N531;Q8N531-2	FBXL6_HUMAN;.	Q	402;408	ENSP00000403873:R402Q;ENSP00000330098:R408Q	ENSP00000330098:R408Q	R	-	2	0	FBXL6	145550770	0.000000	0.05858	1.000000	0.80357	0.021000	0.10359	-0.300000	0.08243	0.656000	0.30886	-0.481000	0.04817	CGG	C|0.932;T|0.068	0.068	strong		0.642	FBXL6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382413.1	NM_024555	
CACNB2	783	hgsc.bcm.edu	37	10	18795465	18795465	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr10:18795465C>T	ENST00000324631.7	+	6	719	c.659C>T	c.(658-660)cCt>cTt	p.P220L	CACNB2_ENST00000377331.2_Missense_Mutation_p.P192L|CACNB2_ENST00000282343.8_Missense_Mutation_p.P192L|CACNB2_ENST00000396576.2_Missense_Mutation_p.P165L|CACNB2_ENST00000352115.6_Missense_Mutation_p.P220L|CACNB2_ENST00000377329.4_Missense_Mutation_p.P166L|CACNB2_ENST00000377315.4_Missense_Mutation_p.P172L|CACNB2_ENST00000377328.1_Intron|CACNB2_ENST00000377319.3_Missense_Mutation_p.P165L	NM_201593.2|NM_201596.2	NP_963887.2|NP_963890.2	Q08289	CACB2_HUMAN	calcium channel, voltage-dependent, beta 2 subunit	220					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|neuromuscular junction development (GO:0007528)|positive regulation of calcium ion transport (GO:0051928)|synaptic transmission (GO:0007268)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|voltage-gated calcium channel complex (GO:0005891)	calcium channel activity (GO:0005262)|voltage-gated calcium channel activity (GO:0005245)	p.P220H(1)|p.P166H(1)|p.P165H(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(12)|prostate(1)|skin(3)|stomach(2)	31					Amlodipine(DB00381)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	AAATCAACACCTCCATCATCT	0.363																																					p.P220L		Atlas-SNP	.											CACNB2_ENST00000377329,NS,carcinoma,0,3	CACNB2	220	3	3	Substitution - Missense(3)	lung(3)	c.C659T						scavenged	.						115.0	105.0	109.0					10																	18795465		2203	4300	6503	SO:0001583	missense	783	exon6			CAACACCTCCATC	U95019	CCDS7125.1, CCDS7126.1, CCDS7127.1, CCDS7128.1, CCDS7129.1, CCDS41493.1, CCDS41494.1	10p12	2014-09-17			ENSG00000165995	ENSG00000165995		"""Calcium channel subunits"""	1402	protein-coding gene	gene with protein product		600003		MYSB, CACNLB2		9254841, 8494331	Standard	NM_201596		Approved		uc001ipr.2	Q08289	OTTHUMG00000017764	ENST00000324631.7:c.659C>T	10.37:g.18795465C>T	ENSP00000320025:p.Pro220Leu	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	95	3	0.0315789	NM_201597	A6PVM5|A6PVM7|A6PVM8|O00304|Q5QJ99|Q5QJA0|Q5VVG9|Q5VVH0|Q5VWV6|Q6TME1|Q6TME2|Q6TME3|Q8WX81|Q96NZ3|Q96NZ4|Q96NZ5|Q9BWU2|Q9HD32|Q9Y340|Q9Y341	Missense_Mutation	SNP	ENST00000324631.7	37	CCDS7125.1	.	.	.	.	.	.	.	.	.	.	C	34	5.314495	0.95655	.	.	ENSG00000165995	ENST00000324631;ENST00000352115;ENST00000282343;ENST00000377331;ENST00000396576;ENST00000377319;ENST00000377329;ENST00000377315	D;D;D;D;D;D;D;D	0.84730	-1.89;-1.71;-1.87;-1.71;-1.86;-1.71;-1.86;-1.86	5.9	5.9	0.94986	Src homology-3 domain (1);	0.000000	0.85682	D	0.000000	D	0.93390	0.7892	M	0.83118	2.625	0.80722	D	1	B;D;D;D;D;D;P;D;D;D;D;P;D;D;D	0.89917	0.365;0.999;0.985;0.999;0.997;0.984;0.941;0.991;0.991;0.985;0.996;0.944;1.0;0.997;0.984	B;D;P;D;D;P;P;D;P;P;D;P;D;D;P	0.91635	0.08;0.991;0.722;0.991;0.928;0.889;0.685;0.948;0.889;0.809;0.937;0.882;0.999;0.972;0.889	D	0.93437	0.6790	10	0.87932	D	0	-16.3254	20.2626	0.98452	0.0:1.0:0.0:0.0	.	172;172;166;166;192;172;166;166;176;165;192;192;220;220;220	B7Z1U5;B7Z2U3;Q5QJ99;Q6TME0;Q5QJA0;Q5VVH1;Q6TME1;Q08289-3;Q59H42;Q08289-6;A6PVM7;Q08289-4;Q08289-7;Q08289-8;Q08289	.;.;.;.;.;.;.;.;.;.;.;.;.;.;CACB2_HUMAN	L	220;220;192;192;165;165;166;172	ENSP00000320025:P220L;ENSP00000344474:P220L;ENSP00000282343:P192L;ENSP00000366548:P192L;ENSP00000379821:P165L;ENSP00000366536:P165L;ENSP00000366546:P166L;ENSP00000366532:P172L	ENSP00000282343:P192L	P	+	2	0	CACNB2	18835471	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.280000	0.78610	2.802000	0.96397	0.650000	0.86243	CCT	.	.	none		0.363	CACNB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047072.2	NM_000724	
PCDHB1	29930	hgsc.bcm.edu	37	5	140432615	140432615	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:140432615G>A	ENST00000306549.3	+	1	1637	c.1560G>A	c.(1558-1560)atG>atA	p.M520I		NM_013340.2	NP_037472.2	Q9Y5F3	PCDB1_HUMAN	protocadherin beta 1	520	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)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|liver(1)|lung(13)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	53			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGAGAACCATGGATTATGAGG	0.433																																					p.M520I		Atlas-SNP	.											.	PCDHB1	148	.	0			c.G1560A						PASS	.						76.0	77.0	77.0					5																	140432615		2203	4300	6503	SO:0001583	missense	29930	exon1			AACCATGGATTAT	AF152488	CCDS4243.1	5q31	2010-01-26			ENSG00000171815	ENSG00000171815		"""Cadherins / Protocadherins : Clustered"""	8680	other	protocadherin		606327				10380929	Standard	NM_013340		Approved	PCDH-BETA1	uc003lik.1	Q9Y5F3	OTTHUMG00000129627	ENST00000306549.3:c.1560G>A	5.37:g.140432615G>A	ENSP00000307234:p.Met520Ile	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	143	62	0.433566	NM_013340	Q2M257	Missense_Mutation	SNP	ENST00000306549.3	37	CCDS4243.1	.	.	.	.	.	.	.	.	.	.	G	11.31	1.601493	0.28534	.	.	ENSG00000171815	ENST00000306549	T	0.47177	0.85	6.11	5.24	0.73138	Cadherin (5);Cadherin-like (1);	0.000000	0.53938	D	0.000046	T	0.32704	0.0838	N	0.17674	0.51	0.35001	D	0.755995	B	0.02656	0.0	B	0.06405	0.002	T	0.38585	-0.9654	10	0.62326	D	0.03	.	10.0729	0.42343	0.0:0.1218:0.5105:0.3678	.	520	Q9Y5F3	PCDB1_HUMAN	I	520	ENSP00000307234:M520I	ENSP00000307234:M520I	M	+	3	0	PCDHB1	140412799	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.839000	0.48207	1.579000	0.49836	0.655000	0.94253	ATG	.	.	none		0.433	PCDHB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251822.2	NM_013340	
SIRPA	140885	hgsc.bcm.edu	37	20	1895965	1895965	+	Missense_Mutation	SNP	C	C	A	rs17855614|rs373583167|rs386811662	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	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	360	19	0.0527778		WXS	Illumina HiSeq	Phase_I	387	37	0.0956072	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	
ALK	238	hgsc.bcm.edu	37	2	29498090	29498090	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:29498090C>T	ENST00000389048.3	-	11	2822	c.1916G>A	c.(1915-1917)aGc>aAc	p.S639N	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	639					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)	GTCCTCTCCGCTAACTGCAAT	0.498			"""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																												p.S639N		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"""L, E, M"""	ALK,NS,carcinoma,+1,1	ALK	533	1	0			c.G1916A						scavenged	.						77.0	77.0	77.0					2																	29498090		2203	4300	6503	SO:0001583	missense	238	exon11	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	TCTCCGCTAACTG	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.1916G>A	2.37:g.29498090C>T	ENSP00000373700:p.Ser639Asn	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	209	3	0.0143541	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Missense_Mutation	SNP	ENST00000389048.3	37	CCDS33172.1	.	.	.	.	.	.	.	.	.	.	C	3.512	-0.099550	0.07010	.	.	ENSG00000171094	ENST00000389048	T	0.77229	-1.08	5.21	3.07	0.35406	.	0.372941	0.22711	U	0.056578	T	0.55909	0.1950	N	0.12182	0.205	0.80722	D	1	B	0.10296	0.003	B	0.08055	0.003	T	0.45396	-0.9264	9	.	.	.	.	8.1773	0.31289	0.0:0.7861:0.0:0.2139	.	639	Q9UM73	ALK_HUMAN	N	639	ENSP00000373700:S639N	.	S	-	2	0	ALK	29351594	0.861000	0.29849	0.994000	0.49952	0.038000	0.13279	1.327000	0.33746	1.202000	0.43218	-0.258000	0.10820	AGC	.	.	none		0.498	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304	
PPP2R5B	5526	hgsc.bcm.edu	37	11	64699058	64699058	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:64699058C>T	ENST00000164133.2	+	10	1595	c.973C>T	c.(973-975)Cca>Tca	p.P325S		NM_006244.3	NP_006235.1	Q15173	2A5B_HUMAN	protein phosphatase 2, regulatory subunit B', beta	325					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)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(9)|ovary(2)	21						CAAATACTGGCCAAAAACCTG	0.597																																					p.P325S		Atlas-SNP	.											.	PPP2R5B	47	.	0			c.C973T						PASS	.						41.0	38.0	39.0					11																	64699058		2201	4297	6498	SO:0001583	missense	5526	exon10			TACTGGCCAAAAA	L42374	CCDS8085.1	11q12	2010-06-18	2010-04-14		ENSG00000068971	ENSG00000068971		"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	9310	protein-coding gene	gene with protein product	"""PP2A, B subunit, B' beta isoform"", ""PP2A, B subunit, B56 beta isoform"", ""PP2A, B subunit, PR61 beta isoform"", ""PP2A, B subunit, R5 beta isoform"", ""serine/threonine protein phosphatase 2A, 56 kDa regulatory subunit, beta isoform"""	601644	"""protein phosphatase 2, regulatory subunit B (B56), beta isoform"", ""protein phosphatase 2, regulatory subunit B', beta isoform"""			7592815	Standard	NM_006244		Approved	FLJ35411, B56B, PR61B	uc001oby.3	Q15173	OTTHUMG00000150043	ENST00000164133.2:c.973C>T	11.37:g.64699058C>T	ENSP00000164133:p.Pro325Ser	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	47	25	0.531915	NM_006244	Q13853	Missense_Mutation	SNP	ENST00000164133.2	37	CCDS8085.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	26.4|26.4	4.729428|4.729428	0.89390|0.89390	.|.	.|.	ENSG00000068971|ENSG00000068971	ENST00000359279|ENST00000164133;ENST00000527441	.|.	.|.	.|.	4.53|4.53	4.53|4.53	0.55603|0.55603	.|Armadillo-type fold (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.83367|0.83367	0.5239|0.5239	M|M	0.90595|0.90595	3.13|3.13	0.80722|0.80722	D|D	1|1	.|D	.|0.67145	.|0.996	.|D	.|0.64410	.|0.925	D|D	0.87185|0.87185	0.2230|0.2230	6|9	0.09338|0.87932	T|D	0.73|0	-8.6715|-8.6715	15.1517|15.1517	0.72706|0.72706	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|325	.|Q15173	.|2A5B_HUMAN	V|S	350|325	.|.	ENSP00000352225:A350V|ENSP00000164133:P325S	A|P	+|+	2|1	0|0	PPP2R5B|PPP2R5B	64455634|64455634	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	5.549000|5.549000	0.67261|0.67261	2.509000|2.509000	0.84616|0.84616	0.462000|0.462000	0.41574|0.41574	GCC|CCA	.	.	none		0.597	PPP2R5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385465.1	NM_006244	
PLA2G4C	8605	hgsc.bcm.edu	37	19	48558246	48558246	+	Missense_Mutation	SNP	C	C	T	rs370150895		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:48558246C>T	ENST00000599921.1	-	15	1675	c.1318G>A	c.(1318-1320)Gag>Aag	p.E440K	PLA2G4C_ENST00000596510.1_5'UTR|PLA2G4C_ENST00000413144.2_Missense_Mutation_p.E440K|PLA2G4C_ENST00000599111.1_Missense_Mutation_p.E450K|PLA2G4C_ENST00000354276.3_Missense_Mutation_p.E440K			Q9UP65	PA24C_HUMAN	phospholipase A2, group IVC (cytosolic, calcium-independent)	440	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid metabolic process (GO:0019369)|glycerophospholipid biosynthetic process (GO:0046474)|glycerophospholipid catabolic process (GO:0046475)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|parturition (GO:0007567)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	calcium-independent phospholipase A2 activity (GO:0047499)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(12)|lung(13)|ovary(2)|prostate(1)|skin(3)	38		all_cancers(25;2.84e-05)|all_lung(116;4.62e-05)|Lung NSC(112;7.61e-05)|all_epithelial(76;0.000192)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;8.09e-05)|all cancers(93;0.000517)|Epithelial(262;0.0135)|GBM - Glioblastoma multiforme(486;0.0717)		AGCTCAGCCTCTTCTACTTGG	0.537																																					p.E450K		Atlas-SNP	.											.	PLA2G4C	76	.	0			c.G1348A						PASS	.	C	LYS/GLU,LYS/GLU,LYS/GLU	2,4404	4.2+/-10.8	0,2,2201	93.0	94.0	94.0		1348,1318,1318	-0.4	0.0	19		94	0,8600		0,0,4300	no	missense,missense,missense	PLA2G4C	NM_001159322.1,NM_001159323.1,NM_003706.2	56,56,56	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	benign,benign,benign	450/552,440/528,440/542	48558246	2,13004	2203	4300	6503	SO:0001583	missense	8605	exon15			CAGCCTCTTCTAC	AF065214	CCDS12710.1, CCDS54286.1, CCDS59403.1	19q13.3	2008-09-19					3.1.1.4		9037	protein-coding gene	gene with protein product		603602				9705332	Standard	NM_003706		Approved	cPLA2-gamma	uc002phx.3	Q9UP65		ENST00000599921.1:c.1318G>A	19.37:g.48558246C>T	ENSP00000469473:p.Glu440Lys	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	145	77	0.531034	NM_001159322	B2RB71|B4DI40|O75457|Q6IBI8|Q9UG68	Missense_Mutation	SNP	ENST00000599921.1	37	CCDS12710.1	.	.	.	.	.	.	.	.	.	.	C	2.940	-0.219120	0.06101	4.54E-4	0.0	ENSG00000105499	ENST00000354276;ENST00000413144	T;T	0.04317	3.65;3.65	3.19	-0.385	0.12470	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (2);	0.170328	0.37809	U	0.001933	T	0.03783	0.0107	L	0.41236	1.265	0.09310	N	1	B;B	0.10296	0.003;0.002	B;B	0.08055	0.003;0.003	T	0.35400	-0.9790	10	0.41790	T	0.15	-12.1445	5.3436	0.15996	0.0:0.5724:0.0:0.4276	.	450;440	B4DI40;Q9UP65	.;PA24C_HUMAN	K	440	ENSP00000346228:E440K;ENSP00000400036:E440K	ENSP00000346228:E440K	E	-	1	0	PLA2G4C	53250058	0.011000	0.17503	0.002000	0.10522	0.020000	0.10135	0.887000	0.28254	0.033000	0.15463	-0.474000	0.04947	GAG	.	.	weak		0.537	PLA2G4C-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465551.1		
FNBP4	23360	hgsc.bcm.edu	37	11	47744591	47744591	+	Silent	SNP	A	A	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:47744591A>T	ENST00000263773.5	-	15	2754	c.2742T>A	c.(2740-2742)ccT>ccA	p.P914P		NM_015308.2	NP_056123.2	Q8N3X1	FNBP4_HUMAN	formin binding protein 4	914	Pro-rich.					nucleus (GO:0005634)		p.P914P(1)		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						gtggtggtggaggaggaggag	0.463																																					p.P914P		Atlas-SNP	.											FNBP4,NS,carcinoma,0,1	FNBP4	99	1	1	Substitution - coding silent(1)	endometrium(1)	c.T2742A						PASS	.						15.0	15.0	15.0					11																	47744591		1997	4159	6156	SO:0001819	synonymous_variant	23360	exon15			TGGTGGAGGAGGA	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.2742T>A	11.37:g.47744591A>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	53	4	0.0754717	NM_015308	Q9H985|Q9NT81|Q9Y2L7	Silent	SNP	ENST00000263773.5	37	CCDS41644.1																																																																																			.	.	none		0.463	FNBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390237.3		
KMT2D	8085	hgsc.bcm.edu	37	12	49427679	49427679	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:49427679C>T	ENST00000301067.7	-	39	10808	c.10809G>A	c.(10807-10809)caG>caA	p.Q3603Q	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	3603	Gln-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.Q3603Q(1)|p.Q3333Q(1)									gctgctgctgctgttgttgct	0.582																																					p.Q3603Q		Atlas-SNP	.											MLL2_ENST00000301067,NS,carcinoma,0,2	MLL2	1173	2	2	Substitution - coding silent(2)	endometrium(2)	c.G10809A						scavenged	.						10.0	10.0	10.0					12																	49427679		2174	4260	6434	SO:0001819	synonymous_variant	8085	exon39			CTGCTGCTGTTGT	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.10809G>A	12.37:g.49427679C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	44	3	0.0681818	NM_003482	O14687	Silent	SNP	ENST00000301067.7	37	CCDS44873.1																																																																																			.	.	none		0.582	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
UNC45B	146862	hgsc.bcm.edu	37	17	33504529	33504529	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr17:33504529C>T	ENST00000268876.5	+	17	2258	c.2161C>T	c.(2161-2163)Cgg>Tgg	p.R721W	UNC45B_ENST00000433649.1_Missense_Mutation_p.R719W|UNC45B_ENST00000378449.1_Missense_Mutation_p.R640W|UNC45B_ENST00000591048.1_Missense_Mutation_p.R640W|UNC45B_ENST00000394570.2_Missense_Mutation_p.R719W	NM_173167.2	NP_775259.1	Q8IWX7	UN45B_HUMAN	unc-45 homolog B (C. elegans)	721					cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(10)|lung(24)|ovary(3)|prostate(2)|skin(1)|stomach(1)|urinary_tract(3)	59		Ovarian(249;0.17)				TGAGGTGGTGCGGCCCCTTGT	0.542																																					p.R721W		Atlas-SNP	.											UNC45B,NS,carcinoma,-1,2	UNC45B	133	2	0			c.C2161T						PASS	.						44.0	30.0	35.0					17																	33504529		2201	4293	6494	SO:0001583	missense	146862	exon17			GTGGTGCGGCCCC	AW755253	CCDS11292.1, CCDS45648.1	17q12	2008-02-05	2005-11-17	2005-11-17	ENSG00000141161	ENSG00000141161			14304	protein-coding gene	gene with protein product		611220	"""cardiomyopathy associated 4"""	CMYA4		12356907	Standard	NM_001267052		Approved	UNC45	uc002hja.3	Q8IWX7	OTTHUMG00000132931	ENST00000268876.5:c.2161C>T	17.37:g.33504529C>T	ENSP00000268876:p.Arg721Trp	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	101	41	0.405941	NM_173167	Q495Q8|Q495Q9	Missense_Mutation	SNP	ENST00000268876.5	37	CCDS11292.1	.	.	.	.	.	.	.	.	.	.	C	17.90	3.502276	0.64298	.	.	ENSG00000141161	ENST00000394570;ENST00000268876;ENST00000433649;ENST00000378449	T;T;T	0.51325	3.54;1.52;0.71	5.3	3.21	0.36854	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.73877	0.3643	M	0.92923	3.36	0.51482	D	0.999929	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.998	T	0.79729	-0.1681	10	0.87932	D	0	-29.8644	12.8752	0.57986	0.4433:0.5567:0.0:0.0	.	640;719;721	Q8IWX7-2;Q8IWX7-3;Q8IWX7	.;.;UN45B_HUMAN	W	721;721;719;640	ENSP00000268876:R721W;ENSP00000412840:R719W;ENSP00000367710:R640W	ENSP00000268876:R721W	R	+	1	2	UNC45B	30528642	0.984000	0.35163	1.000000	0.80357	0.787000	0.44495	1.138000	0.31491	0.725000	0.32318	0.563000	0.77884	CGG	.	.	none		0.542	UNC45B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256458.2	NM_173167	
PRB2	653247	hgsc.bcm.edu	37	12	11546598	11546598	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:11546598C>T	ENST00000389362.4	-	3	449	c.414G>A	c.(412-414)aaG>aaA	p.K138K	PRB2_ENST00000545829.1_5'Flank|PRB1_ENST00000546254.1_Intron	NM_006248.3	NP_006239.3	P02812	PRB2_HUMAN	proline-rich protein BstNI subfamily 2	138	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)			GTCCTTGTGGCTTTCCTGGAG	0.597																																					p.K138K		Atlas-SNP	.											PRB2_ENST00000389362,NS,carcinoma,0,2	PRB2	168	2	0			c.G414A						scavenged	.						241.0	220.0	227.0					12																	11546598		2201	4296	6497	SO:0001819	synonymous_variant	653247	exon3			TTGTGGCTTTCCT	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.414G>A	12.37:g.11546598C>T		Somatic	261	2	0.00766284		WXS	Illumina HiSeq	Phase_I	334	6	0.0179641	NM_006248	O00599|P02811|P04281	Silent	SNP	ENST00000389362.4	37	CCDS41757.2																																																																																			.	.	none		0.597	PRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346925.2	NM_006248	
ZNF175	7728	hgsc.bcm.edu	37	19	52084729	52084729	+	Missense_Mutation	SNP	G	G	A	rs200667551		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:52084729G>A	ENST00000262259.2	+	3	516	c.158G>A	c.(157-159)cGg>cAg	p.R53Q	ZNF175_ENST00000436511.2_Missense_Mutation_p.R53Q|ZNF175_ENST00000596504.1_Missense_Mutation_p.R53Q	NM_007147.2	NP_009078.1	Q9Y473	ZN175_HUMAN	zinc finger protein 175	53	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)		TGCCTGTACCGGGATGTGATG	0.552																																					p.R53Q		Atlas-SNP	.											ZNF175,colon,carcinoma,+1,1	ZNF175	65	1	0			c.G158A						scavenged	.						119.0	104.0	109.0					19																	52084729		2203	4300	6503	SO:0001583	missense	7728	exon3			TGTACCGGGATGT	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.158G>A	19.37:g.52084729G>A	ENSP00000262259:p.Arg53Gln	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	232	3	0.012931	NM_007147	A8K9H2	Missense_Mutation	SNP	ENST00000262259.2	37	CCDS12837.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	7.001	0.554892	0.13436	.	.	ENSG00000105497	ENST00000262259;ENST00000436511	T;T	0.02579	4.24;4.24	2.47	-0.884	0.10597	Krueppel-associated box (4);	.	.	.	.	T	0.02494	0.0076	L	0.33339	1.005	0.18873	N	0.999986	B	0.02656	0.0	B	0.01281	0.0	T	0.43294	-0.9400	9	0.37606	T	0.19	.	6.7679	0.23576	0.6284:0.0:0.3716:0.0	.	53	Q9Y473	ZN175_HUMAN	Q	53	ENSP00000262259:R53Q;ENSP00000440578:R53Q	ENSP00000262259:R53Q	R	+	2	0	ZNF175	56776541	0.000000	0.05858	0.853000	0.33588	0.359000	0.29487	-1.222000	0.02965	-0.334000	0.08463	-0.294000	0.09567	CGG	A|0.000;G|1.000	0.000	strong		0.552	ZNF175-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396205.1	NM_007147	
DMGDH	29958	hgsc.bcm.edu	37	5	78359591	78359591	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:78359591A>G	ENST00000255189.3	-	2	149	c.121T>C	c.(121-123)Tct>Cct	p.S41P	DMGDH_ENST00000380311.4_5'UTR|DMGDH_ENST00000540686.1_5'UTR|DMGDH_ENST00000520388.1_Intron	NM_013391.2	NP_037523.2	Q9UI17	M2GD_HUMAN	dimethylglycine dehydrogenase	41					amino-acid betaine catabolic process (GO:0006579)|choline metabolic process (GO:0019695)|glycine catabolic process (GO:0006546)|glycine metabolic process (GO:0006544)	mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|dimethylglycine dehydrogenase activity (GO:0047865)|electron carrier activity (GO:0009055)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|kidney(2)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	34		all_lung(232;0.000638)|Lung NSC(167;0.00173)|Ovarian(174;0.0262)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;6.52e-45)|Epithelial(54;5.96e-40)|all cancers(79;3.56e-35)		GTTTCTGCAGATAAGGGTGGT	0.468																																					p.S41P		Atlas-SNP	.											DMGDH,rectum,carcinoma,+1,1	DMGDH	88	1	0			c.T121C						scavenged	.						234.0	198.0	210.0					5																	78359591		2203	4300	6503	SO:0001583	missense	29958	exon2			CTGCAGATAAGGG	AF111858	CCDS4044.1	5q14.1	2008-02-05			ENSG00000132837	ENSG00000132837	1.5.99.2		24475	protein-coding gene	gene with protein product		605849				10767172, 11231903	Standard	NM_013391		Approved		uc003kfs.3	Q9UI17	OTTHUMG00000108159	ENST00000255189.3:c.121T>C	5.37:g.78359591A>G	ENSP00000255189:p.Ser41Pro	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	265	4	0.0150943	NM_013391	B2RBN0|B4E1J9	Missense_Mutation	SNP	ENST00000255189.3	37	CCDS4044.1	.	.	.	.	.	.	.	.	.	.	A	10.12	1.263408	0.23051	.	.	ENSG00000132837	ENST00000255189	T	0.75050	-0.9	5.25	-7.77	0.01227	.	1.238380	0.05342	N	0.530281	T	0.49508	0.1561	N	0.08118	0	0.09310	N	0.999996	B	0.02656	0.0	B	0.01281	0.0	T	0.37126	-0.9719	10	0.33141	T	0.24	.	9.3477	0.38118	0.3955:0.0:0.5012:0.1033	.	41	Q9UI17	M2GD_HUMAN	P	41	ENSP00000255189:S41P	ENSP00000255189:S41P	S	-	1	0	DMGDH	78395347	0.000000	0.05858	0.000000	0.03702	0.053000	0.15095	-0.360000	0.07622	-1.315000	0.02297	-0.379000	0.06801	TCT	.	.	none		0.468	DMGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226963.3	NM_013391	
AR	367	hgsc.bcm.edu	37	X	66905872	66905872	+	Missense_Mutation	SNP	G	G	A	rs137852569		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:66905872G>A	ENST00000374690.3	+	3	2313	c.1789G>A	c.(1789-1791)Gcc>Acc	p.A597T	AR_ENST00000396043.2_Missense_Mutation_p.A65T|AR_ENST00000513847.1_3'UTR|AR_ENST00000396044.3_Missense_Mutation_p.A597T|AR_ENST00000504326.1_Missense_Mutation_p.A597T	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	596	Interaction with HIPK3. {ECO:0000250}.|Interaction with LPXN.		S -> G (in PAIS; high dissociation rate; associated with P-617 in a PAIS patient; partially restores DNA-binding activity of P-617 mutant receptors). {ECO:0000269|PubMed:1316540}.|S -> T (in a patient with severe hypospadias). {ECO:0000269|PubMed:10092153}.		androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	GTACCTGTGCGCCAGCAGAAA	0.413									Androgen Insensitivity Syndrome																												p.A597T		Atlas-SNP	.											.	AR	249	.	0			c.G1789A	GRCh37	CM920071	AR	M	rs137852569	PASS	.						106.0	93.0	97.0					X																	66905872		2203	4300	6503	SO:0001583	missense	367	exon3	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	CTGTGCGCCAGCA	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"""Nuclear hormone receptors"""	644	protein-coding gene	gene with protein product	"""testicular feminization"", ""Kennedy disease"""	313700	"""dihydrotestosterone receptor"", ""spinal and bulbar muscular atrophy"""	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.1789G>A	X.37:g.66905872G>A	ENSP00000363822:p.Ala597Thr	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	59	4	0.0677966	NM_000044	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	37	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	G	16.77	3.214457	0.58452	.	.	ENSG00000169083	ENST00000544984;ENST00000374690;ENST00000504326;ENST00000396044;ENST00000396043	D;D;D;D	0.97209	-4.29;-4.29;-4.29;-4.29	5.32	4.47	0.54385	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (3);	0.000000	0.85682	D	0.000000	D	0.97155	0.9070	L	0.45352	1.415	0.80722	D	1	P;P;D;B	0.89917	0.881;0.881;1.0;0.343	B;B;D;B	0.97110	0.175;0.175;1.0;0.076	D	0.97171	0.9844	10	0.87932	D	0	.	10.6719	0.45764	0.0936:0.0:0.9064:0.0	.	597;597;65;596	E7EVX6;D3YPQ2;F1D8N5;P10275	.;.;.;ANDR_HUMAN	T	407;597;597;597;65	ENSP00000363822:A597T;ENSP00000421155:A597T;ENSP00000379359:A597T;ENSP00000379358:A65T	ENSP00000363822:A597T	A	+	1	0	AR	66822597	1.000000	0.71417	0.987000	0.45799	0.102000	0.19082	9.050000	0.93843	1.228000	0.43614	-0.306000	0.09157	GCC	.	.	weak		0.413	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044	
SEMG1	6406	hgsc.bcm.edu	37	20	43837052	43837052	+	Missense_Mutation	SNP	C	C	A	rs199672858	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	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	174	0	0		WXS	Illumina HiSeq	Phase_I	203	3	0.0147783	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	
PRAMEF11	440560	hgsc.bcm.edu	37	1	12887174	12887174	+	Missense_Mutation	SNP	C	C	T	rs61777003		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:12887174C>T	ENST00000535591.1	-	3	878	c.683G>A	c.(682-684)cGc>cAc	p.R228H		NM_001146344.1	NP_001139816.1	O60813	PRA11_HUMAN	PRAME family member 11	228					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.R228H(1)		NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|lung(7)|pancreas(2)|skin(4)|urinary_tract(1)	27						TTGGAGGCAGCGCAGCTTGAG	0.527																																					p.R228H		Atlas-SNP	.											PRAMEF11,extremity,malignant_melanoma,0,1	PRAMEF11	72	1	1	Substitution - Missense(1)	skin(1)	c.G683A						scavenged	.																																			SO:0001583	missense	440560	exon3			AGGCAGCGCAGCT	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.683G>A	1.37:g.12887174C>T	ENSP00000439551:p.Arg228His	Somatic	21	1	0.047619		WXS	Illumina HiSeq	Phase_I	16	3	0.1875	NM_001146344		Missense_Mutation	SNP	ENST00000535591.1	37	CCDS53268.1	.	.	.	.	.	.	.	.	.	.	.	0.026	-1.374502	0.01214	.	.	ENSG00000204513	ENST00000535591;ENST00000331684;ENST00000437584	T;T	0.53206	0.63;0.63	1.48	-1.16	0.09678	.	1.511700	0.03844	N	0.271170	T	0.15349	0.0370	N	0.01134	-0.995	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.25012	-1.0144	10	0.05959	T	0.93	.	4.3434	0.11120	0.0:0.4269:0.0:0.5731	rs61777003	228	O60813	PRA11_HUMAN	H	228;269;228	ENSP00000439551:R228H;ENSP00000391839:R228H	ENSP00000328783:R269H	R	-	2	0	PRAMEF11	12809761	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.181000	0.01257	-0.346000	0.08312	-0.939000	0.02691	CGC	C|0.833;T|0.167	0.167	weak		0.527	PRAMEF11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_496341	
BEST3	144453	hgsc.bcm.edu	37	12	70087575	70087575	+	Silent	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:70087575G>A	ENST00000330891.5	-	4	586	c.360C>T	c.(358-360)caC>caT	p.H120H	BEST3_ENST00000266661.4_Silent_p.H14H|BEST3_ENST00000553096.1_Silent_p.H14H|BEST3_ENST00000551160.1_Silent_p.H14H|BEST3_ENST00000331471.4_Silent_p.H120H|BEST3_ENST00000533674.1_5'UTR|BEST3_ENST00000393365.1_Silent_p.H14H|BEST3_ENST00000476098.1_De_novo_Start_OutOfFrame	NM_001282613.1|NM_032735.2	NP_001269542.1|NP_116124.2	Q8N1M1	BEST3_HUMAN	bestrophin 3	120					negative regulation of ion transport (GO:0043271)	chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			cervix(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(2)	12	Breast(13;2.31e-06)|Esophageal squamous(21;0.187)		Lung(24;0.000278)|OV - Ovarian serous cystadenocarcinoma(12;0.0019)|STAD - Stomach adenocarcinoma(21;0.00694)			GCAGGCGCCCGTGCTCGTCGC	0.532																																					p.H120H		Atlas-SNP	.											.	BEST3	129	.	0			c.C360T						PASS	.						103.0	89.0	93.0					12																	70087575		2203	4300	6503	SO:0001819	synonymous_variant	144453	exon4			GCGCCCGTGCTCG	AF440758	CCDS8992.2, CCDS41810.1, CCDS61192.1, CCDS61193.1, CCDS73496.1	12q14.2-q15	2012-09-26	2006-10-18	2006-10-18	ENSG00000127325	ENSG00000127325		"""Ion channels / Chloride channels : Calcium activated : Bestrophins"""	17105	protein-coding gene	gene with protein product		607337	"""vitelliform macular dystrophy 2-like 3"""	VMD2L3		12032738	Standard	NM_032735		Approved	MGC40411, MGC13168	uc001svg.3	Q8N1M1	OTTHUMG00000149919	ENST00000330891.5:c.360C>T	12.37:g.70087575G>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	162	60	0.37037	NM_032735	B5MDI8|F8VVZ2|Q53YQ7|Q8N356|Q8NFT9|Q9BR80	Silent	SNP	ENST00000330891.5	37	CCDS8992.2																																																																																			.	.	none		0.532	BEST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313908.2	NM_152439	
KAT6A	7994	hgsc.bcm.edu	37	8	41790513	41790513	+	Missense_Mutation	SNP	C	C	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr8:41790513C>A	ENST00000396930.3	-	18	5768	c.5225G>T	c.(5224-5226)gGc>gTc	p.G1742V	KAT6A_ENST00000265713.2_Missense_Mutation_p.G1742V|KAT6A_ENST00000406337.1_Missense_Mutation_p.G1742V	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	1742					aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										AGAGTAGCTGCCGGCACCAAA	0.502																																					p.G1742V		Atlas-SNP	.											MYST3,NS,carcinoma,+1,1	.	.	1	0			c.G5225T						scavenged	.						169.0	170.0	169.0					8																	41790513		2203	4300	6503	SO:0001583	missense	7994	exon18			TAGCTGCCGGCAC	U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Zinc fingers, C2HC-type containing"", ""Zinc fingers, PHD-type"""	13013	protein-coding gene	gene with protein product	"""Monocytic leukemia zinc finger protein"""	601408	"""runt-related transcription factor binding protein 2"", ""MYST histone acetyltransferase (monocytic leukemia) 3"""	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.5225G>T	8.37:g.41790513C>A	ENSP00000380136:p.Gly1742Val	Somatic	101	1	0.00990099		WXS	Illumina HiSeq	Phase_I	148	2	0.0135135	NM_001099412	Q76L81	Missense_Mutation	SNP	ENST00000396930.3	37	CCDS6124.1	.	.	.	.	.	.	.	.	.	.	C	13.31	2.200043	0.38905	.	.	ENSG00000083168	ENST00000265713;ENST00000406337;ENST00000396930	T;T;T	0.70516	-0.49;-0.49;-0.49	5.63	5.63	0.86233	.	0.220723	0.39475	N	0.001342	T	0.69088	0.3072	L	0.32530	0.975	0.80722	D	1	D	0.56521	0.976	P	0.47102	0.537	T	0.73148	-0.4074	10	0.72032	D	0.01	-8.0146	19.69	0.95996	0.0:1.0:0.0:0.0	.	1742	Q92794	KAT6A_HUMAN	V	1742	ENSP00000265713:G1742V;ENSP00000385888:G1742V;ENSP00000380136:G1742V	ENSP00000265713:G1742V	G	-	2	0	KAT6A	41909670	1.000000	0.71417	0.998000	0.56505	0.950000	0.60333	7.437000	0.80417	2.643000	0.89663	0.650000	0.86243	GGC	.	.	none		0.502	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766	
MUC4	4585	hgsc.bcm.edu	37	3	195509843	195509843	+	Missense_Mutation	SNP	C	C	T	rs200739317		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:195509843C>T	ENST00000463781.3	-	2	9067	c.8608G>A	c.(8608-8610)Gct>Act	p.A2870T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A2870T|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACTGAGGAAGCGTCGGTGACA	0.597																																					p.A2870T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	0			c.G8608A						scavenged	.						24.0	21.0	22.0					3																	195509843		675	1566	2241	SO:0001583	missense	4585	exon2			AGGAAGCGTCGGT	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.8608G>A	3.37:g.195509843C>T	ENSP00000417498:p.Ala2870Thr	Somatic	291	3	0.0103093		WXS	Illumina HiSeq	Phase_I	283	14	0.04947	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	15.45	2.838365	0.51057	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31769	1.48;1.48	.	.	.	.	.	.	.	.	T	0.28499	0.0705	N	0.14661	0.345	0.20821	N	0.999847	D	0.69078	0.997	D	0.65573	0.936	T	0.15925	-1.0420	7	.	.	.	.	4.8018	0.13301	0.3429:0.657:0.0:1.0E-4	.	2742	E7ESK3	.	T	2870	ENSP00000417498:A2870T;ENSP00000420243:A2870T	.	A	-	1	0	MUC4	196994622	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.830000	0.00355	-0.000000	0.14550	0.000000	0.15137	GCT	.	.	weak		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
DACH1	1602	hgsc.bcm.edu	37	13	72440219	72440219	+	Missense_Mutation	SNP	G	G	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr13:72440219G>C	ENST00000359684.2	-	1	688	c.689C>G	c.(688-690)aCg>aGg	p.T230R	DACH1_ENST00000354591.4_Missense_Mutation_p.T230R|DACH1_ENST00000305425.4_Missense_Mutation_p.T230R|DACH1_ENST00000313174.7_Missense_Mutation_p.T230R			Q9UI36	DACH1_HUMAN	dachshund family transcription factor 1	230	DACHbox-N.|Interaction with SIX6 and HDAC3. {ECO:0000250}.				cell proliferation (GO:0008283)|development of primary female sexual characteristics (GO:0046545)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of transcription by competitive promoter binding (GO:0010944)|respiratory gaseous exchange (GO:0007585)|suckling behavior (GO:0001967)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity involved in preinitiation complex assembly (GO:0001075)	p.T230fs*6(1)		NS(1)|breast(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(23)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Acute lymphoblastic leukemia(28;0.0503)|Breast(118;0.198)		GBM - Glioblastoma multiforme(99;0.00032)		GGTGTAGACCGTATGCAAGCC	0.617																																					p.T230R		Atlas-SNP	.											.	DACH1	123	.	1	Deletion - Frameshift(1)	lung(1)	c.C689G						PASS	.						79.0	85.0	83.0					13																	72440219		2070	4222	6292	SO:0001583	missense	1602	exon1			TAGACCGTATGCA	AJ005670	CCDS41899.1, CCDS53874.1, CCDS53873.1	13q22	2014-02-03	2014-02-03	2004-04-02	ENSG00000165659	ENSG00000276644			2663	protein-coding gene	gene with protein product		603803	"""dachshund homolog (Drosophila)"", ""dachshund homolog 1 (Drosophila)"""	DACH		9933575, 10395809, 15057823	Standard	NM_004392		Approved		uc021rkj.1	Q9UI36	OTTHUMG00000017063	ENST00000359684.2:c.689C>G	13.37:g.72440219G>C	ENSP00000352712:p.Thr230Arg	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	133	66	0.496241	NM_080759	D0FY35|D0FY36|O75523|O75687|Q5VYY3|Q5VYY4|Q96SG3|Q96SG4|Q9H524|Q9UMH4	Missense_Mutation	SNP	ENST00000359684.2	37		.	.	.	.	.	.	.	.	.	.	G	18.36	3.606479	0.66445	.	.	ENSG00000165659	ENST00000305425;ENST00000313174;ENST00000354591;ENST00000359684;ENST00000377826	D;D;D;D	0.83506	-1.73;-1.73;-1.73;-1.73	4.08	4.08	0.47627	.	0.000000	0.85682	D	0.000000	D	0.91012	0.7173	M	0.80982	2.52	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.997;0.999	D	0.92697	0.6171	10	0.87932	D	0	-6.469	15.8733	0.79141	0.0:0.0:1.0:0.0	.	228;228;228	Q9UI36-4;Q9UI36-3;Q9UI36-2	.;.;.	R	230	ENSP00000304994:T230R;ENSP00000318506:T230R;ENSP00000346604:T230R;ENSP00000352712:T230R	ENSP00000304994:T230R	T	-	2	0	DACH1	71338220	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	9.144000	0.94629	1.803000	0.52742	0.313000	0.20887	ACG	.	.	none		0.617	DACH1-002	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000045240.1	NM_004392	
HIST1H1C	3006	hgsc.bcm.edu	37	6	26056385	26056385	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr6:26056385C>T	ENST00000343677.2	-	1	314	c.272G>A	c.(271-273)gGc>gAc	p.G91D		NM_005319.3	NP_005310.1	P16403	H12_HUMAN	histone cluster 1, H1c	91	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(4)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	34						CACCAGAGTGCCCTTGCTCAC	0.542																																					p.G91D		Atlas-SNP	.											.	HIST1H1C	80	.	0			c.G272A						PASS	.						111.0	115.0	114.0					6																	26056385		2203	4300	6503	SO:0001583	missense	3006	exon1			AGAGTGCCCTTGC	X57129	CCDS4577.1	6p21.3	2012-10-02	2006-10-11	2003-02-21	ENSG00000187837	ENSG00000187837		"""Histones / Replication-dependent"""	4716	protein-coding gene	gene with protein product		142710	"""H1 histone family, member 2"", ""histone 1, H1c"""	H1F2		2759094, 12408966	Standard	NM_005319		Approved	H1.2, H1s-1, H1c	uc003nfw.3	P16403	OTTHUMG00000016140	ENST00000343677.2:c.272G>A	6.37:g.26056385C>T	ENSP00000339566:p.Gly91Asp	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	188	87	0.462766	NM_005319	A8K4I2	Missense_Mutation	SNP	ENST00000343677.2	37	CCDS4577.1	.	.	.	.	.	.	.	.	.	.	C	18.78	3.696243	0.68386	.	.	ENSG00000187837	ENST00000343677	T	0.59083	0.29	5.63	5.63	0.86233	Histone H1/H5 (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.107097	0.64402	D	0.000006	T	0.79902	0.4526	M	0.92026	3.265	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.83425	0.0035	10	0.87932	D	0	-22.419	19.032	0.92961	0.0:1.0:0.0:0.0	.	91	P16403	H12_HUMAN	D	91	ENSP00000339566:G91D	ENSP00000339566:G91D	G	-	2	0	HIST1H1C	26164364	1.000000	0.71417	1.000000	0.80357	0.311000	0.27955	5.879000	0.69690	2.814000	0.96858	0.655000	0.94253	GGC	.	.	none		0.542	HIST1H1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043372.1	NM_005319	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144856817	144856817	+	Splice_Site	SNP	T	T	C	rs3844239		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:144856817T>C	ENST00000369354.3	-	40	6857	c.6668A>G	c.(6667-6669)gAg>gGg	p.E2223G	PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000530740.1_Splice_Site_p.E2308G|PDE4DIP_ENST00000369356.4_Splice_Site_p.E2223G|PDE4DIP_ENST00000313382.9_Splice_Site_p.E2117G|RP4-791M13.4_ENST00000532137.1_RNA|PDE4DIP_ENST00000369359.4_Splice_Site_p.E2359G			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2223					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.E2223G(2)		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)		TGTGATTACCTCTGTGCCTTG	0.478			T	PDGFRB	MPD																																p.E2223G		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	PDE4DIP_ENST00000369356,caecum,carcinoma,0,4	PDE4DIP	817	4	2	Substitution - Missense(2)	prostate(2)	c.A6668G						scavenged	.						52.0	38.0	43.0					1																	144856817		2202	4294	6496	SO:0001630	splice_region_variant	9659	exon40			ATTACCTCTGTGC	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.6669+1A>G	1.37:g.144856817T>C		Somatic	176	11	0.0625		WXS	Illumina HiSeq	Phase_I	172	14	0.0813954	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	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	14.30|14.30	2.495079|2.495079	0.44352|0.44352	.|.	.|.	ENSG00000178104|ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359|ENST00000530130	T;T;T;T;T|.	0.01871|.	4.59;4.69;4.67;4.69;4.69|.	4.52|4.52	3.39|3.39	0.38822|0.38822	.|.	.|.	.|.	.|.	.|.	T|T	0.52885|0.52885	0.1762|0.1762	M|M	0.73598|0.73598	2.24|2.24	0.80722|0.80722	D|D	1|1	B;B|.	0.17852|.	0.0;0.024|.	B;B|.	0.20184|.	0.0;0.028|.	T|T	0.54193|0.54193	-0.8330|-0.8330	9|5	0.59425|.	D|.	0.04|.	.|.	8.6174|8.6174	0.33840|0.33840	0.0:0.0946:0.0:0.9054|0.0:0.0946:0.0:0.9054	rs3844239|rs3844239	2117;2223|.	Q5VU43-3;Q5VU43|.	.;MYOME_HUMAN|.	G|G	2117;2223;2223;2308;2359|300	ENSP00000327209:E2117G;ENSP00000358360:E2223G;ENSP00000358363:E2223G;ENSP00000435654:E2308G;ENSP00000358366:E2359G|.	ENSP00000327209:E2117G|.	E|R	-|-	2|1	0|2	PDE4DIP|PDE4DIP	143568174|143568174	1.000000|1.000000	0.71417|0.71417	0.886000|0.886000	0.34754|0.34754	0.224000|0.224000	0.24922|0.24922	3.513000|3.513000	0.53414|0.53414	0.702000|0.702000	0.31825|0.31825	-0.566000|-0.566000	0.04163|0.04163	GAG|AGG	.	.	weak		0.478	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	Missense_Mutation
CYP2C19	1557	hgsc.bcm.edu	37	10	96580331	96580331	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr10:96580331G>A	ENST00000371321.3	+	6	980	c.898G>A	c.(898-900)Gag>Aag	p.E300K	CYP2C19_ENST00000464755.1_3'UTR	NM_000769.1	NP_000760	P33261	CP2CJ_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 19	300					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|heterocycle metabolic process (GO:0046483)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	(R)-limonene 6-monooxygenase activity (GO:0052741)|(S)-limonene 6-monooxygenase activity (GO:0018675)|(S)-limonene 7-monooxygenase activity (GO:0018676)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxygen binding (GO:0019825)|steroid hydroxylase activity (GO:0008395)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	43		Colorectal(252;0.09)		all cancers(201;6.02e-07)|KIRC - Kidney renal clear cell carcinoma(50;0.0672)|Kidney(138;0.0838)	Acenocoumarol(DB01418)|Acetylsalicylic acid(DB00945)|Adinazolam(DB00546)|Almotriptan(DB00918)|Aminoglutethimide(DB00357)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amoxicillin(DB01060)|Amprenavir(DB00701)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Arformoterol(DB01274)|Artemether(DB06697)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Benzatropine(DB00245)|Bicalutamide(DB01128)|Bifonazole(DB04794)|Bortezomib(DB00188)|Bromazepam(DB01558)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Carisoprodol(DB00395)|Chloramphenicol(DB00446)|Chlorpropamide(DB00672)|Cholecalciferol(DB00169)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cisapride(DB00604)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clevidipine(DB04920)|Clobazam(DB00349)|Clomipramine(DB01242)|Clopidogrel(DB00758)|Clotiazepam(DB01559)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronabinol(DB00470)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enfuvirtide(DB00109)|Enzalutamide(DB08899)|Escitalopram(DB01175)|Esomeprazole(DB00736)|Estradiol(DB00783)|Ethanol(DB00898)|Ethotoin(DB00754)|Etoricoxib(DB01628)|Etravirine(DB06414)|Famotidine(DB00927)|Felbamate(DB00949)|Fluconazole(DB00196)|Flunitrazepam(DB01544)|Fluoxetine(DB00472)|Flutamide(DB00499)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Fosphenytoin(DB01320)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Gliclazide(DB01120)|Glucosamine(DB01296)|Glyburide(DB01016)|Guanfacine(DB01018)|Haloperidol(DB00502)|Hexobarbital(DB01355)|Ibuprofen(DB01050)|Ifosfamide(DB01181)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Indomethacin(DB00328)|Isoniazid(DB00951)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Levomilnacipran(DB08918)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Losartan(DB00678)|Lovastatin(DB00227)|LULICONAZOLE(DB08933)|Lumiracoxib(DB01283)|MACITENTAN(DB08932)|Melatonin(DB01065)|Memantine(DB01043)|Meprobamate(DB00371)|Methadone(DB00333)|Methazolamide(DB00703)|Methimazole(DB00763)|Methsuximide(DB05246)|Methylphenobarbital(DB00849)|Metoprolol(DB00264)|Miconazole(DB01110)|Moclobemide(DB01171)|Modafinil(DB00745)|Nelfinavir(DB00220)|Nicardipine(DB00622)|Nicotine(DB00184)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Norethindrone(DB00717)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ospemifene(DB04938)|Oxcarbazepine(DB00776)|Oxiconazole(DB00239)|Pantoprazole(DB00213)|Pegvisomant(DB00082)|Pentamidine(DB00738)|Pentobarbital(DB00312)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phensuximide(DB00832)|Phenytoin(DB00252)|Pimozide(DB01100)|Pioglitazone(DB01132)|Pipotiazine(DB01621)|Podofilox(DB01179)|Prasugrel(DB06209)|Praziquantel(DB01058)|Prednisone(DB00635)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Propofol(DB00818)|Propranolol(DB00571)|Quazepam(DB01589)|Quetiapine(DB01224)|Quinine(DB00468)|Rabeprazole(DB01129)|Ramelteon(DB00980)|Ranitidine(DB00863)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sitaxentan(DB06268)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Tamoxifen(DB00675)|Tapentadol(DB06204)|Telmisartan(DB00966)|Temazepam(DB00231)|Teniposide(DB00444)|Terbinafine(DB00857)|Testosterone(DB00624)|Thalidomide(DB01041)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Timolol(DB00373)|Tioconazole(DB01007)|Tipranavir(DB00932)|Tofacitinib(DB08895)|Tolbutamide(DB01124)|Tolterodine(DB01036)|Topiramate(DB00273)|Torasemide(DB00214)|Trabectedin(DB05109)|Tranylcypromine(DB00752)|Trimethadione(DB00347)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vismodegib(DB08828)|Voriconazole(DB00582)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zidovudine(DB00495)|Zolpidem(DB00425)|Zonisamide(DB00909)	AGCTGGGACAGAGACAACAAG	0.428																																					p.E300K		Atlas-SNP	.											.	CYP2C19	88	.	0			c.G898A						PASS	.						193.0	174.0	181.0					10																	96580331		2203	4300	6503	SO:0001583	missense	1557	exon6			GGGACAGAGACAA	M61854	CCDS7436.1	10q24	2007-12-14	2003-01-14		ENSG00000165841	ENSG00000165841		"""Cytochrome P450s"""	2621	protein-coding gene	gene with protein product		124020	"""cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 19"""	CYP2C		2009263, 8530044	Standard	NM_000769		Approved	P450IIC19, CPCJ	uc010qnz.2	P33261	OTTHUMG00000018799	ENST00000371321.3:c.898G>A	10.37:g.96580331G>A	ENSP00000360372:p.Glu300Lys	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	102	30	0.294118	NM_000769	P33259|Q8WZB1|Q8WZB2|Q9UCD4	Missense_Mutation	SNP	ENST00000371321.3	37	CCDS7436.1	.	.	.	.	.	.	.	.	.	.	G	15.31	2.796723	0.50208	.	.	ENSG00000165841	ENST00000371321	T	0.17213	2.29	3.95	3.95	0.45737	.	0.074405	0.51477	U	0.000091	T	0.47488	0.1448	M	0.92604	3.325	0.29808	N	0.831907	D	0.89917	1.0	D	0.69654	0.965	T	0.56768	-0.7924	10	0.87932	D	0	.	11.4092	0.49915	0.0:0.0:1.0:0.0	.	300	P33261	CP2CJ_HUMAN	K	300	ENSP00000360372:E300K	ENSP00000360372:E300K	E	+	1	0	CYP2C19	96570321	1.000000	0.71417	0.996000	0.52242	0.192000	0.23643	5.180000	0.65048	2.016000	0.59253	0.400000	0.26472	GAG	.	.	none		0.428	CYP2C19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049490.1	NM_000769	
PMPCA	23203	hgsc.bcm.edu	37	9	139306549	139306549	+	Missense_Mutation	SNP	A	A	G	rs367845329		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr9:139306549A>G	ENST00000371717.3	+	2	181	c.172A>G	c.(172-174)Aca>Gca	p.T58A	SDCCAG3_ENST00000371725.3_5'Flank|PMPCA_ENST00000371720.1_Missense_Mutation_p.T58A|SDCCAG3_ENST00000357365.3_5'Flank|PMPCA_ENST00000399219.3_5'UTR|SDCCAG3_ENST00000298537.7_5'Flank	NM_001282946.1|NM_015160.1	NP_001269875.1|NP_055975.1	Q10713	MPPA_HUMAN	peptidase (mitochondrial processing) alpha	58					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)		TGTTTTTGCTACAGTTGATGG	0.473																																					p.T58A		Atlas-SNP	.											.	PMPCA	29	.	0			c.A172G						PASS	.	A	ALA/THR	0,4406		0,0,2203	177.0	163.0	167.0		172	3.3	0.8	9		167	1,8599	1.2+/-3.3	0,1,4299	no	missense	PMPCA	NM_015160.1	58	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign	58/526	139306549	1,13005	2203	4300	6503	SO:0001583	missense	23203	exon2			TTTGCTACAGTTG	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.172A>G	9.37:g.139306549A>G	ENSP00000360782:p.Thr58Ala	Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	288	72	0.25	NM_015160	B4DKL3|E7ET61|Q16639|Q5SXM9|Q8N513	Missense_Mutation	SNP	ENST00000371717.3	37	CCDS35180.1	.	.	.	.	.	.	.	.	.	.	A	8.346	0.829805	0.16749	0.0	1.16E-4	ENSG00000165688	ENST00000371720;ENST00000371717	T	0.11821	2.74	4.46	3.31	0.37934	.	0.246395	0.41396	D	0.000886	T	0.09158	0.0226	L	0.28556	0.865	0.80722	D	1	B;B	0.13145	0.007;0.001	B;B	0.09377	0.004;0.002	T	0.21245	-1.0251	10	0.20046	T	0.44	.	8.9219	0.35617	0.8332:0.0:0.0:0.1668	.	58;58	B4DRK5;Q10713	.;MPPA_HUMAN	A	58	ENSP00000360782:T58A	ENSP00000360782:T58A	T	+	1	0	PMPCA	138426370	0.602000	0.26916	0.813000	0.32504	0.911000	0.54048	1.358000	0.34102	0.670000	0.31165	-0.368000	0.07277	ACA	.	.	weak		0.473	PMPCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055054.1	NM_015160	
MUC16	94025	hgsc.bcm.edu	37	19	9002597	9002597	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:9002597C>T	ENST00000397910.4	-	51	40422	c.40219G>A	c.(40219-40221)Gac>Aac	p.D13407N	MUC16_ENST00000380951.5_Missense_Mutation_p.D48N	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13409	SEA 9. {ECO:0000255|PROSITE- ProRule:PRU00188}.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CGCTCTCTGTCCAGTCCAGGG	0.592																																					p.D13407N		Atlas-SNP	.											MUC16_ENST00000397910,NS,lymphoid_neoplasm,0,2	MUC16	4315	2	0			c.G40219A						scavenged	.																																			SO:0001583	missense	94025	exon51			CTCTGTCCAGTCC	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.40219G>A	19.37:g.9002597C>T	ENSP00000381008:p.Asp13407Asn	Somatic	194	9	0.0463918		WXS	Illumina HiSeq	Phase_I	197	12	0.0609137	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	11.51|11.51	1.659878|1.659878	0.29515|0.29515	.|.	.|.	ENSG00000181143|ENSG00000181143	ENST00000397910;ENST00000380951|ENST00000542240	T;T|.	0.45668|.	0.89;0.89|.	2.75|2.75	-0.839|-0.839	0.10759|0.10759	SEA (1);|.	.|.	.|.	.|.	.|.	T|.	0.43344|.	0.1243|.	L|L	0.52759|0.52759	1.655|1.655	.|.	.|.	.|.	B;D|.	0.60575|.	0.007;0.988|.	B;D|.	0.75020|.	0.014;0.985|.	T|.	0.51236|.	-0.8731|.	8|.	0.54805|.	T|.	0.06|.	-11.8857|-11.8857	6.8102|6.8102	0.23801|0.23801	0.0:0.8029:0.0:0.1971|0.0:0.8029:0.0:0.1971	.|.	21052;13407|.	Q8WXI7;B5ME49|.	MUC16_HUMAN;.|.	N|X	13407;48|246	ENSP00000381008:D13407N;ENSP00000370338:D48N|.	ENSP00000370338:D48N|.	D|W	-|-	1|3	0|0	MUC16|MUC16	8863597|8863597	0.045000|0.045000	0.20229|0.20229	0.003000|0.003000	0.11579|0.11579	0.000000|0.000000	0.00434|0.00434	1.258000|1.258000	0.32944|0.32944	-0.029000|-0.029000	0.13827|0.13827	-3.921000|-3.921000	0.00016|0.00016	GAC|TGG	.	.	none		0.592	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
KRT8	3856	hgsc.bcm.edu	37	12	53298675	53298675	+	Missense_Mutation	SNP	A	A	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:53298675A>C	ENST00000552551.1	-	2	523	c.91T>G	c.(91-93)Tcc>Gcc	p.S31A	KRT8_ENST00000546897.1_Missense_Mutation_p.S31A|KRT8_ENST00000293308.6_Missense_Mutation_p.S31A|KRT8_ENST00000552150.1_Missense_Mutation_p.S59A			P05787	K2C8_HUMAN	keratin 8	31	Head.|Ser-rich.				cell differentiation involved in embryonic placenta development (GO:0060706)|extrinsic apoptotic signaling pathway (GO:0097191)|hepatocyte apoptotic process (GO:0097284)|response to hydrostatic pressure (GO:0051599)|response to other organism (GO:0051707)|sarcomere organization (GO:0045214)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|viral process (GO:0016032)	cell-cell junction (GO:0005911)|costamere (GO:0043034)|cytoplasm (GO:0005737)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	scaffold protein binding (GO:0097110)|structural molecule activity (GO:0005198)	p.S31A(4)		endometrium(5)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	13				BRCA - Breast invasive adenocarcinoma(357;0.108)	Tenecteplase(DB00031)	CTGATGCGGGAACCGGGCCCA	0.662																																					p.S59A		Atlas-SNP	.											KRT8,NS,carcinoma,0,5	KRT8	41	5	4	Substitution - Missense(4)	endometrium(2)|prostate(1)|liver(1)	c.T175G						scavenged	.						12.0	14.0	13.0					12																	53298675		2120	4158	6278	SO:0001583	missense	3856	exon2			TGCGGGAACCGGG	BC000654	CCDS8841.1, CCDS58234.1	12q13.13	2013-01-16			ENSG00000170421	ENSG00000170421		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6446	protein-coding gene	gene with protein product		148060				2434381, 1705144, 16831889	Standard	NM_002273		Approved	CARD2, K8, CK8, CYK8, K2C8, KO	uc009zmk.1	P05787	OTTHUMG00000169881	ENST00000552551.1:c.91T>G	12.37:g.53298675A>C	ENSP00000447566:p.Ser31Ala	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	98	5	0.0510204	NM_001256282	A8K4H3|B0AZN5|F8VXB4|Q14099|Q14716|Q14717|Q53GJ0|Q6DHW5|Q6GMY0|Q6P4C7|Q96J60	Missense_Mutation	SNP	ENST00000552551.1	37	CCDS8841.1	.	.	.	.	.	.	.	.	.	.	-	0.012	-1.651707	0.00785	.	.	ENSG00000170421	ENST00000552551;ENST00000293308;ENST00000547916;ENST00000546897;ENST00000552150;ENST00000546826;ENST00000548998;ENST00000547413;ENST00000546542	T;T;T;T;T;T;T;T	0.80393	-1.37;-1.37;-1.37;-1.37;-1.37;-1.37;-1.37;-1.37	4.05	-8.11	0.01082	.	0.706613	0.13676	N	0.370518	T	0.40619	0.1124	N	0.01197	-0.965	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.43589	-0.9382	10	0.05351	T	0.99	.	6.5956	0.22672	0.4212:0.312:0.0:0.2668	.	59;31;31	F8VXB4;F8VU64;P05787	.;.;K2C8_HUMAN	A	31;31;31;31;59;31;71;31;109	ENSP00000447566:S31A;ENSP00000293308:S31A;ENSP00000447402:S31A;ENSP00000449404:S59A;ENSP00000447881:S31A;ENSP00000447040:S71A;ENSP00000448681:S31A;ENSP00000450228:S109A	ENSP00000293308:S31A	S	-	1	0	KRT8	51584942	0.005000	0.15991	0.000000	0.03702	0.065000	0.16274	-0.018000	0.12568	-3.264000	0.00201	-0.290000	0.09829	TCC	.	.	none		0.662	KRT8-001	KNOWN	alternative_5_UTR|overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406385.1	NM_002273	
CTR9	9646	hgsc.bcm.edu	37	11	10777233	10777233	+	Missense_Mutation	SNP	G	G	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:10777233G>T	ENST00000361367.2	+	4	819	c.393G>T	c.(391-393)ttG>ttT	p.L131F		NM_014633.3	NP_055448.1	Q6PD62	CTR9_HUMAN	CTR9, Paf1/RNA polymerase II complex component	131					cellular response to lipopolysaccharide (GO:0071222)|endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone H3-K4 trimethylation (GO:0080182)|histone monoubiquitination (GO:0010390)|interleukin-6-mediated signaling pathway (GO:0070102)|JAK-STAT cascade (GO:0007259)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K79 methylation (GO:2001162)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|transcriptionally active chromatin (GO:0035327)				breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(12)|ovary(2)|pancreas(1)|stomach(1)	40				all cancers(16;1.64e-07)|Epithelial(150;2.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		AGAACCATTTGTTGGGAAGAG	0.383																																					p.L131F		Atlas-SNP	.											.	CTR9	94	.	0			c.G393T						PASS	.						139.0	136.0	137.0					11																	10777233		2201	4294	6495	SO:0001583	missense	9646	exon4			CCATTTGTTGGGA	D63875	CCDS7805.1	11p15.3	2013-07-03	2013-07-03	2006-05-22	ENSG00000198730	ENSG00000198730		"""Tetratricopeptide (TTC) repeat domain containing"""	16850	protein-coding gene	gene with protein product		609366	"""SH2 domain binding protein 1 (tetratricopeptide repeat containing)"", ""Ctr9, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)"""	SH2BP1		8590280, 8636124	Standard	NM_014633		Approved	KIAA0155, TSBP, p150TSP	uc001mja.3	Q6PD62	OTTHUMG00000165789	ENST00000361367.2:c.393G>T	11.37:g.10777233G>T	ENSP00000355013:p.Leu131Phe	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	116	48	0.413793	NM_014633	D3DQV8|Q15015	Missense_Mutation	SNP	ENST00000361367.2	37	CCDS7805.1	.	.	.	.	.	.	.	.	.	.	G	14.44	2.536972	0.45176	.	.	ENSG00000198730	ENST00000361367;ENST00000524523	T;T	0.78707	-1.2;1.12	5.97	2.57	0.30868	Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.69088	0.3072	M	0.77820	2.39	0.80722	D	1	P	0.40834	0.73	B	0.31547	0.132	T	0.64474	-0.6399	10	0.19590	T	0.45	-8.2928	8.3402	0.32239	0.1941:0.0:0.6841:0.1217	.	131	Q6PD62	CTR9_HUMAN	F	131;118	ENSP00000355013:L131F;ENSP00000431458:L118F	ENSP00000355013:L131F	L	+	3	2	CTR9	10733809	1.000000	0.71417	1.000000	0.80357	0.420000	0.31355	1.477000	0.35431	0.814000	0.34374	0.591000	0.81541	TTG	.	.	none		0.383	CTR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386215.1	NM_014633	
CLMN	79789	hgsc.bcm.edu	37	14	95669923	95669923	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr14:95669923T>C	ENST00000298912.4	-	9	1876	c.1763A>G	c.(1762-1764)gAg>gGg	p.E588G		NM_024734.3	NP_079010.2	Q96JQ2	CLMN_HUMAN	calmin (calponin-like, transmembrane)	588					negative regulation of cell proliferation (GO:0008285)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)		p.E588G(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(17)|prostate(3)|skin(3)	44				Epithelial(152;0.193)		AGGTTTTGTCTCATGAGGTGA	0.398																																					p.E588G		Atlas-SNP	.											CLMN,NS,carcinoma,-1,2	CLMN	103	2	1	Substitution - Missense(1)	endometrium(1)	c.A1763G						scavenged	.						84.0	82.0	83.0					14																	95669923		2203	4300	6503	SO:0001583	missense	79789	exon9			TTTGTCTCATGAG	AB033014	CCDS9933.1	14q32.13	2012-10-02			ENSG00000165959	ENSG00000165959			19972	protein-coding gene	gene with protein product		611121				11386753	Standard	NM_024734		Approved	FLJ12383, KIAA1188, KIAA0500	uc001yef.2	Q96JQ2	OTTHUMG00000171629	ENST00000298912.4:c.1763A>G	14.37:g.95669923T>C	ENSP00000298912:p.Glu588Gly	Somatic	190	1	0.00526316		WXS	Illumina HiSeq	Phase_I	153	3	0.0196078	NM_024734	B2RAR7|Q9H713|Q9HA23|Q9HA57|Q9UFP4|Q9ULN2	Missense_Mutation	SNP	ENST00000298912.4	37	CCDS9933.1	.	.	.	.	.	.	.	.	.	.	T	11.62	1.693062	0.30052	.	.	ENSG00000165959	ENST00000298912	D	0.94184	-3.37	5.48	4.35	0.52113	.	0.175417	0.27622	N	0.018549	D	0.90277	0.6959	M	0.64997	1.995	0.22001	N	0.999426	B	0.12630	0.006	B	0.09377	0.004	T	0.81788	-0.0772	10	0.44086	T	0.13	.	8.441	0.32816	0.0:0.0878:0.0:0.9122	.	588	Q96JQ2	CLMN_HUMAN	G	588	ENSP00000298912:E588G	ENSP00000298912:E588G	E	-	2	0	CLMN	94739676	0.042000	0.20092	0.010000	0.14722	0.017000	0.09413	2.624000	0.46444	2.081000	0.62600	0.533000	0.62120	GAG	.	.	none		0.398	CLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414518.2		
PRADC1	84279	hgsc.bcm.edu	37	2	73455927	73455927	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:73455927C>T	ENST00000258083.2	-	4	509	c.442G>A	c.(442-444)Gac>Aac	p.D148N	PRADC1_ENST00000480093.1_Intron	NM_032319.1	NP_115695.1	Q9BSG0	PADC1_HUMAN	protease-associated domain containing 1	148	PA.					extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)				endometrium(1)|large_intestine(1)|lung(2)	4						CCTCACCCGTCTCGGCCGAGC	0.592																																					p.D148N		Atlas-SNP	.											PRADC1,NS,carcinoma,+2,1	PRADC1	15	1	0			c.G442A						scavenged	.						35.0	32.0	33.0					2																	73455927		2203	4300	6503	SO:0001583	missense	84279	exon4			ACCCGTCTCGGCC	BC005069	CCDS1924.1	2p13.2	2012-10-31	2011-04-15	2011-04-15	ENSG00000135617	ENSG00000135617			16047	protein-coding gene	gene with protein product	"""protease-associated domain-containing glycoprotein 21 kDa"""		"""chromosome 2 open reading frame 7"""	C2orf7		15498570	Standard	NM_032319		Approved	MGC13004, PAP21, hPAP21	uc002siy.3	Q9BSG0	OTTHUMG00000129773	ENST00000258083.2:c.442G>A	2.37:g.73455927C>T	ENSP00000258083:p.Asp148Asn	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	96	2	0.0208333	NM_032319	Q2Z1P2	Missense_Mutation	SNP	ENST00000258083.2	37	CCDS1924.1	.	.	.	.	.	.	.	.	.	.	C	16.03	3.006534	0.54361	.	.	ENSG00000135617	ENST00000258083	T	0.08193	3.12	4.64	4.64	0.57946	Protease-associated domain, PA (1);	0.000000	0.85682	D	0.000000	T	0.20700	0.0498	L	0.46614	1.455	0.58432	D	0.999999	D	0.62365	0.991	D	0.80764	0.994	T	0.02958	-1.1089	10	0.16896	T	0.51	.	16.5993	0.84807	0.0:1.0:0.0:0.0	.	148	Q9BSG0	PADC1_HUMAN	N	148	ENSP00000258083:D148N	ENSP00000258083:D148N	D	-	1	0	PRADC1	73309435	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.467000	0.73547	2.576000	0.86940	0.655000	0.94253	GAC	.	.	none		0.592	PRADC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251989.1	NM_032319	
OPN1LW	5956	hgsc.bcm.edu	37	X	153421999	153421999	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:153421999G>A	ENST00000369951.4	+	5	1035	c.975G>A	c.(973-975)atG>atA	p.M325I		NM_020061.4	NP_064445.2	P04000	OPSR_HUMAN	opsin 1 (cone pigments), long-wave-sensitive	325					phototransduction, visible light (GO:0007603)|positive regulation of cytokinesis (GO:0032467)|protein-chromophore linkage (GO:0018298)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	G-protein coupled receptor activity (GO:0004930)|photoreceptor activity (GO:0009881)			endometrium(3)|large_intestine(2)|lung(8)|ovary(1)|skin(1)	15	all_cancers(53;1.83e-16)|all_epithelial(53;2.73e-10)|all_lung(58;6.39e-07)|Lung NSC(58;8.37e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					ATGTCTTTATGAACCGGCAGG	0.522																																					p.M325I		Atlas-SNP	.											.	OPN1LW	87	.	0			c.G975A						PASS	.						160.0	162.0	161.0					X																	153421999		2193	4268	6461	SO:0001583	missense	5956	exon5			CTTTATGAACCGG	Z68193	CCDS14742.1	Xq28	2013-01-08	2008-04-16		ENSG00000102076	ENSG00000102076		"""GPCR / Class A : Opsin receptors"""	9936	protein-coding gene	gene with protein product	"""cone dystrophy 5 (X-linked)"""	300822	"""color blindness, protan"", ""red cone photoreceptor pigment"""	CBBM, RCP, CBP			Standard	NM_020061		Approved	COD5	uc004fjz.4	P04000	OTTHUMG00000034295	ENST00000369951.4:c.975G>A	X.37:g.153421999G>A	ENSP00000358967:p.Met325Ile	Somatic	409	0	0		WXS	Illumina HiSeq	Phase_I	464	71	0.153017	NM_020061		Missense_Mutation	SNP	ENST00000369951.4	37	CCDS14742.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.940464	0.73557	.	.	ENSG00000102076	ENST00000369951	T	0.37752	1.18	4.57	4.57	0.56435	.	0.000000	0.85682	D	0.000000	T	0.66781	0.2824	M	0.89601	3.045	0.58432	D	0.999999	D	0.65815	0.995	D	0.77004	0.989	T	0.75909	-0.3151	10	0.87932	D	0	.	15.5112	0.75782	0.0:0.0:1.0:0.0	.	325	P04000	OPSR_HUMAN	I	325	ENSP00000358967:M325I	ENSP00000358967:M325I	M	+	3	0	OPN1LW	153075193	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	5.384000	0.66225	1.989000	0.58080	0.436000	0.28706	ATG	.	.	none		0.522	OPN1LW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082839.2	NM_020061	
SERINC3	10955	hgsc.bcm.edu	37	20	43129937	43129937	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr20:43129937G>A	ENST00000342374.4	-	9	1217	c.1060C>T	c.(1060-1062)Cgc>Tgc	p.R354C	SERINC3_ENST00000541235.1_Missense_Mutation_p.R299C|SERINC3_ENST00000255175.1_Missense_Mutation_p.R354C	NM_006811.2	NP_006802.1	Q13530	SERC3_HUMAN	serine incorporator 3	354					phosphatidylserine metabolic process (GO:0006658)|positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902237)|sphingolipid metabolic process (GO:0006665)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-serine transmembrane transporter activity (GO:0015194)			endometrium(4)|large_intestine(2)|lung(8)|skin(3)|urinary_tract(1)	18		Myeloproliferative disorder(115;0.0122)	Colorectal(3;0.000291)|COAD - Colon adenocarcinoma(18;0.00189)			GTGGAAGTGCGGATGCTGGAA	0.493																																					p.R354C		Atlas-SNP	.											.	SERINC3	42	.	0			c.C1060T						PASS	.						95.0	78.0	84.0					20																	43129937		2203	4300	6503	SO:0001583	missense	10955	exon9			AAGTGCGGATGCT	U49188	CCDS13333.1	20q13.12	2008-05-14	2005-11-15	2005-11-15	ENSG00000132824	ENSG00000132824			11699	protein-coding gene	gene with protein product		607165	"""tumor differentially expressed 1"""	TDE1		10559794	Standard	NM_006811		Approved	DIFF33, TDE, SBBI99, TMS-1, AIGP1	uc002xme.3	Q13530	OTTHUMG00000033087	ENST00000342374.4:c.1060C>T	20.37:g.43129937G>A	ENSP00000340243:p.Arg354Cys	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	103	50	0.485437	NM_006811	B4DUE9|O43717|Q9BR33	Missense_Mutation	SNP	ENST00000342374.4	37	CCDS13333.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.618830	0.87460	.	.	ENSG00000132824	ENST00000411544;ENST00000255175;ENST00000342374;ENST00000538937;ENST00000541235	T;T;T;T	0.18174	2.23;2.23;2.23;2.23	5.4	4.45	0.53987	.	0.143233	0.64402	N	0.000004	T	0.50871	0.1641	M	0.92970	3.365	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.993;0.996	T	0.64330	-0.6433	10	0.72032	D	0.01	.	14.1243	0.65210	0.0719:0.0:0.9281:0.0	.	354;354	Q53GK8;Q13530	.;SERC3_HUMAN	C	93;354;354;321;299	ENSP00000414197:R93C;ENSP00000255175:R354C;ENSP00000340243:R354C;ENSP00000440966:R299C	ENSP00000255175:R354C	R	-	1	0	SERINC3	42563351	1.000000	0.71417	0.991000	0.47740	0.968000	0.65278	9.480000	0.97931	1.506000	0.48736	0.563000	0.77884	CGC	.	.	none		0.493	SERINC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080544.3	NM_006811	
GTF2H5	404672	hgsc.bcm.edu	37	6	158613139	158613139	+	Nonsense_Mutation	SNP	C	C	T	rs121434364		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr6:158613139C>T	ENST00000607778.1	+	3	244	c.166C>T	c.(166-168)Cga>Tga	p.R56*		NM_207118.2	NP_997001.1	Q6ZYL4	TF2H5_HUMAN	general transcription factor IIH, polypeptide 5	56					cellular response to gamma radiation (GO:0071480)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, preincision complex assembly (GO:0006294)|regulation of transcription, DNA-templated (GO:0006355)|rRNA processing (GO:0006364)|transcription elongation from RNA polymerase I promoter (GO:0006362)	core TFIIH complex (GO:0000439)|nucleolus (GO:0005730)	rDNA binding (GO:0000182)						Breast(66;0.00519)|Ovarian(120;0.123)|Prostate(117;0.178)		OV - Ovarian serous cystadenocarcinoma(65;5.98e-18)|BRCA - Breast invasive adenocarcinoma(81;2.83e-05)		CCTCCAGGAGCGAGTGGGTGA	0.403								Nucleotide excision repair (NER)																													p.R56X		Atlas-SNP	.											.	GTF2H5	1	.	0			c.C166T	GRCh37	CM041784	GTF2H5	M	rs121434364	PASS	.						104.0	97.0	99.0					6																	158613139		2203	4300	6503	SO:0001587	stop_gained	404672	exon3			CAGGAGCGAGTGG	AK055106	CCDS5256.1	6q25.3	2014-09-17	2004-07-15	2004-07-16		ENSG00000272047		"""General transcription factors"", ""General transcription factor IIH complex subunits"""	21157	protein-coding gene	gene with protein product	"""DNA repair syndrome trichothiodystrophy group A"""	608780	"""chromosome 6 open reading frame 175"", ""trichothiodystrophy"""	C6orf175, TTD		15220921	Standard	NM_207118		Approved	FLJ30544, bA120J8.2, TTD-A, TFB5, TFIIH, TTDA	uc003qrd.3	Q6ZYL4		ENST00000607778.1:c.166C>T	6.37:g.158613139C>T	ENSP00000476100:p.Arg56*	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	173	87	0.50289	NM_207118	Q0P5V8	Nonsense_Mutation	SNP	ENST00000607778.1	37	CCDS5256.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.150837	0.78001	.	.	ENSG00000185068	ENST00000438073	.	.	.	6.06	5.15	0.70609	.	0.056997	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09590	T	0.72	-1.3438	7.5749	0.27931	0.1988:0.7139:0.0:0.0873	.	.	.	.	X	56	.	ENSP00000415032:R56X	R	+	1	2	GTF2H5	158533127	1.000000	0.71417	1.000000	0.80357	0.696000	0.40369	3.192000	0.50989	1.482000	0.48325	-0.355000	0.07637	CGA	.	.	weak		0.403	GTF2H5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042865.2	NM_207118	
CLTCL1	8218	hgsc.bcm.edu	37	22	19217421	19217421	+	Silent	SNP	G	G	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr22:19217421G>T	ENST00000263200.10	-	11	1794	c.1722C>A	c.(1720-1722)cgC>cgA	p.R574R	CLTCL1_ENST00000353891.5_Silent_p.R574R|CLTCL1_ENST00000427926.1_Silent_p.R574R	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	574	Distal segment.|Heavy chain arm.				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)					CCTCAGCTGGGCGATTATTCT	0.463			T	?	ALCL																																p.R574R		Atlas-SNP	.		Dom	yes		22	22q11.21	8218	"""clathrin, heavy polypeptide-like 1"""		L	CLTCL1,caecum,adenoma,-2,1	CLTCL1	115	1	0			c.C1722A						scavenged	.						50.0	49.0	49.0					22																	19217421		1952	4162	6114	SO:0001819	synonymous_variant	8218	exon11			AGCTGGGCGATTA		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.1722C>A	22.37:g.19217421G>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	65	2	0.0307692	NM_001835	B7Z7U5|Q14017|Q15808|Q15809	Silent	SNP	ENST00000263200.10	37	CCDS46662.1																																																																																			.	.	none		0.463	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098	
ARHGAP35	2909	hgsc.bcm.edu	37	19	47424847	47424847	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:47424847G>A	ENST00000404338.3	+	1	2915	c.2915G>A	c.(2914-2916)cGg>cAg	p.R972Q		NM_004491.4	NP_004482.4	Q9NRY4	RHG35_HUMAN	Rho GTPase activating protein 35	972					axon guidance (GO:0007411)|camera-type eye development (GO:0043010)|forebrain development (GO:0030900)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular permeability (GO:0043116)|neural tube closure (GO:0001843)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|GTP binding (GO:0005525)|Rho GTPase activator activity (GO:0005100)|transcription corepressor activity (GO:0003714)										AACTCCCCCCGGGCAGGATCA	0.488																																					p.R972Q		Atlas-SNP	.											GRLF1_ENST00000317082,NS,carcinoma,+1,1	.	.	1	0			c.G2915A						scavenged	.						52.0	52.0	52.0					19																	47424847		1932	4132	6064	SO:0001583	missense	2909	exon1			CCCCCCGGGCAGG	M73077	CCDS46127.1	19q13.32	2011-06-29	2011-06-07	2011-06-07	ENSG00000160007	ENSG00000160007		"""Rho GTPase activating proteins"""	4591	protein-coding gene	gene with protein product		605277	"""glucocorticoid receptor DNA binding factor 1"""	GRLF1		1894621, 20675588	Standard	NM_004491		Approved	GRF-1, p190ARhoGAP, P190A, KIAA1722, p190RhoGAP	uc010ekv.3	Q9NRY4		ENST00000404338.3:c.2915G>A	19.37:g.47424847G>A	ENSP00000385720:p.Arg972Gln	Somatic	81	1	0.0123457		WXS	Illumina HiSeq	Phase_I	132	3	0.0227273	NM_004491	A7E2A4|Q14452|Q9C0E1	Missense_Mutation	SNP	ENST00000404338.3	37	CCDS46127.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.820378	0.90873	.	.	ENSG00000160007	ENST00000317082;ENST00000404338	T	0.09073	3.02	5.86	5.86	0.93980	.	0.052258	0.85682	D	0.000000	T	0.22704	0.0548	L	0.52573	1.65	0.58432	D	0.999999	D	0.62365	0.991	P	0.59357	0.856	T	0.00015	-1.2397	10	0.72032	D	0.01	-28.679	18.9487	0.92632	0.0:0.0:1.0:0.0	.	972	Q9NRY4-2	.	Q	972	ENSP00000385720:R972Q	ENSP00000324820:R972Q	R	+	2	0	ARHGAP35	52116687	0.992000	0.36948	1.000000	0.80357	0.980000	0.70556	6.387000	0.73191	2.778000	0.95560	0.655000	0.94253	CGG	.	.	none		0.488	ARHGAP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466652.1	NM_004491	
CYP1A2	1544	hgsc.bcm.edu	37	15	75042485	75042485	+	Missense_Mutation	SNP	C	C	A	rs368187861		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr15:75042485C>A	ENST00000343932.4	+	2	469	c.406C>A	c.(406-408)Cgc>Agc	p.R136S		NM_000761.3	NP_000752.2	P05177	CP1A2_HUMAN	cytochrome P450, family 1, subfamily A, polypeptide 2	136					alkaloid metabolic process (GO:0009820)|arachidonic acid metabolic process (GO:0019369)|cellular respiration (GO:0045333)|cellular response to cadmium ion (GO:0071276)|dibenzo-p-dioxin metabolic process (GO:0018894)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|heterocycle metabolic process (GO:0046483)|hydrogen peroxide biosynthetic process (GO:0050665)|lung development (GO:0030324)|methylation (GO:0032259)|monocarboxylic acid metabolic process (GO:0032787)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|oxidative deethylation (GO:0071615)|oxidative demethylation (GO:0070989)|porphyrin-containing compound metabolic process (GO:0006778)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)|response to estradiol (GO:0032355)|response to lipopolysaccharide (GO:0032496)|small molecule metabolic process (GO:0044281)|steroid catabolic process (GO:0006706)|toxin biosynthetic process (GO:0009403)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|caffeine oxidase activity (GO:0034875)|demethylase activity (GO:0032451)|electron carrier activity (GO:0009055)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	33					"""""""Insulin(DB00071)|Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Agomelatine(DB06594)|Albendazole(DB00518)|Alitretinoin(DB00523)|Almotriptan(DB00918)|Alosetron(DB00969)|Aminoglutethimide(DB00357)|Aminophenazone(DB01424)|Aminophylline(DB01223)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Anagrelide(DB00261)|Anastrozole(DB01217)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Asenapine(DB06216)|Atropine(DB00572)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzyl alcohol(DB06770)|Betaxolol(DB00195)|Bortezomib(DB00188)|Bromazepam(DB01558)|Bromocriptine(DB01200)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Caffeine(DB00201)|Carbamazepine(DB00564)|Carmustine(DB00262)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clenbuterol(DB01407)|Clevidipine(DB04920)|Clobetasol propionate(DB01013)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Conjugated Estrogens(DB00286)|Cyclobenzaprine(DB00924)|Dacarbazine(DB00851)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Diazepam(DB00829)|Diclofenac(DB00586)|Dinoprostone(DB00917)|Diphenhydramine(DB01075)|Domperidone(DB01184)|Dopamine(DB00988)|Doxepin(DB01142)|Duloxetine(DB00476)|Edetic Acid(DB00974)|Efavirenz(DB00625)|Eltrombopag(DB06210)|Enoxacin(DB00467)|Epinephrine(DB00668)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estrone(DB00655)|Estropipate(DB04574)|Ethanol(DB00898)|Etoposide(DB00773)|Etoricoxib(DB01628)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Flutamide(DB00499)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Frovatriptan(DB00998)|Gemfibrozil(DB01241)|Griseofulvin(DB00400)|Guanabenz(DB00629)|Haloperidol(DB00502)|Hesperetin(DB01094)|Hexobarbital(DB01355)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Imiquimod(DB00724)|inhaled insulin(DB05278)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Levobupivacaine(DB01002)|Levofloxacin(DB01137)|Lidocaine(DB00281)|Lomefloxacin(DB00978)|Lopinavir(DB01601)|Lorcaserin(DB04871)|Losartan(DB00678)|Lumiracoxib(DB01283)|Malathion(DB00772)|Maprotiline(DB00934)|Meclizine(DB00737)|Melatonin(DB01065)|Menadione(DB00170)|Methadone(DB00333)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Modafinil(DB00745)|Nabumetone(DB00461)|Nafcillin(DB00607)|Naproxen(DB00788)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niclosamide(DB06803)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitric Oxide(DB00435)|Nitroprusside(DB00325)|Norepinephrine(DB00368)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ofloxacin(DB01165)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxaliplatin(DB00526)|Oxtriphylline(DB01303)|Palonosetron(DB00377)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Pefloxacin(DB00487)|Pentamidine(DB00738)|Pentoxifylline(DB00806)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phentermine(DB00191)|Phenylephrine(DB00388)|Phenylpropanolamine(DB00397)|Pimozide(DB01100)|Pipotiazine(DB01621)|Pomalidomide(DB08910)|Praziquantel(DB01058)|Primaquine(DB01087)|Primidone(DB00794)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Pyrazinamide(DB00339)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ramelteon(DB00980)|Ranitidine(DB00863)|Rasagiline(DB01367)|Rifabutin(DB00615)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Riluzole(DB00740)|Ritonavir(DB00503)|Rizatriptan(DB00953)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Roxithromycin(DB00778)|Secobarbital(DB00418)|Selegiline(DB01037)|Sertraline(DB01104)|SIMEPREVIR(DB06290)|Sorafenib(DB00398)|Streptozocin(DB00428)|Sulindac(DB00605)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Tenofovir(DB00300)|Terbinafine(DB00857)|Thalidomide(DB01041)|Theobromine(DB01412)|Theophylline(DB00277)|Thiabendazole(DB00730)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tizanidine(DB00697)|Tocainide(DB01056)|Toremifene(DB00539)|Tranylcypromine(DB00752)|Triamterene(DB00384)|Trifluoperazine(DB00831)|Valproic Acid(DB00313)|Vemurafenib(DB08881)|Verapamil(DB00661)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zileuton(DB00744)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)|Zolpidem(DB00425)"""	GTGGGCTGCCCGCCGGCGCCT	0.622																																					p.R136S		Atlas-SNP	.											CYP1A2,NS,carcinoma,-1,1	CYP1A2	70	1	0			c.C406A						scavenged	.						91.0	93.0	92.0					15																	75042485		2197	4296	6493	SO:0001583	missense	1544	exon2			GCTGCCCGCCGGC	AF182274	CCDS32293.1	15q24.1	2013-11-11	2003-01-14		ENSG00000140505	ENSG00000140505	1.14.14.1	"""Cytochrome P450s"""	2596	protein-coding gene	gene with protein product		124060	"""cytochrome P450, subfamily I (aromatic compound-inducible), polypeptide 2"""			15128046	Standard	NM_000761		Approved	P3-450, CP12	uc002ayr.1	P05177	OTTHUMG00000172901	ENST00000343932.4:c.406C>A	15.37:g.75042485C>A	ENSP00000342007:p.Arg136Ser	Somatic	70	1	0.0142857		WXS	Illumina HiSeq	Phase_I	68	2	0.0294118	NM_000761	Q16754|Q6NWU5|Q9BXX7|Q9UK49	Missense_Mutation	SNP	ENST00000343932.4	37	CCDS32293.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.893375	0.91889	.	.	ENSG00000140505	ENST00000343932	T	0.79845	-1.31	4.83	4.83	0.62350	.	0.000000	0.85682	D	0.000000	D	0.93090	0.7800	H	0.96015	3.755	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.95243	0.8353	10	0.87932	D	0	.	18.1026	0.89510	0.0:1.0:0.0:0.0	.	136	P05177-2	.	S	136	ENSP00000342007:R136S	ENSP00000342007:R136S	R	+	1	0	CYP1A2	72829538	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.419000	0.80179	2.499000	0.84300	0.561000	0.74099	CGC	.	.	alt		0.622	CYP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421263.2	NM_000761	
LURAP1L	286343	hgsc.bcm.edu	37	9	12775880	12775880	+	Missense_Mutation	SNP	T	T	G	rs201963967		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr9:12775880T>G	ENST00000319264.3	+	1	861	c.166T>G	c.(166-168)Tgc>Ggc	p.C56G	RP11-3L8.3_ENST00000417638.1_RNA|LURAP1L_ENST00000489107.1_3'UTR	NM_203403.1	NP_981948.1	Q8IV03	LUR1L_HUMAN	leucine rich adaptor protein 1-like	59	Gly-rich.							p.C56G(1)									cggcggcggctgcagtagcag	0.687																																					p.C56G		Atlas-SNP	.											C9orf150,caecum,carcinoma,0,3	.	.	3	1	Substitution - Missense(1)	ovary(1)	c.T166G						scavenged	.						4.0	4.0	4.0					9																	12775880		1740	3236	4976	SO:0001583	missense	286343	exon1			GGCGGCTGCAGTA	AK095824	CCDS6473.1	9p22.3	2012-02-01	2012-02-01	2012-02-01	ENSG00000153714	ENSG00000153714			31452	protein-coding gene	gene with protein product	"""similar to DNA segment, Chr 4, Brigham & Womens Genetics 0951 expressed"""		"""chromosome 9 open reading frame 150"""	C9orf150		12766061	Standard	NM_203403		Approved	MGC46502, FLJ38505, bA3L8.2	uc003zkw.3	Q8IV03	OTTHUMG00000019557	ENST00000319264.3:c.166T>G	9.37:g.12775880T>G	ENSP00000321026:p.Cys56Gly	Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	14	3	0.214286	NM_203403	Q5VZX7|Q8N923|Q8NCG2	Missense_Mutation	SNP	ENST00000319264.3	37	CCDS6473.1	.	.	.	.	.	.	.	.	.	.	T	6.415	0.444604	0.12164	.	.	ENSG00000153714	ENST00000319264	T	0.42900	0.96	4.66	0.578	0.17391	.	1.586600	0.03312	N	0.190713	T	0.18087	0.0434	.	.	.	0.51482	P	7.500000000004725E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.20009	-1.0288	8	0.08837	T	0.75	.	1.2788	0.02036	0.1736:0.1011:0.2715:0.4538	.	59	Q8IV03	CI150_HUMAN	G	56	ENSP00000321026:C56G	ENSP00000321026:C56G	C	+	1	0	C9orf150	12765880	0.074000	0.21230	0.846000	0.33378	0.825000	0.46686	-0.127000	0.10547	0.663000	0.31027	0.454000	0.30748	TGC	.	.	weak		0.687	LURAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051730.1	NM_203403	
MST1L	11223	hgsc.bcm.edu	37	1	17086183	17086183	+	RNA	SNP	T	T	G	rs61769735	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	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	235	28	0.119149		WXS	Illumina HiSeq	Phase_I	197	21	0.106599	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	
CCSER1	401145	hgsc.bcm.edu	37	4	91321217	91321217	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr4:91321217C>T	ENST00000509176.1	+	4	1828	c.1540C>T	c.(1540-1542)Ctg>Ttg	p.L514L	CCSER1_ENST00000432775.2_Silent_p.L514L|CCSER1_ENST00000333691.8_Silent_p.L514L	NM_001145065.1	NP_001138537.1	Q9C0I3	CCSE1_HUMAN	coiled-coil serine-rich protein 1	514																	ATCTTGTGAACTGGATGAAGA	0.333																																					p.L514L		Atlas-SNP	.											FAM190A_ENST00000509176,NS,carcinoma,-2,3	.	.	3	0			c.C1540T						scavenged	.						201.0	170.0	180.0					4																	91321217		1846	4111	5957	SO:0001819	synonymous_variant	401145	exon4			TGTGAACTGGATG		CCDS47099.1, CCDS47100.1	4q22.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184305	ENSG00000184305			29349	protein-coding gene	gene with protein product			"""family with sequence similarity 190, member A"""	FAM190A		11214970	Standard	NM_001145065		Approved	KIAA1680	uc003hsv.4	Q9C0I3	OTTHUMG00000160950	ENST00000509176.1:c.1540C>T	4.37:g.91321217C>T		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	182	3	0.0164835	NM_001145065	Q4W5M0|Q86V57	Silent	SNP	ENST00000509176.1	37	CCDS47099.1																																																																																			.	.	none		0.333	CCSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363109.3	NM_001145065	
DTD2	112487	hgsc.bcm.edu	37	14	31926584	31926584	+	Missense_Mutation	SNP	G	G	A	rs17097904	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr14:31926584G>A	ENST00000310850.4	-	1	132	c.16C>T	c.(16-18)Cgg>Tgg	p.R6W	RP11-176H8.1_ENST00000547378.1_Missense_Mutation_p.R6W|DTD2_ENST00000356180.4_Missense_Mutation_p.R6W	NM_080664.2	NP_542395.1	Q96FN9	DTD2_HUMAN	D-tyrosyl-tRNA deacylase 2 (putative)	6			R -> W (in dbSNP:rs17097904).		D-amino acid catabolic process (GO:0019478)	cytoplasm (GO:0005737)	hydrolase activity, acting on ester bonds (GO:0016788)	p.R6W(1)									TGAGGAATCCGGCTACCCTCA	0.697																																					p.R6W		Atlas-SNP	.											C14orf126,third_ventricle,glioma,0,2	.	.	2	1	Substitution - Missense(1)	skin(1)	c.C16T						scavenged	.						12.0	12.0	12.0					14																	31926584		2183	4278	6461	SO:0001583	missense	112487	exon1			GAATCCGGCTACC	BC010618	CCDS9643.1	14q12	2012-09-25	2012-09-25	2012-09-25	ENSG00000129480	ENSG00000129480			20277	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 126"""	C14orf126			Standard	NM_080664		Approved	MGC9912	uc001wrj.3	Q96FN9	OTTHUMG00000140205	ENST00000310850.4:c.16C>T	14.37:g.31926584G>A	ENSP00000312224:p.Arg6Trp	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	48	8	0.166667	NM_080664	D3DS87	Missense_Mutation	SNP	ENST00000310850.4	37	CCDS9643.1	.	.	.	.	.	.	.	.	.	.	G	19.08	3.758136	0.69763	.	.	ENSG00000203546;ENSG00000129480;ENSG00000129480	ENST00000547378;ENST00000310850;ENST00000356180	T;T;T	0.55052	0.54;0.71;0.71	4.84	2.97	0.34412	D-Tyr tRNAtyr deacylase-like domain (1);	0.302778	0.30901	N	0.008651	T	0.52419	0.1733	M	0.69823	2.125	0.36855	D	0.888115	D	0.67145	0.996	B	0.43623	0.425	T	0.65220	-0.6221	10	0.87932	D	0	.	11.9711	0.53063	0.0:0.0:0.5428:0.4572	rs17097904	6	Q96FN9	DTD2_HUMAN	W	6	ENSP00000447056:R6W;ENSP00000312224:R6W;ENSP00000348503:R6W	ENSP00000312224:R6W	R	-	1	2	C14orf126;RP11-176H8.1	30996335	0.001000	0.12720	0.005000	0.12908	0.004000	0.04260	0.080000	0.14802	0.618000	0.30179	0.561000	0.74099	CGG	.	.	weak		0.697	DTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276614.2	NM_080664	
APOBEC3F	200316	hgsc.bcm.edu	37	22	39441197	39441197	+	Silent	SNP	G	G	A	rs200983508	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	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	133	5	0.037594		WXS	Illumina HiSeq	Phase_I	143	5	0.034965	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	
TRPC4AP	26133	hgsc.bcm.edu	37	20	33595429	33595429	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr20:33595429C>T	ENST00000252015.2	-	14	1699	c.1610G>A	c.(1609-1611)cGg>cAg	p.R537Q	TRPC4AP_ENST00000432634.2_Missense_Mutation_p.R498Q|TRPC4AP_ENST00000451813.2_Missense_Mutation_p.R529Q|TRPC4AP_ENST00000539834.1_Missense_Mutation_p.R139Q			Q8TEL6	TP4AP_HUMAN	transient receptor potential cation channel, subfamily C, member 4 associated protein	537					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)	p.R537Q(1)		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)			CTCCACAGCCCGAGCTTGCCA	0.567																																					p.R537Q		Atlas-SNP	.											TRPC4AP,NS,carcinoma,0,1	TRPC4AP	64	1	1	Substitution - Missense(1)	endometrium(1)	c.G1610A						scavenged	.						102.0	97.0	99.0					20																	33595429		2203	4300	6503	SO:0001583	missense	26133	exon14			ACAGCCCGAGCTT	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.1610G>A	20.37:g.33595429C>T	ENSP00000252015:p.Arg537Gln	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	157	2	0.0127389	NM_015638	E1P5Q0|E1P5Q1|Q96H82|Q9BVB8|Q9H429|Q9UFS6	Missense_Mutation	SNP	ENST00000252015.2	37	CCDS13246.1	.	.	.	.	.	.	.	.	.	.	C	35	5.460657	0.96240	.	.	ENSG00000100991	ENST00000252015;ENST00000451813;ENST00000539834;ENST00000432634;ENST00000541994	T;T;T;T	0.32023	1.47;1.47;1.47;1.47	5.35	4.41	0.53225	.	0.049552	0.85682	N	0.000000	T	0.49795	0.1578	M	0.66939	2.045	0.58432	D	0.999995	D;D;D	0.76494	0.997;0.999;0.999	P;P;P	0.61477	0.832;0.889;0.889	T	0.54794	-0.8240	10	0.72032	D	0.01	.	13.8973	0.63781	0.0:0.9275:0.0:0.0725	.	498;529;537	B4E0Q1;E1P5Q0;Q8TEL6	.;.;TP4AP_HUMAN	Q	537;529;139;498;522	ENSP00000252015:R537Q;ENSP00000400614:R529Q;ENSP00000446090:R139Q;ENSP00000400497:R498Q	ENSP00000252015:R537Q	R	-	2	0	TRPC4AP	33059090	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.317000	0.79018	1.491000	0.48482	0.655000	0.94253	CGG	.	.	none		0.567	TRPC4AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078832.2	NM_015638	
RBPJL	11317	hgsc.bcm.edu	37	20	43944983	43944983	+	Splice_Site	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr20:43944983G>A	ENST00000343694.3	+	10	1248		c.e10+1		RBPJL_ENST00000372743.1_Splice_Site|RBPJL_ENST00000372741.3_Splice_Site|RBPJL_ENST00000464504.1_Splice_Site	NM_001281448.1|NM_001281449.1|NM_014276.2	NP_001268377.1|NP_001268378.1|NP_055091.2	Q9UBG7	RBPJL_HUMAN	recombination signal binding protein for immunoglobulin kappa J region-like						positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Myeloproliferative disorder(115;0.0122)				CACCCTAGAGGTGAAGCCGGG	0.657																																					.		Atlas-SNP	.											RBPJL,right_lower_lobe,carcinoma,0,1	RBPJL	67	1	0			c.1176+1G>A						scavenged	.						33.0	32.0	32.0					20																	43944983		2203	4300	6503	SO:0001630	splice_region_variant	11317	exon10			CTAGAGGTGAAGC	AB024964	CCDS13349.1, CCDS63283.1, CCDS63284.1	20q13.12	2013-10-18	2007-02-26	2007-02-26	ENSG00000124232	ENSG00000124232			13761	protein-coding gene	gene with protein product			"""recombining binding protein suppressor of hairless (Drosophila)-like"""	RBPSUHL		9929984	Standard	NM_014276		Approved	RBP-L, SUH, SUHL	uc002xns.3	Q9UBG7	OTTHUMG00000033055	ENST00000343694.3:c.1176+1G>A	20.37:g.43944983G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	125	2	0.016	NM_014276	O95723|Q5QPU9|Q5QPV0|Q9ULV9	Splice_Site	SNP	ENST00000343694.3	37	CCDS13349.1	.	.	.	.	.	.	.	.	.	.	G	19.18	3.776980	0.70107	.	.	ENSG00000124232	ENST00000372743;ENST00000372741;ENST00000343694	.	.	.	4.55	4.55	0.56014	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.5364	0.84373	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	RBPJL	43378397	1.000000	0.71417	1.000000	0.80357	0.800000	0.45204	9.187000	0.94912	2.364000	0.80123	0.555000	0.69702	.	.	.	none		0.657	RBPJL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080391.1	NM_014276	Intron
SI	6476	hgsc.bcm.edu	37	3	164783107	164783107	+	Missense_Mutation	SNP	C	C	T	rs530009542	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:164783107C>T	ENST00000264382.3	-	7	811	c.749G>A	c.(748-750)cGt>cAt	p.R250H		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	250	Isomaltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)	p.R250H(1)		NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	TAAATCATGACGAAATCTCTT	0.338										HNSCC(35;0.089)			C|||	2	0.000399361	0.0	0.0	5008	,	,		9411	0.0		0.0	False		,,,				2504	0.002				p.R250H		Atlas-SNP	.											SI,colon,carcinoma,-1,3	SI	500	3	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.G749A						scavenged	.						76.0	75.0	75.0					3																	164783107		2203	4300	6503	SO:0001583	missense	6476	exon7			TCATGACGAAATC	X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"""Oligosaccharide alpha-1,6-glucosidase"""	609845	"""sucrase-isomaltase"""			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.749G>A	3.37:g.164783107C>T	ENSP00000264382:p.Arg250His	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	162	2	0.0123457	NM_001041	A2RUC3|Q1JQ80|Q1RMC2	Missense_Mutation	SNP	ENST00000264382.3	37	CCDS3196.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.361611	0.82353	.	.	ENSG00000090402	ENST00000264382	D	0.90732	-2.72	5.9	5.9	0.94986	Glycoside hydrolase-type carbohydrate-binding (1);	0.105792	0.64402	D	0.000003	D	0.95118	0.8418	H	0.95470	3.675	0.48762	D	0.999702	D	0.71674	0.998	P	0.51833	0.681	D	0.95739	0.8781	10	0.66056	D	0.02	.	13.4661	0.61254	0.0:0.9291:0.0:0.0709	.	250	P14410	SUIS_HUMAN	H	250	ENSP00000264382:R250H	ENSP00000264382:R250H	R	-	2	0	SI	166265801	0.998000	0.40836	1.000000	0.80357	0.992000	0.81027	3.549000	0.53681	2.788000	0.95919	0.650000	0.86243	CGT	.	.	none		0.338	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041	
CYP2D6	1565	hgsc.bcm.edu	37	22	42523539	42523539	+	Silent	SNP	A	A	G	rs28371726	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr22:42523539A>G	ENST00000360608.5	-	7	1197	c.1083T>C	c.(1081-1083)caT>caC	p.H361H	NDUFA6-AS1_ENST00000536447.2_RNA|NDUFA6-AS1_ENST00000451451.1_RNA|NDUFA6-AS1_ENST00000417327.1_RNA|NDUFA6-AS1_ENST00000439129.1_RNA|NDUFA6-AS1_ENST00000600968.1_RNA|CYP2D6_ENST00000389970.3_Silent_p.H361H|NDUFA6-AS1_ENST00000416037.2_RNA|CYP2D6_ENST00000359033.4_Silent_p.H310H|NDUFA6-AS1_ENST00000434834.1_RNA|NDUFA6-AS1_ENST00000595777.1_RNA|NDUFA6-AS1_ENST00000610250.1_RNA	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	361					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)	GCTGCACCTCATGAATCACGG	0.602																																					p.H361H		Atlas-SNP	.											CYP2D6_ENST00000360608,NS,carcinoma,0,4	CYP2D6	104	4	0			c.T1083C						scavenged	.						119.0	93.0	102.0					22																	42523539		2202	4299	6501	SO:0001819	synonymous_variant	1565	exon7			CACCTCATGAATC	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.1083T>C	22.37:g.42523539A>G		Somatic	219	3	0.0136986		WXS	Illumina HiSeq	Phase_I	169	6	0.035503	NM_000106	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	Silent	SNP	ENST00000360608.5	37	CCDS46721.1																																																																																			A|0.959;G|0.041	0.041	strong		0.602	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320525.1		
ABCA3	21	hgsc.bcm.edu	37	16	2338028	2338028	+	Splice_Site	SNP	G	G	A	rs76519389	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr16:2338028G>A	ENST00000301732.5	-	21	3703	c.3003C>T	c.(3001-3003)ctC>ctT	p.L1001L	ABCA3_ENST00000382381.3_Splice_Site_p.L943L	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	1001					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)	GCCCCTTACCGAGCACCTCGC	0.667													G|||	4	0.000798722	0.0023	0.0	5008	,	,		14175	0.0		0.0	False		,,,				2504	0.001				p.L1001L		Atlas-SNP	.											.	ABCA3	176	.	0			c.C3003T						PASS	.	G		2,4394		0,2,2196	22.0	23.0	23.0		3003	-1.2	1.0	16	dbSNP_131	23	0,8598		0,0,4299	yes	coding-synonymous-near-splice	ABCA3	NM_001089.2		0,2,6495	AA,AG,GG		0.0,0.0455,0.0154		1001/1705	2338028	2,12992	2198	4299	6497	SO:0001630	splice_region_variant	21	exon21			CTTACCGAGCACC	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.3004+1C>T	16.37:g.2338028G>A		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	20	8	0.4	NM_001089	B2RU09|Q54A95|Q6P5P9|Q92473	Silent	SNP	ENST00000301732.5	37	CCDS10466.1																																																																																			G|1.000;A|0.000	0.000	strong		0.667	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089	Silent
NKAIN2	154215	hgsc.bcm.edu	37	6	124676480	124676480	+	Missense_Mutation	SNP	G	G	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr6:124676480G>C	ENST00000368417.1	+	3	320	c.260G>C	c.(259-261)gGg>gCg	p.G87A	NKAIN2_ENST00000546092.1_Missense_Mutation_p.G87A|NKAIN2_ENST00000476571.1_3'UTR|NKAIN2_ENST00000545433.1_Missense_Mutation_p.G72A|NKAIN2_ENST00000368416.1_Missense_Mutation_p.G87A	NM_001040214.1	NP_001035304.1	Q5VXU1	NKAI2_HUMAN	Na+/K+ transporting ATPase interacting 2	87						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|large_intestine(3)|lung(12)|skin(2)	19				GBM - Glioblastoma multiforme(226;0.104)		TTGGAGGCTGGGGACCTCTCA	0.423																																					p.G87A		Atlas-SNP	.											.	NKAIN2	34	.	0			c.G260C						PASS	.						246.0	223.0	231.0					6																	124676480		2203	4300	6503	SO:0001583	missense	154215	exon3			AGGCTGGGGACCT	AB070452	CCDS34526.1	6q21	2008-02-05	2007-10-04	2007-10-04	ENSG00000188580	ENSG00000188580		"""Na+/K+ transporting ATPase interacting"""	16443	protein-coding gene	gene with protein product		609758	"""T-cell lymphoma breakpoint associated target 1"""	TCBA1		17606467	Standard	XM_005266833		Approved	FAM77B	uc003pzo.3	Q5VXU1	OTTHUMG00000015500	ENST00000368417.1:c.260G>C	6.37:g.124676480G>C	ENSP00000357402:p.Gly87Ala	Somatic	283	0	0		WXS	Illumina HiSeq	Phase_I	234	116	0.495726	NM_153355	Q8IYR4|Q8TF67	Missense_Mutation	SNP	ENST00000368417.1	37	CCDS34526.1	.	.	.	.	.	.	.	.	.	.	G	16.34	3.094672	0.56075	.	.	ENSG00000188580	ENST00000368416;ENST00000368417;ENST00000546092;ENST00000539866;ENST00000545433	T;T;T;T	0.38077	1.16;1.16;1.16;1.16	5.74	4.86	0.63082	.	0.382836	0.29100	N	0.013152	T	0.30727	0.0774	M	0.80746	2.51	0.54753	D	0.999985	B;B;B;P	0.38473	0.082;0.452;0.294;0.633	B;B;B;B	0.36289	0.088;0.211;0.132;0.221	T	0.35276	-0.9795	10	0.59425	D	0.04	0.1499	16.0861	0.81049	0.0:0.0:0.8649:0.1351	.	87;86;87;87	F5GY48;Q5VXU1-3;Q5VXU1;Q5VXU1-2	.;.;NKAI2_HUMAN;.	A	87;87;87;86;72	ENSP00000357401:G87A;ENSP00000357402:G87A;ENSP00000440287:G87A;ENSP00000437798:G72A	ENSP00000357401:G87A	G	+	2	0	NKAIN2	124718179	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.421000	0.90259	1.410000	0.46936	0.650000	0.86243	GGG	.	.	none		0.423	NKAIN2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042057.1	NM_001040214	
MUC16	94025	hgsc.bcm.edu	37	19	9067987	9067987	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:9067987A>G	ENST00000397910.4	-	3	19662	c.19459T>C	c.(19459-19461)Tcc>Ccc	p.S6487P		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	6489	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						GTAAGAGTGGACAAATCTAAT	0.483																																					p.S6487P		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,+2,3	MUC16	4315	3	0			c.T19459C						scavenged	.						163.0	163.0	163.0					19																	9067987		1983	4157	6140	SO:0001583	missense	94025	exon3			GAGTGGACAAATC	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.19459T>C	19.37:g.9067987A>G	ENSP00000381008:p.Ser6487Pro	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	165	4	0.0242424	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	a	2.306	-0.359046	0.05138	.	.	ENSG00000181143	ENST00000397910	T	0.27104	1.69	1.83	0.755	0.18415	.	.	.	.	.	T	0.15435	0.0372	N	0.22421	0.69	.	.	.	B	0.24483	0.104	B	0.23275	0.045	T	0.15636	-1.0430	8	0.87932	D	0	.	5.537	0.17018	0.2531:0.0:0.0:0.7469	.	6487	B5ME49	.	P	6487	ENSP00000381008:S6487P	ENSP00000381008:S6487P	S	-	1	0	MUC16	8928987	0.000000	0.05858	0.001000	0.08648	0.015000	0.08874	0.168000	0.16622	-0.214000	0.10078	-2.002000	0.00443	TCC	.	.	none		0.483	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
NLRP5	126206	hgsc.bcm.edu	37	19	56572873	56572873	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:56572873C>T	ENST00000390649.3	+	15	3582	c.3582C>T	c.(3580-3582)gaC>gaT	p.D1194D		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	1194					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)		ATGAAGATGACCGGTACTGGT	0.493																																					p.D1194D		Atlas-SNP	.											NLRP5_ENST00000390649,NS,carcinoma,+1,1	NLRP5	217	1	0			c.C3582T						scavenged	.						151.0	143.0	146.0					19																	56572873		1934	4142	6076	SO:0001819	synonymous_variant	126206	exon15			AGATGACCGGTAC	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.3582C>T	19.37:g.56572873C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	163	3	0.0184049	NM_153447	A8MTY4|Q86W29	Silent	SNP	ENST00000390649.3	37	CCDS12938.1																																																																																			.	.	none		0.493	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447	
SEC22C	9117	hgsc.bcm.edu	37	3	42610481	42610481	+	Missense_Mutation	SNP	C	C	G	rs141431943		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:42610481C>G	ENST00000264454.3	-	2	201	c.58G>C	c.(58-60)Gcc>Ccc	p.A20P	SEC22C_ENST00000493107.1_5'UTR|SEC22C_ENST00000417572.1_Missense_Mutation_p.A20P|SEC22C_ENST00000273156.7_Missense_Mutation_p.A20P|SEC22C_ENST00000536332.1_5'UTR|SEC22C_ENST00000423701.2_Missense_Mutation_p.A20P			Q9BRL7	SC22C_HUMAN	SEC22 vesicle trafficking protein homolog C (S. cerevisiae)	20	Longin. {ECO:0000255|PROSITE- ProRule:PRU00231}.				ER to Golgi vesicle-mediated transport (GO:0006888)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)	3				KIRC - Kidney renal clear cell carcinoma(284;0.222)		TCAGTAGAGGCTGAGAGGGGC	0.517																																					p.A20P		Atlas-SNP	.											.	SEC22C	27	.	0			c.G58C						PASS	.						74.0	72.0	72.0					3																	42610481		2203	4300	6503	SO:0001583	missense	9117	exon2			TAGAGGCTGAGAG	AF039568	CCDS2699.1, CCDS2700.1, CCDS56246.1	3p24.3-p22.1	2006-04-25	2006-04-25	2006-04-25	ENSG00000093183	ENSG00000093183			16828	protein-coding gene	gene with protein product		604028	"""SEC22 vesicle trafficking protein-like 3 (S. cerevisiae)"""	SEC22L3		9501016, 11001058	Standard	NM_004206		Approved	MGC13261, MGC5373	uc003clj.3	Q9BRL7	OTTHUMG00000131797	ENST00000264454.3:c.58G>C	3.37:g.42610481C>G	ENSP00000264454:p.Ala20Pro	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	168	30	0.178571	NM_001201584	O95152|Q68CX3|Q6UW18	Missense_Mutation	SNP	ENST00000264454.3	37	CCDS2700.1	.	.	.	.	.	.	.	.	.	.	C	32	5.146526	0.94603	.	.	ENSG00000093183	ENST00000423701;ENST00000273156;ENST00000417572;ENST00000264454;ENST00000456515;ENST00000450981;ENST00000416880;ENST00000420163	T;T;T;T;T;T;T;T	0.25250	1.81;1.81;1.81;1.81;1.81;1.81;1.81;1.81	5.41	5.41	0.78517	Longin (2);Longin-like (1);	0.000000	0.85682	D	0.000000	T	0.59418	0.2192	M	0.86740	2.835	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.997;0.999	T	0.66670	-0.5865	10	0.87932	D	0	-10.4295	19.1881	0.93653	0.0:1.0:0.0:0.0	.	20;20;20	Q9BRL7-3;Q9BRL7;Q9BRL7-2	.;SC22C_HUMAN;.	P	20	ENSP00000414576:A20P;ENSP00000273156:A20P;ENSP00000407564:A20P;ENSP00000264454:A20P;ENSP00000391170:A20P;ENSP00000397170:A20P;ENSP00000391957:A20P;ENSP00000408242:A20P	ENSP00000264454:A20P	A	-	1	0	SEC22C	42585485	1.000000	0.71417	0.946000	0.38457	0.871000	0.50021	7.246000	0.78247	2.522000	0.85027	0.655000	0.94253	GCC	C|1.000;T|0.000	.	alt		0.517	SEC22C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254734.1	NM_004206	
USP17L10	100287144	hgsc.bcm.edu	37	4	9212697	9212697	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr4:9212697C>T	ENST00000417945.1	+	1	315	c.315C>T	c.(313-315)gcC>gcT	p.A105A	USP17L13_ENST00000421288.2_Intron	NM_001256852.1	NP_001243781.1	C9JJH3	U17LA_HUMAN	ubiquitin specific peptidase 17-like family member 10	105	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)										CGCCACTTGCCAACTACATGC	0.557																																					p.A105A		Atlas-SNP	.											.	.	.	.	0			c.C315T						PASS	.																																			SO:0001819	synonymous_variant	100287144	exon1			ACTTGCCAACTAC		CCDS59454.1	4p16.1	2014-02-12	2012-10-09		ENSG00000231396	ENSG00000231396			44438	protein-coding gene	gene with protein product							Standard	NM_001256852		Approved		uc031sdg.1	C9JJH3	OTTHUMG00000160160	ENST00000417945.1:c.315C>T	4.37:g.9212697C>T		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	19	10	0.526316	NM_001256852		Silent	SNP	ENST00000417945.1	37	CCDS59454.1																																																																																			.	.	none		0.557	USP17L10-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359428.1	NM_001256852	
CCR8	1237	hgsc.bcm.edu	37	3	39374673	39374673	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:39374673T>C	ENST00000326306.4	+	2	989	c.851T>C	c.(850-852)gTc>gCc	p.V284A	CCR8_ENST00000414803.1_3'UTR|CCR8_ENST00000545843.1_Missense_Mutation_p.V201A	NM_005201.3	NP_005192.1	P51685	CCR8_HUMAN	chemokine (C-C motif) receptor 8	284					cell adhesion (GO:0007155)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)|coreceptor activity (GO:0015026)			NS(3)|breast(1)|endometrium(3)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0504)|Kidney(284;0.0635)		GCCACCCATGTCACAGAAATC	0.428																																					p.V284A		Atlas-SNP	.											CCR8,NS,carcinoma,+1,1	CCR8	34	1	0			c.T851C						scavenged	.						111.0	110.0	110.0					3																	39374673		2203	4300	6503	SO:0001583	missense	1237	exon2			CCCATGTCACAGA	D49919	CCDS2684.1	3p22	2012-08-08			ENSG00000179934	ENSG00000179934		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1609	protein-coding gene	gene with protein product		601834		CMKBRL2, CMKBR8		8816377, 8886020	Standard	NM_005201		Approved	CY6, TER1, CKR-L1, GPR-CY6, CDw198	uc010hhr.2	P51685	OTTHUMG00000131290	ENST00000326306.4:c.851T>C	3.37:g.39374673T>C	ENSP00000326432:p.Val284Ala	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	220	3	0.0136364	NM_005201	B2RC64|Q3KNQ8|Q3KNR3|Q9BYX5	Missense_Mutation	SNP	ENST00000326306.4	37	CCDS2684.1	.	.	.	.	.	.	.	.	.	.	T	19.78	3.891728	0.72524	.	.	ENSG00000179934	ENST00000326306;ENST00000545843	T;T	0.39406	1.08;1.08	4.76	4.76	0.60689	GPCR, rhodopsin-like superfamily (1);	0.421090	0.23380	N	0.048811	T	0.54967	0.1891	M	0.64567	1.98	0.41078	D	0.985502	P;P	0.42296	0.775;0.775	P;P	0.54431	0.689;0.752	T	0.54840	-0.8233	10	0.41790	T	0.15	.	13.2519	0.60055	0.0:0.0:0.0:1.0	.	284;201	P51685;Q3KNR3	CCR8_HUMAN;.	A	284;201	ENSP00000326432:V284A;ENSP00000440474:V201A	ENSP00000326432:V284A	V	+	2	0	CCR8	39349677	1.000000	0.71417	0.995000	0.50966	0.985000	0.73830	4.690000	0.61731	2.004000	0.58718	0.533000	0.62120	GTC	.	.	none		0.428	CCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254058.2	NM_005201	
HTR1F	3355	hgsc.bcm.edu	37	3	88040116	88040116	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:88040116G>A	ENST00000319595.4	+	1	271	c.217G>A	c.(217-219)Gct>Act	p.A73T		NM_000866.3	NP_000857.1	P30939	5HT1F_HUMAN	5-hydroxytryptamine (serotonin) receptor 1F, G protein-coupled	73					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)	TTTTCTTGTGGCTGTCCTGGT	0.458																																					p.A73T		Atlas-SNP	.											HTR1F,NS,carcinoma,-1,1	HTR1F	66	1	0			c.G217A						scavenged	.						109.0	102.0	105.0					3																	88040116		2203	4300	6503	SO:0001583	missense	3355	exon2			CTTGTGGCTGTCC	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.217G>A	3.37:g.88040116G>A	ENSP00000322924:p.Ala73Thr	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	205	3	0.0146341	NM_000866		Missense_Mutation	SNP	ENST00000319595.4	37	CCDS2920.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.551349	0.86127	.	.	ENSG00000179097	ENST00000319595	T	0.36699	1.24	5.31	5.31	0.75309	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.65842	0.2730	M	0.89414	3.03	0.58432	D	0.999997	D	0.76494	0.999	D	0.73708	0.981	T	0.70332	-0.4901	10	0.46703	T	0.11	.	16.4743	0.84128	0.0:0.0:1.0:0.0	.	73	P30939	5HT1F_HUMAN	T	73	ENSP00000322924:A73T	ENSP00000322924:A73T	A	+	1	0	HTR1F	88122806	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	9.823000	0.99369	2.495000	0.84180	0.585000	0.79938	GCT	.	.	none		0.458	HTR1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352890.1	NM_000866	
ANKRD36	375248	hgsc.bcm.edu	37	2	97790211	97790211	+	Missense_Mutation	SNP	A	A	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:97790211A>T	ENST00000461153.2	+	5	852	c.608A>T	c.(607-609)cAt>cTt	p.H203L	ANKRD36_ENST00000420699.2_Missense_Mutation_p.H203L			A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	203								p.H203L(2)		endometrium(9)|kidney(5)|liver(1)|lung(3)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23						GCCCTCATACATGCTGTTACT	0.323																																					p.H203L		Atlas-SNP	.											ANKRD36_ENST00000420699,extremity,malignant_melanoma,0,2	ANKRD36	170	2	2	Substitution - Missense(2)	NS(1)|skin(1)	c.A608T						scavenged	.						79.0	60.0	65.0					2																	97790211		692	1589	2281	SO:0001583	missense	375248	exon5			TCATACATGCTGT	BC046186	CCDS54379.1	2q11.2	2013-09-24			ENSG00000135976	ENSG00000135976		"""Ankyrin repeat domain containing"""	24079	protein-coding gene	gene with protein product						12975309	Standard	NM_001164315		Approved	UNQ2430	uc010yva.2	A6QL64	OTTHUMG00000155256	ENST00000461153.2:c.608A>T	2.37:g.97790211A>T	ENSP00000419530:p.His203Leu	Somatic	266	4	0.0150376		WXS	Illumina HiSeq	Phase_I	202	5	0.0247525	NM_001164315	B4E3I8|Q6UX02|Q86X62|Q9HCD1	Missense_Mutation	SNP	ENST00000461153.2	37	CCDS54379.1	.	.	.	.	.	.	.	.	.	.	A	0.010	-1.781271	0.00634	.	.	ENSG00000135976	ENST00000461153;ENST00000420699;ENST00000393513;ENST00000455519	T;T	0.60920	0.15;0.15	0.946	-0.341	0.12639	Ankyrin repeat-containing domain (4);	.	.	.	.	T	0.16642	0.0400	N	0.00855	-1.145	0.47511	D	0.999447	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.37384	-0.9708	9	0.02654	T	1	.	3.0347	0.06118	0.3942:0.0:0.0:0.6058	.	203;203	A6QL64;F2Z332	AN36A_HUMAN;.	L	203	ENSP00000419530:H203L;ENSP00000391950:H203L	ENSP00000377149:H203L	H	+	2	0	ANKRD36	97153938	0.990000	0.36364	0.731000	0.30826	0.427000	0.31564	0.125000	0.15749	-0.131000	0.11578	-1.495000	0.00966	CAT	.	.	none		0.323	ANKRD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339154.5		
SH3GL3	6457	hgsc.bcm.edu	37	15	84287010	84287010	+	Missense_Mutation	SNP	G	G	A	rs376114446		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr15:84287010G>A	ENST00000427482.2	+	9	1321	c.1015G>A	c.(1015-1017)Gtg>Atg	p.V339M	SH3GL3_ENST00000535412.1_3'UTR|SH3GL3_ENST00000564054.1_3'UTR|SH3GL3_ENST00000324537.5_Missense_Mutation_p.V347M|SH3GL3_ENST00000434347.1_Missense_Mutation_p.V347M|AC087738.1_ENST00000411248.1_RNA	NM_003027.3	NP_003018.3	Q99963	SH3G3_HUMAN	SH3-domain GRB2-like 3	339	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				central nervous system development (GO:0007417)|endocytosis (GO:0006897)|signal transduction (GO:0007165)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)			central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	30						CATTAATTACGTGGAAGTGAT	0.393																																					p.V339M		Atlas-SNP	.											SH3GL3_ENST00000427482,NS,carcinoma,0,2	SH3GL3	91	2	0			c.G1015A						PASS	.	G	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	106.0	94.0	98.0		1015	5.6	1.0	15		98	0,8600		0,0,4300	no	missense	SH3GL3	NM_003027.3	21	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	339/348	84287010	1,13005	2203	4300	6503	SO:0001583	missense	6457	exon9			AATTACGTGGAAG	AF036271	CCDS10325.2, CCDS73772.1	15q24	2006-11-24			ENSG00000140600	ENSG00000140600			10832	protein-coding gene	gene with protein product		603362				9169142	Standard	NR_026799		Approved	SH3D2C, SH3P13, CNSA3, EEN-B2, HsT19371	uc002bjw.3	Q99963	OTTHUMG00000147361	ENST00000427482.2:c.1015G>A	15.37:g.84287010G>A	ENSP00000391372:p.Val339Met	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	80	14	0.175	NM_003027	O43553|O43554	Missense_Mutation	SNP	ENST00000427482.2	37	CCDS10325.2	.	.	.	.	.	.	.	.	.	.	G	28.8	4.950836	0.92660	2.27E-4	0.0	ENSG00000140600	ENST00000427482;ENST00000324537;ENST00000434347	T;T;T	0.55234	0.53;0.53;0.53	5.57	5.57	0.84162	Src homology-3 domain (4);	0.264468	0.37483	N	0.002070	D	0.82697	0.5093	H	0.96805	3.885	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.992	D	0.88419	0.3027	10	0.87932	D	0	-31.8197	18.5386	0.91019	0.0:0.0:1.0:0.0	.	339;347	Q99963;Q99963-3	SH3G3_HUMAN;.	M	339;347;347	ENSP00000391372:V339M;ENSP00000320092:V347M;ENSP00000397871:V347M	ENSP00000320092:V347M	V	+	1	0	SH3GL3	82078014	1.000000	0.71417	0.979000	0.43373	0.986000	0.74619	9.300000	0.96151	2.612000	0.88384	0.655000	0.94253	GTG	.	.	weak		0.393	SH3GL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347797.1	NM_003027	
IQCA1	79781	hgsc.bcm.edu	37	2	237374287	237374287	+	Missense_Mutation	SNP	G	G	A	rs35814876	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:237374287G>A	ENST00000409907.3	-	6	1061	c.787C>T	c.(787-789)Cgg>Tgg	p.R263W	IQCA1_ENST00000309507.5_Missense_Mutation_p.R259W|IQCA1_ENST00000431676.2_Missense_Mutation_p.R263W	NM_024726.4	NP_079002.3	Q86XH1	IQCA1_HUMAN	IQ motif containing with AAA domain 1	263							ATP binding (GO:0005524)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)	26						ACCTCATTCCGCAGGCGGTCC	0.448													G|||	4	0.000798722	0.0	0.0014	5008	,	,		19395	0.0		0.002	False		,,,				2504	0.001				p.R270W		Atlas-SNP	.											IQCA1_ENST00000409907,NS,carcinoma,+1,4	IQCA1	170	4	0			c.C808T						scavenged	.	G	TRP/ARG	4,3850		0,4,1923	131.0	119.0	123.0		787	1.3	0.0	2	dbSNP_126	123	21,8257		0,21,4118	yes	missense	IQCA1	NM_024726.3	101	0,25,6041	AA,AG,GG		0.2537,0.1038,0.2061	probably-damaging	263/823	237374287	25,12107	1927	4139	6066	SO:0001583	missense	79781	exon6			CATTCCGCAGGCG	AK026180	CCDS46549.1, CCDS59441.1, CCDS74677.1	2q37.3	2014-07-18	2008-07-02	2008-07-02	ENSG00000132321	ENSG00000132321		"""ATPases / AAA-type"""	26195	protein-coding gene	gene with protein product	"""dynein regulatory complex subunit 11"""		"""IQ motif containing with AAA domain"""	IQCA		23427265	Standard	NM_024726		Approved	FLJ22527, DRC11	uc002vwb.3	Q86XH1	OTTHUMG00000153058	ENST00000409907.3:c.787C>T	2.37:g.237374287G>A	ENSP00000387347:p.Arg263Trp	Somatic	202	1	0.00495049		WXS	Illumina HiSeq	Phase_I	255	40	0.156863	NM_001270585	B4DFH9|E7EWQ0|Q4G164|Q53R37|Q53RV3|Q96NS7|Q9H680	Missense_Mutation	SNP	ENST00000409907.3	37	CCDS46549.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.73|15.73	2.918853|2.918853	0.52546|0.52546	0.001038|0.001038	0.002537|0.002537	ENSG00000132321|ENSG00000132321	ENST00000418802|ENST00000409907;ENST00000457693;ENST00000309507;ENST00000431676;ENST00000412437	.|D;D;D	.|0.96041	.|-3.86;-3.89;-3.89	5.37|5.37	1.31|1.31	0.21738|0.21738	.|.	.|0.120895	.|0.37393	.|N	.|0.002106	D|D	0.97770|0.97770	0.9268|0.9268	M|M	0.88906|0.88906	2.99|2.99	0.09310|0.09310	N|N	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.91635	.|0.999;0.995;0.998	D|D	0.94404|0.94404	0.7625|0.7625	5|10	.|0.87932	.|D	.|0	.|.	15.7632|15.7632	0.78103|0.78103	0.0:0.0:0.3887:0.6113|0.0:0.0:0.3887:0.6113	rs35814876|rs35814876	.|263;270;263	.|E7EWQ0;E9PH78;Q86XH1	.|.;.;IQCA1_HUMAN	V|W	281|263;270;259;263;259	.|ENSP00000387347:R263W;ENSP00000311951:R259W;ENSP00000407213:R263W	.|ENSP00000254653:R263W	A|R	-|-	2|1	0|2	IQCA1|IQCA1	237039026|237039026	0.017000|0.017000	0.18338|0.18338	0.022000|0.022000	0.16811|0.16811	0.026000|0.026000	0.11368|0.11368	0.527000|0.527000	0.22987|0.22987	-0.043000|-0.043000	0.13513|0.13513	0.563000|0.563000	0.77884|0.77884	GCG|CGG	G|0.986;A|0.014	0.014	weak		0.448	IQCA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000329266.1	NM_024726	
CA10	56934	hgsc.bcm.edu	37	17	49713329	49713329	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr17:49713329A>G	ENST00000285273.4	-	8	1787	c.676T>C	c.(676-678)Tat>Cat	p.Y226H	CA10_ENST00000451037.2_Missense_Mutation_p.Y226H|CA10_ENST00000571918.1_5'UTR|CA10_ENST00000442502.2_Missense_Mutation_p.Y226H|CA10_ENST00000340813.6_Missense_Mutation_p.Y232H|CA10_ENST00000570565.1_Missense_Mutation_p.Y151H	NM_001082533.1	NP_001076002.1	Q9NS85	CAH10_HUMAN	carbonic anhydrase X	226					brain development (GO:0007420)					cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(21)|ovary(1)|skin(3)|stomach(2)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(22;4.74e-06)		Zonisamide(DB00909)	GTCTCTGGATATAGTTCCTCT	0.388																																					p.Y226H		Atlas-SNP	.											.	CA10	84	.	0			c.T676C						PASS	.						114.0	109.0	110.0					17																	49713329		2203	4300	6503	SO:0001583	missense	56934	exon8			CTGGATATAGTTC	AF288385	CCDS32684.1	17q21	2012-08-21			ENSG00000154975	ENSG00000154975		"""Carbonic anhydrases"""	1369	protein-coding gene	gene with protein product		604642				8673298, 9921901	Standard	NM_020178		Approved	CARPX, CA-RPX, HUCEP-15	uc002itx.4	Q9NS85	OTTHUMG00000177544	ENST00000285273.4:c.676T>C	17.37:g.49713329A>G	ENSP00000285273:p.Tyr226His	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	93	4	0.0430108	NM_001082534	B2R7J0|B4DGL6	Missense_Mutation	SNP	ENST00000285273.4	37	CCDS32684.1	.	.	.	.	.	.	.	.	.	.	A	29.6	5.021686	0.93462	.	.	ENSG00000154975	ENST00000442502;ENST00000285273;ENST00000451037;ENST00000340813	T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23	6.16	6.16	0.99307	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.000000	0.85682	D	0.000000	T	0.79569	0.4468	L	0.59436	1.845	0.58432	D	0.999999	D;D;D	0.89917	1.0;0.999;0.994	D;D;P	0.76071	0.987;0.987;0.873	T	0.81070	-0.1099	10	0.87932	D	0	.	15.9872	0.80168	1.0:0.0:0.0:0.0	.	226;232;151	Q9NS85;Q68D28;B4DGL6	CAH10_HUMAN;.;.	H	226;226;226;232	ENSP00000390666:Y226H;ENSP00000285273:Y226H;ENSP00000405388:Y226H;ENSP00000340363:Y232H	ENSP00000285273:Y226H	Y	-	1	0	CA10	47068328	1.000000	0.71417	0.985000	0.45067	0.985000	0.73830	9.157000	0.94714	2.367000	0.80283	0.528000	0.53228	TAT	.	.	none		0.388	CA10-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000437480.1	NM_020178	
RHOJ	57381	hgsc.bcm.edu	37	14	63757685	63757685	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr14:63757685C>T	ENST00000316754.3	+	5	1050	c.588C>T	c.(586-588)caC>caT	p.H196H		NM_020663.4	NP_065714.1	Q9H4E5	RHOJ_HUMAN	ras homolog family member J	196					actin cytoskeleton organization (GO:0030036)|GTP catabolic process (GO:0006184)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|upper_aerodigestive_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(108;0.00326)|all cancers(60;0.031)|BRCA - Breast invasive adenocarcinoma(234;0.119)		CCATTTTCCACCCCAAGAAAA	0.473																																					p.H196H		Atlas-SNP	.											RHOJ,NS,malignant_melanoma,+2,1	RHOJ	45	1	0			c.C588T						scavenged	.						125.0	121.0	122.0					14																	63757685		2203	4300	6503	SO:0001819	synonymous_variant	57381	exon5			TTTCCACCCCAAG	AK027351	CCDS9757.1	14q23.1	2012-02-27	2012-02-27	2004-03-24	ENSG00000126785	ENSG00000126785			688	protein-coding gene	gene with protein product		607653	"""RAS-like, family 7, member B"", ""ras homolog gene family, member J"""	RASL7B, ARHJ		10967094	Standard	NM_020663		Approved	FLJ14445, TCL	uc001xgb.2	Q9H4E5	OTTHUMG00000140342	ENST00000316754.3:c.588C>T	14.37:g.63757685C>T		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	113	2	0.0176991	NM_020663	Q96KC1	Silent	SNP	ENST00000316754.3	37	CCDS9757.1																																																																																			.	.	none		0.473	RHOJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276975.3		
UGT1A6	54578	hgsc.bcm.edu	37	2	234601918	234601918	+	Missense_Mutation	SNP	C	C	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:234601918C>A	ENST00000305139.6	+	1	407	c.268C>A	c.(268-270)Cgt>Agt	p.R90S	UGT1A9_ENST00000354728.4_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A6_ENST00000480628.1_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A6_ENST00000406651.1_5'Flank|UGT1A1_ENST00000373450.4_Intron|AC114812.8_ENST00000439336.1_RNA	NM_001072.3	NP_001063.2	P19224	UD16_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A6	90					cellular glucuronidation (GO:0052695)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;5.86e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000384)|Lung(119;0.00306)|LUSC - Lung squamous cell carcinoma(224;0.00702)	Acetaminophen(DB00316)|Deferiprone(DB08826)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Propofol(DB00818)|Valproic Acid(DB00313)	GCTGAAGAACCGTTACCAATC	0.398																																					p.R90S		Atlas-SNP	.											UGT1A6,colon,carcinoma,-1,1	UGT1A6	63	1	0			c.C268A						scavenged	.						112.0	105.0	107.0					2																	234601918		2203	4300	6503	SO:0001583	missense	54578	exon1			AAGAACCGTTACC	M84130	CCDS2507.1, CCDS2508.1	2q37	2010-03-05	2005-07-20		ENSG00000167165	ENSG00000167165		"""UDP glucuronosyltransferases"""	12538	other	complex locus constituent		606431	"""UDP glycosyltransferase 1 family, polypeptide A6"""			9295054, 1339448	Standard	NM_001072		Approved	HLUGP, GNT1, UGT1F		P19224	OTTHUMG00000059122	ENST00000305139.6:c.268C>A	2.37:g.234601918C>A	ENSP00000303174:p.Arg90Ser	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	161	2	0.0124224	NM_001072	A6NKK6|B8K289|Q96TE7	Missense_Mutation	SNP	ENST00000305139.6	37	CCDS2507.1	.	.	.	.	.	.	.	.	.	.	C	8.635	0.894527	0.17613	.	.	ENSG00000167165	ENST00000441351;ENST00000305139	T;T	0.06218	3.33;3.33	5.17	5.17	0.71159	.	.	.	.	.	T	0.06462	0.0166	N	0.25647	0.755	0.26024	N	0.981824	B;B	0.14438	0.01;0.003	B;B	0.23018	0.043;0.022	T	0.33420	-0.9869	9	0.18276	T	0.48	.	15.5189	0.75851	0.0:0.852:0.148:0.0	.	90;90	B8K289;P19224	.;UD16_HUMAN	S	90	ENSP00000389637:R90S;ENSP00000303174:R90S	ENSP00000303174:R90S	R	+	1	0	UGT1A6	234266657	0.000000	0.05858	0.028000	0.17463	0.333000	0.28666	-0.554000	0.06006	2.678000	0.91216	0.655000	0.94253	CGT	.	.	none		0.398	UGT1A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130988.1	NM_205862	
SEMA6D	80031	hgsc.bcm.edu	37	15	48063877	48063877	+	Silent	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr15:48063877G>A	ENST00000316364.5	+	19	3556	c.3117G>A	c.(3115-3117)agG>agA	p.R1039R	SEMA6D_ENST00000536845.2_Silent_p.R1039R|SEMA6D_ENST00000358066.4_Silent_p.R977R|SEMA6D_ENST00000389428.3_Silent_p.R964R|SEMA6D_ENST00000537942.1_Silent_p.R977R|SEMA6D_ENST00000354744.4_Silent_p.R983R|SEMA6D_ENST00000389432.2_Silent_p.R996R|SEMA6D_ENST00000355997.3_3'UTR|SEMA6D_ENST00000558014.1_Silent_p.R977R|SEMA6D_ENST00000389433.2_Silent_p.R1020R|SEMA6D_ENST00000558816.1_3'UTR	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	1039					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)		CTCTTCCTAGGACGGGACTAA	0.512																																					p.R1039R		Atlas-SNP	.											.	SEMA6D	322	.	0			c.G3117A						PASS	.						167.0	165.0	165.0					15																	48063877		2198	4297	6495	SO:0001819	synonymous_variant	80031	exon19			TCCTAGGACGGGA	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.3117G>A	15.37:g.48063877G>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	146	8	0.0547945	NM_153618	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Silent	SNP	ENST00000316364.5	37	CCDS32225.1																																																																																			.	.	none		0.512	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966	
FRG1	2483	hgsc.bcm.edu	37	4	190878551	190878551	+	Splice_Site	SNP	A	A	G			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr4:190878551A>G	ENST00000226798.4	+	6	654		c.e6-1		FRG1_ENST00000514482.1_Splice_Site	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1						mRNA splicing, via spliceosome (GO:0000398)|muscle organ development (GO:0007517)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.?(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1)	32		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		TGTTTCACTTAGGGGAAAATG	0.358																																					.		Atlas-SNP	.											FRG1,NS,malignant_melanoma,0,1	FRG1	76	1	1	Unknown(1)	NS(1)	c.433-2A>G						scavenged	.						10.0	16.0	14.0					4																	190878551		2077	4234	6311	SO:0001630	splice_region_variant	2483	exon6			TCACTTAGGGGAA	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.433-1A>G	4.37:g.190878551A>G		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	227	2	0.00881057	NM_004477	A8K775	Splice_Site	SNP	ENST00000226798.4	37	CCDS34121.1	.	.	.	.	.	.	.	.	.	.	N	13.17	2.156273	0.38021	.	.	ENSG00000109536	ENST00000226798;ENST00000524583;ENST00000531991	.	.	.	3.8	3.8	0.43715	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.8823	0.46946	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FRG1	191115545	1.000000	0.71417	1.000000	0.80357	0.407000	0.30961	9.035000	0.93752	1.517000	0.48917	0.373000	0.22412	.	.	.	none		0.358	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359622.4	NM_004477	Intron
MED13L	23389	hgsc.bcm.edu	37	12	116413345	116413345	+	Missense_Mutation	SNP	C	C	T	rs182752795	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:116413345C>T	ENST00000281928.3	-	24	5769	c.5563G>A	c.(5563-5565)Gtt>Att	p.V1855I		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	1855						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		ATATTTACAACGCAGGTCTCT	0.418													C|||	2	0.000399361	0.0	0.0014	5008	,	,		19304	0.001		0.0	False		,,,				2504	0.0				p.V1855I		Atlas-SNP	.											MED13L,colon,carcinoma,0,1	MED13L	193	1	0			c.G5563A						scavenged	.						65.0	61.0	62.0					12																	116413345		2203	4300	6503	SO:0001583	missense	23389	exon24			TTACAACGCAGGT	AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"""thyroid hormone receptor associated protein 2"""	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.5563G>A	12.37:g.116413345C>T	ENSP00000281928:p.Val1855Ile	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	169	3	0.0177515	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Missense_Mutation	SNP	ENST00000281928.3	37	CCDS9177.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0017482517482517483|0.0017482517482517483	0|0	0.0|0.0	C|C	5.802|5.802	0.332346|0.332346	0.10956|0.10956	.|.	.|.	ENSG00000123066|ENSG00000123066	ENST00000552447|ENST00000281928	.|D	.|0.82344	.|-1.6	5.86|5.86	-0.741|-0.741	0.11112|0.11112	.|.	.|0.306722	.|0.39475	.|N	.|0.001356	T|T	0.53384|0.53384	0.1793|0.1793	N|N	0.02129|0.02129	-0.67|-0.67	0.32347|0.32347	N|N	0.558907|0.558907	.|B	.|0.02656	.|0.0	.|B	.|0.06405	.|0.002	T|T	0.54364|0.54364	-0.8305|-0.8305	5|10	.|0.02654	.|T	.|1	-3.037|-3.037	12.0632|12.0632	0.53574|0.53574	0.0:0.4747:0.0:0.5253|0.0:0.4747:0.0:0.5253	.|.	.|1855	.|Q71F56	.|MD13L_HUMAN	H|I	47|1855	.|ENSP00000281928:V1855I	.|ENSP00000281928:V1855I	R|V	-|-	2|1	0|0	MED13L|MED13L	114897728|114897728	1.000000|1.000000	0.71417|0.71417	0.964000|0.964000	0.40570|0.40570	0.995000|0.995000	0.86356|0.86356	1.907000|1.907000	0.39897|0.39897	-0.275000|-0.275000	0.09219|0.09219	-0.145000|-0.145000	0.13849|0.13849	CGT|GTT	C|1.000;T|0.000	0.000	strong		0.418	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3		
HLA-C	3107	hgsc.bcm.edu	37	6	31238930	31238930	+	Missense_Mutation	SNP	A	A	T	rs79636386	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr6:31238930A>T	ENST00000376228.5	-	3	553	c.539T>A	c.(538-540)cTg>cAg	p.L180Q	HLA-C_ENST00000383329.3_Missense_Mutation_p.L180Q	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	180	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						GTAGGCTCTCAGCTGCTCCGC	0.687																																					p.L180Q		Atlas-SNP	.											HLA-C_ENST00000383329,NS,carcinoma,0,2	HLA-C	92	2	0			c.T539A						scavenged	.						44.0	31.0	35.0					6																	31238930		2196	4292	6488	SO:0001583	missense	3107	exon3			GCTCTCAGCTGCT	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.539T>A	6.37:g.31238930A>T	ENSP00000365402:p.Leu180Gln	Somatic	278	5	0.0179856		WXS	Illumina HiSeq	Phase_I	210	7	0.0333333	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	.	.	.	.	.	.	.	.	.	.	.	0.527	-0.859406	0.02610	.	.	ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	T;T	0.00010	9.42;9.42	2.81	-5.62	0.02481	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	115.764000	0.00166	U	0.000008	T	0.00012	0.0000	N	0.11284	0.12	0.09310	N	1	B;B;B;B	0.30406	0.278;0.024;0.024;0.024	B;B;B;B	0.31016	0.123;0.04;0.04;0.04	T	0.35847	-0.9772	10	0.23302	T	0.38	.	0.7503	0.00989	0.3702:0.2557:0.1128:0.2613	rs2308592;rs9264655;rs17839942;rs28367578	180;180;180;180	A2AEA4;A6H578;A2AEA2;P10321	.;.;.;1C07_HUMAN	Q	180;180;180;217	ENSP00000365402:L180Q;ENSP00000372819:L180Q	ENSP00000365402:L180Q	L	-	2	0	HLA-C	31346909	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.015000	0.00160	-3.815000	0.00103	-3.321000	0.00044	CTG	T|0.001;C|0.301;A|0.698	0.001	weak		0.687	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
BRINP1	1620	hgsc.bcm.edu	37	9	121929513	121929513	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr9:121929513G>A	ENST00000265922.3	-	8	2596	c.2135C>T	c.(2134-2136)cCg>cTg	p.P712L	BRINP1_ENST00000482797.1_Intron	NM_014618.2	NP_055433.2	O60477	BRNP1_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 1	712			P -> T (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell cycle (GO:0045786)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	cytoplasm (GO:0005737)		p.P712L(1)									GGGTTTCCCCGGGGCCACAGG	0.557																																					p.P712L		Atlas-SNP	.											DBC1,rectum,carcinoma,0,4	DBC1	194	4	1	Substitution - Missense(1)	kidney(1)	c.C2135T						PASS	.						86.0	94.0	91.0					9																	121929513		2203	4300	6503	SO:0001583	missense	1620	exon8			TTCCCCGGGGCCA	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.2135C>T	9.37:g.121929513G>A	ENSP00000265922:p.Pro712Leu	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	226	79	0.349558	NM_014618	Q6IPV6|Q6P1A0|Q8WU22	Missense_Mutation	SNP	ENST00000265922.3	37	CCDS6822.1	.	.	.	.	.	.	.	.	.	.	G	18.02	3.531209	0.64972	.	.	ENSG00000078725	ENST00000373969;ENST00000265922	T	0.19250	2.16	5.64	4.73	0.59995	.	0.100848	0.64402	D	0.000001	T	0.23727	0.0574	M	0.61703	1.905	0.80722	D	1	P	0.35433	0.501	B	0.28011	0.085	T	0.07121	-1.0789	10	0.87932	D	0	-22.0002	16.2315	0.82344	0.0:0.0:0.8659:0.1341	.	712	O60477	DBC1_HUMAN	L	712	ENSP00000265922:P712L	ENSP00000265922:P712L	P	-	2	0	DBC1	120969334	1.000000	0.71417	0.961000	0.40146	0.998000	0.95712	7.234000	0.78134	1.508000	0.48769	0.585000	0.79938	CCG	.	.	none		0.557	BRINP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055440.2	NM_014618	
NELL2	4753	hgsc.bcm.edu	37	12	44915940	44915940	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:44915940C>T	ENST00000429094.2	-	18	2522	c.2018G>A	c.(2017-2019)cGa>cAa	p.R673Q	NELL2_ENST00000395487.2_Missense_Mutation_p.R672Q|NELL2_ENST00000452445.2_Missense_Mutation_p.R673Q|NELL2_ENST00000549027.1_Missense_Mutation_p.R672Q|NELL2_ENST00000551601.1_Missense_Mutation_p.R625Q|NELL2_ENST00000437801.2_Missense_Mutation_p.R723Q|NELL2_ENST00000333837.4_Missense_Mutation_p.R696Q	NM_001145108.1	NP_001138580.1	Q99435	NELL2_HUMAN	NEL-like 2 (chicken)	673	VWFC 2. {ECO:0000255|PROSITE- ProRule:PRU00220}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(16)|lung(30)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	65	Lung SC(27;0.192)	Lung NSC(34;0.144)		GBM - Glioblastoma multiforme(48;0.092)		GACCATCCGTCGACACATAAC	0.438																																					p.R723Q		Atlas-SNP	.											NELL2_ENST00000437801,colon,carcinoma,-1,2	NELL2	286	2	0			c.G2168A						scavenged	.						95.0	87.0	90.0					12																	44915940		2203	4300	6503	SO:0001583	missense	4753	exon19			ATCCGTCGACACA	D83018	CCDS8746.1, CCDS44863.1, CCDS44864.1, CCDS53781.1	12q12	2012-01-30	2001-11-28		ENSG00000184613	ENSG00000184613			7751	protein-coding gene	gene with protein product		602320	"""nel (chicken)-like 2"""			19249368	Standard	NM_006159		Approved	NRP2	uc010skz.1	Q99435	OTTHUMG00000169464	ENST00000429094.2:c.2018G>A	12.37:g.44915940C>T	ENSP00000390680:p.Arg673Gln	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	64	3	0.046875	NM_001145107	B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2	Missense_Mutation	SNP	ENST00000429094.2	37	CCDS8746.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.940970	0.73557	.	.	ENSG00000184613	ENST00000395487;ENST00000429094;ENST00000551601;ENST00000452445;ENST00000549027;ENST00000333837;ENST00000437801	D;T;T;T;D;T;D	0.81821	-1.5;-1.47;-1.18;-1.47;-1.5;-1.43;-1.54	5.7	4.81	0.61882	von Willebrand factor, type C (2);EGF-like region, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.70937	0.3281	L	0.53617	1.68	0.58432	D	0.999997	P;P;B;B;B	0.42827	0.539;0.791;0.056;0.009;0.258	B;B;B;B;B	0.28232	0.024;0.087;0.018;0.005;0.053	T	0.69978	-0.4998	10	0.21014	T	0.42	-9.7144	14.8365	0.70187	0.0:0.931:0.0:0.069	.	696;723;625;673;672	B7Z2U7;B7Z9U3;F8VVB6;Q99435;Q96JS2	.;.;.;NELL2_HUMAN;.	Q	672;673;625;673;672;696;723	ENSP00000378866:R672Q;ENSP00000390680:R673Q;ENSP00000449332:R625Q;ENSP00000394612:R673Q;ENSP00000447927:R672Q;ENSP00000327988:R696Q;ENSP00000416341:R723Q	ENSP00000327988:R696Q	R	-	2	0	NELL2	43202207	1.000000	0.71417	0.973000	0.42090	0.938000	0.57974	7.814000	0.86154	1.405000	0.46838	0.650000	0.86243	CGA	.	.	none		0.438	NELL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404180.1	NM_006159	
ACN9	57001	hgsc.bcm.edu	37	7	96810429	96810429	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr7:96810429C>T	ENST00000432641.2	+	2	1414	c.280C>T	c.(280-282)Cgt>Tgt	p.R94C	ACN9_ENST00000479853.1_3'UTR|ACN9_ENST00000360382.4_3'UTR	NM_020186.2	NP_064571.1			ACN9 homolog (S. cerevisiae)											large_intestine(1)|lung(4)|ovary(1)|skin(1)|urinary_tract(3)	10	all_cancers(62;2.54e-08)|all_epithelial(64;2.24e-08)|Esophageal squamous(72;0.00507)|all_lung(186;0.154)|Lung NSC(181;0.159)					TAATGACTTTCGTGATGAACA	0.388																																					p.R94C		Atlas-SNP	.											ACN9,NS,malignant_melanoma,0,1	ACN9	19	1	0			c.C280T						scavenged	.						71.0	73.0	73.0					7																	96810429		2203	4300	6503	SO:0001583	missense	57001	exon2			GACTTTCGTGATG	BC028409	CCDS5648.1	7q22.1	2006-02-09			ENSG00000196636	ENSG00000196636			21752	protein-coding gene	gene with protein product		615773					Standard	NM_020186		Approved	DC11	uc003uoo.4	Q9NRP4	OTTHUMG00000154064	ENST00000432641.2:c.280C>T	7.37:g.96810429C>T	ENSP00000414066:p.Arg94Cys	Somatic	322	0	0		WXS	Illumina HiSeq	Phase_I	365	4	0.0109589	NM_020186		Missense_Mutation	SNP	ENST00000432641.2	37	CCDS5648.1	.	.	.	.	.	.	.	.	.	.	C	14.14	2.446155	0.43429	.	.	ENSG00000196636	ENST00000432641	.	.	.	5.13	2.97	0.34412	.	0.202544	0.46145	D	0.000320	T	0.47764	0.1463	L	0.46157	1.445	0.80722	D	1	B	0.22346	0.068	B	0.17722	0.019	T	0.50923	-0.8770	9	0.62326	D	0.03	-2.2131	9.6707	0.40011	0.4515:0.5485:0.0:0.0	.	94	Q9NRP4	ACN9_HUMAN	C	94	.	ENSP00000414066:R94C	R	+	1	0	ACN9	96648365	0.999000	0.42202	1.000000	0.80357	0.985000	0.73830	3.201000	0.51059	1.249000	0.43950	0.591000	0.81541	CGT	.	.	none		0.388	ACN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333685.3	NM_020186	
CUX1	1523	hgsc.bcm.edu	37	7	101845432	101845432	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr7:101845432T>C	ENST00000292535.7	+	18	2893	c.2855T>C	c.(2854-2856)gTt>gCt	p.V952A	CUX1_ENST00000546411.2_Missense_Mutation_p.V850A|CUX1_ENST00000547394.2_Intron|CUX1_ENST00000556210.1_Missense_Mutation_p.V794A|CUX1_ENST00000550008.2_Missense_Mutation_p.V896A|CUX1_ENST00000292538.4_Intron|CUX1_ENST00000425244.2_Intron|CUX1_ENST00000549414.2_Missense_Mutation_p.V930A|CUX1_ENST00000360264.3_Missense_Mutation_p.V963A|CUX1_ENST00000437600.4_Intron|CUX1_ENST00000393824.3_Intron|CUX1_ENST00000560541.1_Intron	NM_181552.3	NP_853530.2	P39880	CUX1_HUMAN	cut-like homeobox 1	952					auditory receptor cell differentiation (GO:0042491)|kidney development (GO:0001822)|lung development (GO:0030324)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retrograde transport, vesicle recycling within Golgi (GO:0000301)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						ACCCGGCAGGTTAAGGAAAAG	0.587																																					p.V963A		Atlas-SNP	.											.	CUX1	253	.	0			c.T2888C						PASS	.						93.0	99.0	97.0					7																	101845432		2203	4300	6503	SO:0001583	missense	1523	exon18			GGCAGGTTAAGGA	M74099	CCDS5720.1, CCDS5721.1, CCDS47672.1, CCDS56498.1, CCDS56499.1, CCDS56500.1, CCDS59071.1	7q22.1	2012-10-03	2007-11-07	2007-11-07	ENSG00000257923	ENSG00000257923		"""Homeoboxes / CUT class"""	2557	protein-coding gene	gene with protein product	"""golgi integral membrane protein 6"""	116896	"""cut (Drosophila)-like 1 (CCAAT displacement protein)"", ""cut-like 1, CCAAT displacement protein (Drosophila)"""	CUTL1		8468066, 9799793, 15004235	Standard	NM_001202543		Approved	CDP, CDP1, CUX, CUT, Clox, CDP/Cut, CDP/Cux, Cux/CDP, CASP, GOLIM6	uc003uyx.4	P39880	OTTHUMG00000157129	ENST00000292535.7:c.2855T>C	7.37:g.101845432T>C	ENSP00000292535:p.Val952Ala	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	96	4	0.0416667	NM_001202543	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Missense_Mutation	SNP	ENST00000292535.7	37	CCDS5721.1	.	.	.	.	.	.	.	.	.	.	T	18.82	3.704680	0.68615	.	.	ENSG00000257923	ENST00000360264;ENST00000292535;ENST00000549414;ENST00000550008;ENST00000546411;ENST00000556210	T;T;T;T;T;T	0.71461	-0.55;-0.52;-0.55;-0.57;-0.52;-0.53	5.29	5.29	0.74685	Homeodomain protein CUT (2);Lambda repressor-like, DNA-binding (2);	0.162599	0.40554	N	0.001077	T	0.77955	0.4208	M	0.75615	2.305	0.80722	D	1	P;D	0.55385	0.78;0.971	P;P	0.50934	0.471;0.654	T	0.81908	-0.0717	10	0.87932	D	0	-24.5424	15.2336	0.73411	0.0:0.0:0.0:1.0	.	952;963	P39880;P39880-3	CUX1_HUMAN;.	A	963;952;930;896;850;794	ENSP00000353401:V963A;ENSP00000292535:V952A;ENSP00000446630:V930A;ENSP00000447373:V896A;ENSP00000450125:V850A;ENSP00000451558:V794A	ENSP00000292535:V952A	V	+	2	0	CUX1	101632152	1.000000	0.71417	0.955000	0.39395	0.969000	0.65631	7.698000	0.84413	2.010000	0.58986	0.533000	0.62120	GTT	.	.	none		0.587	CUX1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347535.1	NM_001913	
KDM4C	23081	hgsc.bcm.edu	37	9	6880041	6880041	+	Missense_Mutation	SNP	G	G	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr9:6880041G>T	ENST00000381309.3	+	6	1224	c.659G>T	c.(658-660)cGa>cTa	p.R220L	KDM4C_ENST00000442236.2_Missense_Mutation_p.R39L|KDM4C_ENST00000543771.1_Missense_Mutation_p.R220L|KDM4C_ENST00000536108.1_Missense_Mutation_p.R39L|KDM4C_ENST00000535193.1_Missense_Mutation_p.R242L|KDM4C_ENST00000489243.1_3'UTR|KDM4C_ENST00000381306.3_Missense_Mutation_p.R220L	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C	220	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				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)	p.R220Q(1)		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						CATGGAAAACGACTTGAAAGA	0.303																																					p.R242L		Atlas-SNP	.											KDM4C_ENST00000381306,colon,carcinoma,+1,4	KDM4C	186	4	1	Substitution - Missense(1)	large_intestine(1)	c.G725T						scavenged	.						64.0	64.0	64.0					9																	6880041		2203	4299	6502	SO:0001583	missense	23081	exon6			GAAAACGACTTGA	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.659G>T	9.37:g.6880041G>T	ENSP00000370710:p.Arg220Leu	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	124	2	0.016129	NM_001146696	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Missense_Mutation	SNP	ENST00000381309.3	37	CCDS6471.1	.	.	.	.	.	.	.	.	.	.	G	34	5.355061	0.95854	.	.	ENSG00000107077	ENST00000535193;ENST00000543771;ENST00000381309;ENST00000381306;ENST00000442236;ENST00000536108	T;T;T;T;T;T	0.72725	-0.68;-0.68;-0.68;-0.68;-0.68;-0.68	5.16	5.16	0.70880	Transcription factor jumonji/aspartyl beta-hydroxylase (2);Transcription factor jumonji (1);	0.153645	0.46442	D	0.000287	D	0.84334	0.5449	M	0.73753	2.245	0.80722	D	1	D;D;P;P;D;D	0.89917	1.0;0.999;0.873;0.85;0.999;0.999	D;D;P;B;D;D	0.80764	0.994;0.993;0.723;0.435;0.962;0.965	D	0.85891	0.1428	10	0.87932	D	0	-0.0458	18.8266	0.92122	0.0:0.0:1.0:0.0	.	39;220;220;242;220;220	E7EV17;F5H347;B4E1Y4;F5H7P0;Q9H3R0;Q9H3R0-2	.;.;.;.;KDM4C_HUMAN;.	L	242;220;220;220;39;39	ENSP00000442382:R242L;ENSP00000445427:R220L;ENSP00000370710:R220L;ENSP00000370707:R220L;ENSP00000409353:R39L;ENSP00000440656:R39L	ENSP00000370707:R220L	R	+	2	0	KDM4C	6870041	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.040000	0.93783	2.677000	0.91161	0.591000	0.81541	CGA	.	.	none		0.303	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061	
SEH1L	81929	hgsc.bcm.edu	37	18	12955467	12955467	+	Silent	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr18:12955467T>C	ENST00000262124.11	+	3	295	c.168T>C	c.(166-168)caT>caC	p.H56H	SEH1L_ENST00000399892.2_Silent_p.H56H	NM_031216.3	NP_112493.2	Q96EE3	SEH1_HUMAN	SEH1-like (S. cerevisiae)	56					attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation (GO:0051315)|carbohydrate metabolic process (GO:0005975)|cytokine production involved in inflammatory response (GO:0002534)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-positive bacterium (GO:0050830)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore organization (GO:0006999)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear envelope (GO:0005635)|nuclear pore outer ring (GO:0031080)		p.H56H(2)		central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1)	11						CCCAGACACATAGTGGATCTG	0.398																																					p.H56H		Atlas-SNP	.											SEH1L,NS,carcinoma,0,3	SEH1L	33	3	2	Substitution - coding silent(2)	prostate(1)|central_nervous_system(1)	c.T168C						scavenged	.						150.0	135.0	140.0					18																	12955467		2203	4300	6503	SO:0001819	synonymous_variant	81929	exon3			GACACATAGTGGA	BC012430	CCDS32791.1, CCDS45832.1	18p11.21	2013-01-10				ENSG00000085415		"""WD repeat domain containing"""	30379	protein-coding gene	gene with protein product	"""sec13 like protein"", ""nucleoporin Seh1"""	609263				12196509, 14517296	Standard	XM_005258152		Approved	SEH1A, SEH1B, Seh1, SEC13L	uc002krq.3	Q96EE3		ENST00000262124.11:c.168T>C	18.37:g.12955467T>C		Somatic	201	1	0.00497512		WXS	Illumina HiSeq	Phase_I	185	9	0.0486486	NM_001013437	A8K5B1|Q8NFU6|Q96MH3|Q9C069	Silent	SNP	ENST00000262124.11	37	CCDS45832.1																																																																																			.	.	weak		0.398	SEH1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458254.1	NM_031216	
DNAH10	196385	hgsc.bcm.edu	37	12	124395178	124395178	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:124395178T>C	ENST00000409039.3	+	58	9764	c.9739T>C	c.(9739-9741)Tac>Cac	p.Y3247H		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	3247	Stalk. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		TGTAATGGGCTACTGTGATGT	0.463																																					p.Y3247H		Atlas-SNP	.											DNAH10_same_name,NS,carcinoma,-2,2	DNAH10	888	2	0			c.T9739C						scavenged	.						89.0	92.0	91.0					12																	124395178		1942	4135	6077	SO:0001583	missense	196385	exon58			ATGGGCTACTGTG	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.9739T>C	12.37:g.124395178T>C	ENSP00000386770:p.Tyr3247His	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	93	2	0.0215054	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	T	22.0	4.224128	0.79576	.	.	ENSG00000197653	ENST00000409039	T	0.75050	-0.9	4.96	4.96	0.65561	Dynein heavy chain, coiled coil stalk (1);	0.142976	0.49305	D	0.000158	D	0.90865	0.7130	H	0.97340	3.985	0.58432	D	0.999995	D	0.89917	1.0	D	0.91635	0.999	D	0.93972	0.7250	10	0.87932	D	0	.	14.632	0.68663	0.0:0.0:0.0:1.0	.	3247	Q8IVF4	DYH10_HUMAN	H	3247	ENSP00000386770:Y3247H	ENSP00000386770:Y3247H	Y	+	1	0	DNAH10	122961131	1.000000	0.71417	1.000000	0.80357	0.770000	0.43624	7.774000	0.85478	1.867000	0.54127	0.533000	0.62120	TAC	.	.	none		0.463	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
GRN	2896	hgsc.bcm.edu	37	17	42430050	42430050	+	Missense_Mutation	SNP	C	C	T	rs63750116		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr17:42430050C>T	ENST00000053867.3	+	13	1728	c.1666C>T	c.(1666-1668)Cgc>Tgc	p.R556C	GRN_ENST00000589265.1_Missense_Mutation_p.R399C	NM_002087.2	NP_002078.1	P28799	GRN_HUMAN	granulin	556					blastocyst hatching (GO:0001835)|cell death (GO:0008219)|embryo implantation (GO:0007566)|positive regulation of epithelial cell proliferation (GO:0050679)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)	growth factor activity (GO:0008083)|poly(A) RNA binding (GO:0044822)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.189)		TGCTGATCGGCGCCACTGCTG	0.682																																					p.R556C		Atlas-SNP	.											.	GRN	51	.	0			c.C1666T						PASS	.						62.0	65.0	64.0					17																	42430050		2203	4300	6503	SO:0001583	missense	2896	exon13			GATCGGCGCCACT	M75161	CCDS11483.1	17q21.32	2014-09-17				ENSG00000030582			4601	protein-coding gene	gene with protein product	"""progranulin"""	138945				1417868, 9826678	Standard	XM_005257253		Approved	PCDGF, PGRN, CLN11	uc002igp.1	P28799		ENST00000053867.3:c.1666C>T	17.37:g.42430050C>T	ENSP00000053867:p.Arg556Cys	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	62	30	0.483871	NM_002087	D3DX55|P23781|P23782|P23783|P23784|Q53HQ8|Q53Y88|Q540U8|Q9BWE7|Q9H8S1|Q9UCH0	Missense_Mutation	SNP	ENST00000053867.3	37	CCDS11483.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.388125	0.82902	.	.	ENSG00000030582	ENST00000053867;ENST00000357351;ENST00000393566	T	0.72725	-0.68	5.53	4.52	0.55395	Granulin (3);	0.909924	0.09476	N	0.797014	T	0.82148	0.4974	M	0.78801	2.425	0.09310	N	0.999999	D	0.76494	0.999	D	0.67725	0.953	T	0.68765	-0.5322	10	0.39692	T	0.17	-19.1959	9.4761	0.38873	0.1587:0.6877:0.1536:0.0	rs63750116	556	P28799	GRN_HUMAN	C	556;401;376	ENSP00000053867:R556C	ENSP00000053867:R556C	R	+	1	0	GRN	39785576	0.000000	0.05858	0.021000	0.16686	0.641000	0.38312	0.559000	0.23485	2.599000	0.87857	0.561000	0.74099	CGC	.	.	weak		0.682	GRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457766.1	NM_002087	
TSKS	60385	hgsc.bcm.edu	37	19	50251699	50251699	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:50251699C>T	ENST00000246801.3	-	3	509	c.427G>A	c.(427-429)Gcc>Acc	p.A143T	TSKS_ENST00000358830.3_5'Flank	NM_021733.1	NP_068379.1	Q9UJT2	TSKS_HUMAN	testis-specific serine kinase substrate	143					negative regulation of phosphatase activity (GO:0010923)	centriole (GO:0005814)	protein kinase binding (GO:0019901)	p.A143S(1)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(9)|prostate(3)|skin(3)	38		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(134;0.0145)		GAGTCTTTGGCGCGGACCAAT	0.562																																					p.A143T		Atlas-SNP	.											TSKS,NS,carcinoma,0,1	TSKS	97	1	1	Substitution - Missense(1)	liver(1)	c.G427A						scavenged	.						117.0	96.0	103.0					19																	50251699		2203	4300	6503	SO:0001583	missense	60385	exon3			CTTTGGCGCGGAC	BC058862	CCDS12780.1	19q13.3	2014-06-13							30719	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 161"""	608253				11444856, 18495105	Standard	NM_021733		Approved	TSSKS, PPP1R161	uc002ppm.3	Q9UJT2		ENST00000246801.3:c.427G>A	19.37:g.50251699C>T	ENSP00000246801:p.Ala143Thr	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	256	4	0.015625	NM_021733	Q8WXJ0	Missense_Mutation	SNP	ENST00000246801.3	37	CCDS12780.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.629111	0.87560	.	.	ENSG00000126467	ENST00000246801	T	0.45276	0.9	4.85	4.85	0.62838	.	0.000000	0.53938	D	0.000057	T	0.51568	0.1682	L	0.29908	0.895	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.48937	-0.8990	10	0.42905	T	0.14	-22.8746	14.9962	0.71433	0.0:1.0:0.0:0.0	.	143	Q9UJT2	TSKS_HUMAN	T	143	ENSP00000246801:A143T	ENSP00000246801:A143T	A	-	1	0	TSKS	54943511	0.992000	0.36948	0.959000	0.39883	0.990000	0.78478	3.860000	0.55995	2.525000	0.85131	0.462000	0.41574	GCC	.	.	none		0.562	TSKS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465795.1	NM_021733	
TNN	63923	hgsc.bcm.edu	37	1	175097789	175097789	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:175097789C>T	ENST00000239462.4	+	15	3350	c.3237C>T	c.(3235-3237)gcC>gcT	p.A1079A		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	1079	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)		ACAGCAATGCCGCCAGTGGTC	0.582																																					p.A1079A		Atlas-SNP	.											TNN,NS,carcinoma,+2,1	TNN	297	1	0			c.C3237T						scavenged	.						102.0	97.0	99.0					1																	175097789		2203	4300	6503	SO:0001819	synonymous_variant	63923	exon15			CAATGCCGCCAGT	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.3237C>T	1.37:g.175097789C>T		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	190	2	0.0105263	NM_022093	B9EGP3|Q5R360	Silent	SNP	ENST00000239462.4	37	CCDS30943.1																																																																																			.	.	none		0.582	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527	
D2HGDH	728294	hgsc.bcm.edu	37	2	242681924	242681924	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:242681924T>C	ENST00000321264.4	+	4	634	c.425T>C	c.(424-426)gTc>gCc	p.V142A	D2HGDH_ENST00000403782.1_Missense_Mutation_p.V8A|D2HGDH_ENST00000342518.6_Missense_Mutation_p.V142A|D2HGDH_ENST00000537090.1_Missense_Mutation_p.V142A	NM_152783.3	NP_689996.4	Q8N465	D2HDH_HUMAN	D-2-hydroxyglutarate dehydrogenase	142	FAD-binding PCMH-type. {ECO:0000255|PROSITE-ProRule:PRU00718}.				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)		AGCGTCCCCGTCTTTGACGAG	0.647																																					p.V142A		Atlas-SNP	.											D2HGDH,NS,carcinoma,+1,1	D2HGDH	39	1	0			c.T425C						scavenged	.						103.0	79.0	87.0					2																	242681924		2203	4296	6499	SO:0001583	missense	728294	exon4			TCCCCGTCTTTGA	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.425T>C	2.37:g.242681924T>C	ENSP00000315351:p.Val142Ala	Somatic	309	1	0.00323625		WXS	Illumina HiSeq	Phase_I	395	6	0.0151899	NM_152783	B4E3L6|E7ENP2|Q6IQ24|Q8N5Q8	Missense_Mutation	SNP	ENST00000321264.4	37	CCDS33426.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.356896	0.82243	.	.	ENSG00000180902	ENST00000537090;ENST00000321264;ENST00000403782;ENST00000342518;ENST00000437164;ENST00000454048	D;D;D;D;D;D	0.95756	-3.8;-3.8;-3.8;-3.8;-3.8;-3.73	5.06	5.06	0.68205	FAD-binding, type 2, subdomain 1 (1);FAD-binding, type 2 (2);FAD linked oxidase, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.97201	0.9085	M	0.76170	2.325	0.80722	D	1	D	0.61080	0.989	D	0.68039	0.955	D	0.97882	1.0292	10	0.87932	D	0	.	14.8133	0.70010	0.0:0.0:0.0:1.0	.	142	Q8N465	D2HDH_HUMAN	A	142;142;8;142;26;12	ENSP00000442796:V142A;ENSP00000315351:V142A;ENSP00000384723:V8A;ENSP00000339536:V142A;ENSP00000412511:V26A;ENSP00000404596:V12A	ENSP00000315351:V142A	V	+	2	0	D2HGDH	242330597	1.000000	0.71417	0.971000	0.41717	0.635000	0.38103	7.367000	0.79558	1.913000	0.55393	0.454000	0.30748	GTC	.	.	none		0.647	D2HGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322794.2	NM_152783	
CHTF18	63922	hgsc.bcm.edu	37	16	840179	840179	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr16:840179C>T	ENST00000262315.9	+	5	672	c.609C>T	c.(607-609)ggC>ggT	p.G203G	CHTF18_ENST00000317063.6_Silent_p.G400G|RPUSD1_ENST00000007264.2_5'Flank|CHTF18_ENST00000455171.2_Silent_p.G231G|RPUSD1_ENST00000567114.1_5'Flank|CHTF18_ENST00000491530.1_3'UTR|RPUSD1_ENST00000561734.1_5'Flank|RPUSD1_ENST00000565809.1_5'Flank	NM_022092.2	NP_071375.1	Q8WVB6	CTF18_HUMAN	CTF18, chromosome transmission fidelity factor 18 homolog (S. cerevisiae)	203					cell cycle (GO:0007049)|DNA replication (GO:0006260)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(1)|kidney(3)|liver(2)|lung(4)|prostate(1)	11		Hepatocellular(780;0.00335)				CCCCACAGGGCTCTCTCCTCC	0.657																																					p.G203G		Atlas-SNP	.											.	CHTF18	52	.	0			c.C609T						PASS	.						32.0	36.0	35.0					16																	840179		2048	4196	6244	SO:0001819	synonymous_variant	63922	exon5			ACAGGGCTCTCTC	BC018184	CCDS45371.1	16p13.3	2010-04-21	2003-12-09		ENSG00000127586	ENSG00000127586		"""ATPases / AAA-type"""	18435	protein-coding gene	gene with protein product		613201	"""chromosome 16 open reading frame 41"""	C16orf41		12171929	Standard	NM_022092		Approved	CHL12, C321D2.4, Ctf18	uc002cke.4	Q8WVB6	OTTHUMG00000047838	ENST00000262315.9:c.609C>T	16.37:g.840179C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	91	23	0.252747	NM_022092	B7ZBA2|D3DU68|Q7Z6Y4|Q7Z6Y6|Q9BR83|Q9BRG5|Q9H7K3	Silent	SNP	ENST00000262315.9	37	CCDS45371.1	.	.	.	.	.	.	.	.	.	.	C	6.013	0.370712	0.11409	.	.	ENSG00000127586	ENST00000426047	.	.	.	4.9	-2.96	0.05547	.	.	.	.	.	T	0.20210	0.0486	.	.	.	0.19945	N	0.999945	.	.	.	.	.	.	T	0.28522	-1.0041	4	.	.	.	-9.3545	3.1824	0.06589	0.3147:0.2606:0.0:0.4247	.	.	.	.	F	99	.	.	L	+	1	0	CHTF18	780180	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.736000	0.04882	-0.299000	0.08909	-0.455000	0.05494	CTC	.	.	none		0.657	CHTF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109061.3	NM_022092	
NEFH	4744	hgsc.bcm.edu	37	22	29885567	29885567	+	Silent	SNP	A	A	C	rs147489453|rs75808076|rs59279731		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr22:29885567A>C	ENST00000310624.6	+	4	1971	c.1938A>C	c.(1936-1938)gcA>gcC	p.A646A		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	652	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AGGAGGAAGCAAAGTCCCCTG	0.567																																					p.A646A		Atlas-SNP	.											NEFH,rectum,carcinoma,0,1	NEFH	178	1	0			c.A1938C						PASS	.						78.0	77.0	77.0					22																	29885567		2133	4127	6260	SO:0001819	synonymous_variant	4744	exon4			GGAAGCAAAGTCC		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1938A>C	22.37:g.29885567A>C		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	72	17	0.236111	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Silent	SNP	ENST00000310624.6	37	CCDS13858.1																																																																																			.	.	weak		0.567	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
ADAMTS12	81792	hgsc.bcm.edu	37	5	33576895	33576895	+	Missense_Mutation	SNP	C	C	T	rs202204545		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:33576895C>T	ENST00000504830.1	-	19	3571	c.3236G>A	c.(3235-3237)cGc>cAc	p.R1079H	ADAMTS12_ENST00000352040.3_Missense_Mutation_p.R994H|ADAMTS12_ENST00000504582.1_5'Flank	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	1079	Spacer 2.				cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						AATGAGATAGCGAGAGCTCAG	0.517										HNSCC(64;0.19)																											p.R1079H		Atlas-SNP	.											ADAMTS12,NS,carcinoma,-1,1	ADAMTS12	464	1	0			c.G3236A						scavenged	.						120.0	113.0	116.0					5																	33576895		2203	4300	6503	SO:0001583	missense	81792	exon19			AGATAGCGAGAGC	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.3236G>A	5.37:g.33576895C>T	ENSP00000422554:p.Arg1079His	Somatic	140	1	0.00714286		WXS	Illumina HiSeq	Phase_I	214	4	0.0186916	NM_030955	A2RRN9|A5D6V6|Q6UWL3	Missense_Mutation	SNP	ENST00000504830.1	37	CCDS34140.1	.	.	.	.	.	.	.	.	.	.	c	3.366	-0.129536	0.06753	.	.	ENSG00000151388	ENST00000504830;ENST00000352040	T;T	0.43294	0.95;0.95	4.93	-6.33	0.01988	.	1.928310	0.01728	N	0.028718	T	0.14270	0.0345	N	0.01576	-0.805	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.16837	-1.0389	10	0.15499	T	0.54	.	6.279	0.20997	0.0:0.2804:0.3558:0.3638	.	994;1079	P58397-3;P58397	.;ATS12_HUMAN	H	1079;994	ENSP00000422554:R1079H;ENSP00000344847:R994H	ENSP00000344847:R994H	R	-	2	0	ADAMTS12	33612652	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.456000	0.06754	-0.869000	0.04052	-1.122000	0.02009	CGC	.	.	weak		0.517	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955	
SIRPA	140885	hgsc.bcm.edu	37	20	1895963	1895963	+	Missense_Mutation	SNP	A	A	G	rs373583167|rs386811662|rs17855613	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr20:1895963A>G	ENST00000358771.4	+	2	450	c.298A>G	c.(298-300)Aac>Gac	p.N100D	SIRPA_ENST00000356025.3_Missense_Mutation_p.N100D|SIRPA_ENST00000400068.3_Missense_Mutation_p.N100D	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	100	Ig-like V-type.		N -> E (requires 2 nucleotide substitutions). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9062191, ECO:0000269|PubMed:9070220}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		CACAAAGAGAAACAACATGGA	0.522																																					p.N100D	GBM(155;1668 1920 5945 42733 48121)	Atlas-SNP	.											SIRPA,brain,glioma,-2,4	SIRPA	83	4	0			c.A298G						scavenged	.																																			SO:0001583	missense	140885	exon3			AAGAGAAACAACA	D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	9662	protein-coding gene	gene with protein product		602461	"""protein tyrosine phosphatase, non-receptor type substrate 1"""	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.298A>G	20.37:g.1895963A>G	ENSP00000351621:p.Asn100Asp	Somatic	363	20	0.0550964		WXS	Illumina HiSeq	Phase_I	389	38	0.0976864	NM_001040022	A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	Missense_Mutation	SNP	ENST00000358771.4	37	CCDS13022.1	.	.	.	.	.	.	.	.	.	.	A	10.72	1.430951	0.25726	.	.	ENSG00000198053	ENST00000400068;ENST00000356025;ENST00000358771	T;T;T	0.02236	4.38;4.38;4.38	5.11	-5.69	0.02428	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.743450	0.02696	N	0.111247	T	0.03651	0.0104	L	0.55481	1.735	0.09310	N	1	B;B;B	0.17465	0.0;0.022;0.0	B;B;B	0.24701	0.004;0.055;0.007	T	0.41875	-0.9484	10	0.51188	T	0.08	.	10.2665	0.43457	0.2384:0.1377:0.6239:0.0	rs17855613	80;100;100	B4DP97;P78324-2;P78324	.;.;SHPS1_HUMAN	D	100	ENSP00000382941:N100D;ENSP00000348307:N100D;ENSP00000351621:N100D	ENSP00000348307:N100D	N	+	1	0	SIRPA	1843963	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-1.479000	0.02327	-1.294000	0.02360	-0.388000	0.06559	AAC	.	.	weak		0.522	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792	
DSPP	1834	hgsc.bcm.edu	37	4	88537081	88537081	+	Silent	SNP	C	C	T	rs367717407|rs370267258	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr4:88537081C>T	ENST00000282478.7	+	4	3300	c.3267C>T	c.(3265-3267)gaC>gaT	p.D1089D	DSPP_ENST00000399271.1_Silent_p.D1089D|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1089	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)		atagcagtgacagcagcaata	0.537													c|||	838	0.167332	0.2292	0.2133	5008	,	,		14171	0.1131		0.1461	False		,,,				2504	0.1288				p.D1089D		Atlas-SNP	.											.	DSPP	174	.	0			c.C3267T						PASS	.	C		1383,707		577,229,239	19.0	24.0	22.0		3267	0.6	0.0	4		22	2123,1867		754,615,626	no	coding-synonymous	DSPP	NM_014208.3		1331,844,865	TT,TC,CC		46.792,33.8278,42.3355		1089/1302	88537081	3506,2574	1045	1995	3040	SO:0001819	synonymous_variant	1834	exon5			CAGTGACAGCAGC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3267C>T	4.37:g.88537081C>T		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	57	13	0.22807	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	weak		0.537	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
WDR78	79819	hgsc.bcm.edu	37	1	67299296	67299296	+	Missense_Mutation	SNP	G	G	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:67299296G>T	ENST00000371026.3	-	13	2040	c.1985C>A	c.(1984-1986)cCt>cAt	p.P662H	WDR78_ENST00000431318.1_Missense_Mutation_p.P408H	NM_024763.4	NP_079039.4	Q5VTH9	WDR78_HUMAN	WD repeat domain 78	662					hematopoietic progenitor cell differentiation (GO:0002244)					NS(1)|endometrium(3)|kidney(6)|large_intestine(6)|lung(10)|ovary(3)|skin(3)	32						ACACATTCCAGGAGCCTGTCG	0.343																																					p.P662H		Atlas-SNP	.											WDR78,face,carcinoma,-1,1	WDR78	102	1	0			c.C1985A						scavenged	.						147.0	150.0	149.0					1																	67299296		2203	4300	6503	SO:0001583	missense	79819	exon13			ATTCCAGGAGCCT	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.1985C>A	1.37:g.67299296G>T	ENSP00000360065:p.Pro662His	Somatic	192	1	0.00520833		WXS	Illumina HiSeq	Phase_I	199	2	0.0100503	NM_024763	A8K9W5|B5MDT3|H7BY80|Q5VTI0|Q8N5G5|Q9H5R9|Q9UF44	Missense_Mutation	SNP	ENST00000371026.3	37	CCDS635.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.012914	0.75161	.	.	ENSG00000152763	ENST00000371026;ENST00000431318;ENST00000464352	T;T;T	0.74632	-0.86;-0.2;-0.2	5.84	5.84	0.93424	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.050731	0.85682	D	0.000000	D	0.83811	0.5335	M	0.65975	2.015	0.58432	D	0.999998	D;D	0.89917	1.0;0.999	D;D	0.74023	0.982;0.96	D	0.84084	0.0386	10	0.72032	D	0.01	-20.6504	20.1346	0.98019	0.0:0.0:1.0:0.0	.	408;662	Q5VTH9-3;Q5VTH9	.;WDR78_HUMAN	H	662;408;428	ENSP00000360065:P662H;ENSP00000393182:P408H;ENSP00000433682:P428H	ENSP00000360065:P662H	P	-	2	0	WDR78	67071884	1.000000	0.71417	1.000000	0.80357	0.592000	0.36648	8.039000	0.88947	2.765000	0.95021	0.655000	0.94253	CCT	.	.	none		0.343	WDR78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025404.1	NM_024763	
DSPP	1834	hgsc.bcm.edu	37	4	88537123	88537123	+	Silent	SNP	C	C	T	rs372453629	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr4:88537123C>T	ENST00000282478.7	+	4	3342	c.3309C>T	c.(3307-3309)agC>agT	p.S1103S	DSPP_ENST00000399271.1_Silent_p.S1103S|RP11-742B18.1_ENST00000506480.1_RNA			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	31	18	0.580645		WXS	Illumina HiSeq	Phase_I	49	44	0.897959	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	
PITX2	5308	hgsc.bcm.edu	37	4	111539469	111539469	+	Missense_Mutation	SNP	C	C	T	rs149181425		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr4:111539469C>T	ENST00000354925.2	-	7	2471	c.766G>A	c.(766-768)Gcg>Acg	p.A256T	PITX2_ENST00000556049.1_5'Flank|PITX2_ENST00000394598.2_Missense_Mutation_p.A256T|RP11-380D23.2_ENST00000503456.1_lincRNA|PITX2_ENST00000355080.5_Missense_Mutation_p.A210T|PITX2_ENST00000306732.3_Missense_Mutation_p.A263T|PITX2_ENST00000394595.3_3'UTR	NM_001204397.1	NP_001191326.1	Q99697	PITX2_HUMAN	paired-like homeodomain 2	256					atrial cardiac muscle tissue morphogenesis (GO:0055009)|atrioventricular valve development (GO:0003171)|camera-type eye development (GO:0043010)|cardiac neural crest cell migration involved in outflow tract morphogenesis (GO:0003253)|cell proliferation involved in outflow tract morphogenesis (GO:0061325)|deltoid tuberosity development (GO:0035993)|determination of left/right symmetry (GO:0007368)|embryonic camera-type eye development (GO:0031076)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic hindlimb morphogenesis (GO:0035116)|endodermal digestive tract morphogenesis (GO:0061031)|extraocular skeletal muscle development (GO:0002074)|female gonad development (GO:0008585)|hair cell differentiation (GO:0035315)|hypothalamus cell migration (GO:0021855)|in utero embryonic development (GO:0001701)|iris morphogenesis (GO:0061072)|left lung morphogenesis (GO:0060460)|left/right axis specification (GO:0070986)|male gonad development (GO:0008584)|myoblast fusion (GO:0007520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|odontogenesis (GO:0042476)|odontogenesis of dentin-containing tooth (GO:0042475)|patterning of blood vessels (GO:0001569)|positive regulation of DNA binding (GO:0043388)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prolactin secreting cell differentiation (GO:0060127)|pulmonary myocardium development (GO:0003350)|pulmonary vein morphogenesis (GO:0060577)|regulation of cell migration (GO:0030334)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to hormone (GO:0009725)|response to vitamin A (GO:0033189)|somatotropin secreting cell differentiation (GO:0060126)|spleen development (GO:0048536)|subthalamic nucleus development (GO:0021763)|superior vena cava morphogenesis (GO:0060578)|vascular smooth muscle cell differentiation (GO:0035886)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell development (GO:0055015)|ventricular septum morphogenesis (GO:0060412)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin DNA binding (GO:0031490)|phosphoprotein binding (GO:0051219)|protein homodimerization activity (GO:0042803)|ribonucleoprotein complex binding (GO:0043021)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|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)|transcription factor binding (GO:0008134)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|endometrium(3)|large_intestine(1)|lung(5)	10		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00222)		GTCGGCACCGCGGAATTCAGC	0.592																																					p.A263T		Atlas-SNP	.											.	PITX2	73	.	0			c.G787A						PASS	.						45.0	49.0	48.0					4																	111539469		2203	4300	6503	SO:0001583	missense	5308	exon3			GCACCGCGGAATT	U69961	CCDS3692.1, CCDS3693.1, CCDS3694.1	4q25	2011-06-20	2007-07-12		ENSG00000164093	ENSG00000164093		"""Homeoboxes / PRD class"""	9005	protein-coding gene	gene with protein product		601542	"""paired-like homeodomain transcription factor 2"""	IRID2, IHG2, RIEG, RIEG1, RGS		9539779, 7581385	Standard	NM_000325		Approved	IGDS, RS, Brx1, Otlx2, ARP1	uc021xqr.1	Q99697	OTTHUMG00000132837	ENST00000354925.2:c.766G>A	4.37:g.111539469C>T	ENSP00000347004:p.Ala256Thr	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	162	40	0.246914	NM_000325	A8K6C6|B2RA02|B3KXS0|O60578|O60579|O60580|Q3KQX9|Q9BY17	Missense_Mutation	SNP	ENST00000354925.2	37	CCDS3692.1	.	.	.	.	.	.	.	.	.	.	C	17.15	3.315299	0.60524	.	.	ENSG00000164093	ENST00000306732;ENST00000394598;ENST00000355080;ENST00000354925;ENST00000511837	D;D;D;D;D	0.93366	-2.86;-2.99;-3.13;-2.99;-3.21	5.68	4.84	0.62591	.	0.267779	0.42548	D	0.000699	D	0.91334	0.7267	L	0.54908	1.71	0.80722	D	1	P;B;P;P	0.48162	0.802;0.104;0.906;0.701	B;B;B;B	0.42738	0.355;0.016;0.283;0.396	D	0.89846	0.4006	10	0.33141	T	0.24	.	14.5613	0.68140	0.0:0.9297:0.0:0.0703	.	210;210;256;263	A8K6C6;Q99697-3;Q99697;Q99697-2	.;.;PITX2_HUMAN;.	T	263;256;210;256;256	ENSP00000304169:A263T;ENSP00000378097:A256T;ENSP00000347192:A210T;ENSP00000347004:A256T;ENSP00000421454:A256T	ENSP00000304169:A263T	A	-	1	0	PITX2	111758918	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	7.818000	0.86416	1.405000	0.46838	0.655000	0.94253	GCG	C|1.000;A|0.000	.	alt		0.592	PITX2-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256308.2		
UBQLN2	29978	hgsc.bcm.edu	37	X	56591532	56591532	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:56591532T>C	ENST00000338222.5	+	1	1507	c.1226T>C	c.(1225-1227)aTg>aCg	p.M409T		NM_013444.3	NP_038472.2	Q9UHD9	UBQL2_HUMAN	ubiquilin 2	409					cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|endometrium(3)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(1)	21						GCTGCACAGATGATGCTGAAT	0.527																																					p.M409T	Esophageal Squamous(104;218 1492 6022 10838 28884)	Atlas-SNP	.											.	UBQLN2	55	.	0			c.T1226C						PASS	.						39.0	33.0	35.0					X																	56591532		2203	4300	6503	SO:0001583	missense	29978	exon1			CACAGATGATGCT	AF189009	CCDS14374.1	Xp11.21	2014-09-17			ENSG00000188021	ENSG00000188021		"""Ubiquilin family"""	12509	protein-coding gene	gene with protein product	"""NEDD4 binding protein 4"""	300264				10675567	Standard	NM_013444		Approved	Chap1, Dsk2, RIHFB2157, LIC-2, CHAP1/DSK2, PLIC-2, N4BP4, PLIC2	uc004dus.3	Q9UHD9	OTTHUMG00000021669	ENST00000338222.5:c.1226T>C	X.37:g.56591532T>C	ENSP00000345195:p.Met409Thr	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	131	57	0.435115	NM_013444	O94798|Q5D027|Q9H3W6|Q9HAZ4	Missense_Mutation	SNP	ENST00000338222.5	37	CCDS14374.1	.	.	.	.	.	.	.	.	.	.	T	12.66	2.004951	0.35415	.	.	ENSG00000188021	ENST00000338222;ENST00000535171	D	0.85088	-1.94	4.73	4.73	0.59995	Heat shock chaperonin-binding (1);	0.145633	0.49916	D	0.000140	D	0.84028	0.5382	M	0.80616	2.505	0.47245	D	0.999362	P;P	0.42649	0.786;0.61	B;B	0.37451	0.25;0.191	D	0.85805	0.1376	10	0.59425	D	0.04	-10.2918	11.3192	0.49410	0.0:0.0:0.0:1.0	.	409;409	B4DZF1;Q9UHD9	.;UBQL2_HUMAN	T	409	ENSP00000345195:M409T	ENSP00000345195:M409T	M	+	2	0	UBQLN2	56608257	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.816000	0.86201	1.874000	0.54306	0.481000	0.45027	ATG	.	.	none		0.527	UBQLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056891.1	NM_013444	
TFAP2A	7020	hgsc.bcm.edu	37	6	10398806	10398806	+	Silent	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr6:10398806G>A	ENST00000482890.1	-	8	1510	c.1158C>T	c.(1156-1158)ttC>ttT	p.F386F	TFAP2A_ENST00000379604.2_Silent_p.F386F|TFAP2A_ENST00000379608.3_Silent_p.F380F|TFAP2A_ENST00000379613.3_Silent_p.F388F|TFAP2A_ENST00000319516.4_Silent_p.F382F|TFAP2A_ENST00000497266.1_5'Flank			P05549	AP2A_HUMAN	transcription factor AP-2 alpha (activating enhancer binding protein 2 alpha)	386	H-S-H (helix-span-helix), dimerization.				anterior neuropore closure (GO:0021506)|basement membrane organization (GO:0071711)|bone morphogenesis (GO:0060349)|cellular response to iron ion (GO:0071281)|cornea development in camera-type eye (GO:0061303)|embryonic body morphogenesis (GO:0010172)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|embryonic pattern specification (GO:0009880)|epidermis morphogenesis (GO:0048730)|eyelid development in camera-type eye (GO:0061029)|face morphogenesis (GO:0060325)|forebrain neuron development (GO:0021884)|inner ear morphogenesis (GO:0042472)|keratinocyte development (GO:0003334)|kidney development (GO:0001822)|lens induction in camera-type eye (GO:0060235)|metanephric nephron development (GO:0072210)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell development (GO:0014032)|oculomotor nerve formation (GO:0021623)|optic cup structural organization (GO:0003409)|optic vesicle morphogenesis (GO:0003404)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cell migration (GO:0030335)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of tooth mineralization (GO:0070172)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell differentiation (GO:0045595)|regulation of neuron differentiation (GO:0045664)|retina layer formation (GO:0010842)|sensory perception of sound (GO:0007605)|sympathetic nervous system development (GO:0048485)|transcription from RNA polymerase II promoter (GO:0006366)|trigeminal nerve development (GO:0021559)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|endometrium(1)|large_intestine(5)|lung(5)|ovary(1)	13	Breast(50;0.0427)|Ovarian(93;0.0991)	all_hematologic(90;0.107)				CGGGGCTGCCGAAGCCGTGGG	0.627																																					p.F386F		Atlas-SNP	.											TFAP2A_ENST00000379604,right_upper_lobe,carcinoma,0,3	TFAP2A	129	3	0			c.C1158T						scavenged	.						157.0	170.0	166.0					6																	10398806		2203	4300	6503	SO:0001819	synonymous_variant	7020	exon7			GCTGCCGAAGCCG	X52611	CCDS4510.1, CCDS34337.1, CCDS43422.1	6p24.3	2013-09-19	2001-11-28		ENSG00000137203	ENSG00000137203			11742	protein-coding gene	gene with protein product		107580	"""transcription factor AP-2 alpha (activating enhancer-binding protein 2 alpha)"""	TFAP2, AP2TF		1916817, 3063603	Standard	NM_001032280		Approved	AP-2	uc003myr.3	P05549	OTTHUMG00000014235	ENST00000482890.1:c.1158C>T	6.37:g.10398806G>A		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	163	4	0.0245399	NM_003220	Q13777|Q5TAV5|Q8N1C6	Silent	SNP	ENST00000482890.1	37	CCDS4510.1																																																																																			.	.	none		0.627	TFAP2A-007	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353619.2	NM_003220	
SEMA5B	54437	hgsc.bcm.edu	37	3	122632728	122632728	+	Silent	SNP	G	G	A			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:122632728G>A	ENST00000357599.3	-	15	2495	c.2109C>T	c.(2107-2109)tgC>tgT	p.C703C	SEMA5B_ENST00000451055.2_Silent_p.C757C|SEMA5B_ENST00000195173.4_Silent_p.C703C	NM_001031702.3|NM_001256348.1	NP_001026872.2|NP_001243277.1	Q9P283	SEM5B_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	703	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.			C -> F (in Ref. 2; AAQ88491). {ECO:0000305}.	cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(13)|lung(26)|ovary(2)|pancreas(3)|skin(2)|upper_aerodigestive_tract(3)	55				GBM - Glioblastoma multiforme(114;0.0367)		TCTTGCCCACGCAGATGCGGC	0.657																																					p.C757C		Atlas-SNP	.											.	SEMA5B	303	.	0			c.C2271T						PASS	.						49.0	53.0	51.0					3																	122632728		2203	4299	6502	SO:0001819	synonymous_variant	54437	exon15			GCCCACGCAGATG	AB040878	CCDS35491.1, CCDS58848.1, CCDS74995.1	3q21.1	2008-07-18			ENSG00000082684	ENSG00000082684		"""Semaphorins"""	10737	protein-coding gene	gene with protein product		609298		SEMAG		8817451	Standard	NM_001256346		Approved	SemG, KIAA1445, FLJ10372	uc031sbm.1	Q9P283	OTTHUMG00000140392	ENST00000357599.3:c.2109C>T	3.37:g.122632728G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	80	38	0.475	NM_001256347	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Silent	SNP	ENST00000357599.3	37	CCDS35491.1																																																																																			.	.	none		0.657	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277165.1	NM_001031702	
ERAP1	51752	hgsc.bcm.edu	37	5	96129142	96129142	+	Silent	SNP	C	C	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:96129142C>T	ENST00000443439.2	-	7	1215	c.1149G>A	c.(1147-1149)gaG>gaA	p.E383E	ERAP1_ENST00000296754.3_Silent_p.E383E	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	383					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)		CAGACACAAACTCCATAAATT	0.373																																					p.E383E		Atlas-SNP	.											ERAP1,colon,carcinoma,-2,1	ERAP1	59	1	0			c.G1149A						scavenged	.						106.0	88.0	94.0					5																	96129142		2203	4300	6503	SO:0001819	synonymous_variant	51752	exon7			CACAAACTCCATA	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.1149G>A	5.37:g.96129142C>T		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	259	3	0.011583	NM_001198541	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Silent	SNP	ENST00000443439.2	37	CCDS47250.1																																																																																			.	.	none		0.373	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442	
SYT10	341359	hgsc.bcm.edu	37	12	33579301	33579301	+	Missense_Mutation	SNP	G	G	T			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:33579301G>T	ENST00000228567.3	-	2	577	c.281C>A	c.(280-282)aCt>aAt	p.T94N	SYT10_ENST00000535526.1_5'UTR|SYT10_ENST00000567656.1_5'Flank	NM_198992.3	NP_945343.1	Q6XYQ8	SYT10_HUMAN	synaptotagmin X	94					regulation of calcium ion-dependent exocytosis (GO:0017158)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(3)|skin(4)|urinary_tract(1)	42	Lung NSC(5;8.37e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0334)					TGGAAGCGTAGTGATGTTGGA	0.423																																					p.T94N		Atlas-SNP	.											.	SYT10	109	.	0			c.C281A						PASS	.						91.0	90.0	90.0					12																	33579301		2203	4300	6503	SO:0001583	missense	341359	exon2			AGCGTAGTGATGT	AY198413	CCDS8732.1	12p11	2013-01-21			ENSG00000110975	ENSG00000110975		"""Synaptotagmins"""	19266	protein-coding gene	gene with protein product							Standard	NM_198992		Approved		uc001rll.1	Q6XYQ8	OTTHUMG00000169269	ENST00000228567.3:c.281C>A	12.37:g.33579301G>T	ENSP00000228567:p.Thr94Asn	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	135	21	0.155556	NM_198992	Q495U2	Missense_Mutation	SNP	ENST00000228567.3	37	CCDS8732.1	.	.	.	.	.	.	.	.	.	.	G	0.496	-0.873133	0.02570	.	.	ENSG00000110975	ENST00000228567	T	0.46451	0.87	4.1	-2.4	0.06583	.	0.459403	0.18019	N	0.154304	T	0.21468	0.0517	N	0.19112	0.55	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.09378	-1.0677	10	0.36615	T	0.2	.	6.502	0.22174	0.0:0.3531:0.4103:0.2366	.	94	Q6XYQ8	SYT10_HUMAN	N	94	ENSP00000228567:T94N	ENSP00000228567:T94N	T	-	2	0	SYT10	33470568	0.000000	0.05858	0.000000	0.03702	0.174000	0.22865	-0.030000	0.12308	-0.492000	0.06687	-0.147000	0.13772	ACT	.	.	none		0.423	SYT10-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403222.1	NM_198992	
HLA-B	3106	hgsc.bcm.edu	37	6	31322910	31322910	+	Missense_Mutation	SNP	G	G	A	rs74189305		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr6:31322910G>A	ENST00000412585.2	-	5	1014	c.986C>T	c.(985-987)gCt>gTt	p.A329V		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	329			A -> T (in dbSNP:rs1051488).		antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)	p.A329V(4)		endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						ACACATCACAGCAGCGACCAC	0.587									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.A329V		Atlas-SNP	.											HLA-B,NS,carcinoma,-1,7	HLA-B	54	7	4	Substitution - Missense(4)	kidney(4)	c.C986T						scavenged	.						102.0	101.0	101.0					6																	31322910		1511	2709	4220	SO:0001583	missense	3106	exon5	Familial Cancer Database	;Lichen Sclerosis, Familial	ATCACAGCAGCGA	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.986C>T	6.37:g.31322910G>A	ENSP00000399168:p.Ala329Val	Somatic	166	2	0.0120482		WXS	Illumina HiSeq	Phase_I	186	7	0.0376344	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	.	.	.	.	.	.	.	.	.	.	N	9.051	0.992087	0.18966	.	.	ENSG00000234745	ENST00000412585;ENST00000428231	T	0.00622	6.16	3.73	-3.02	0.05446	.	.	.	.	.	T	0.00109	0.0003	N	0.00729	-1.24	0.09310	N	1	B	0.20052	0.041	B	0.29077	0.098	T	0.22906	-1.0203	9	0.49607	T	0.09	.	5.2273	0.15401	0.4363:0.3516:0.2121:0.0	.	329	P01889	1B07_HUMAN	V	329;208	ENSP00000399168:A329V	ENSP00000399168:A329V	A	-	2	0	HLA-B	31430889	0.000000	0.05858	0.128000	0.21923	0.021000	0.10359	0.033000	0.13754	-0.241000	0.09681	0.448000	0.29417	GCT	.	.	weak		0.587	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
ATP12A	479	hgsc.bcm.edu	37	13	25283889	25283889	+	Missense_Mutation	SNP	C	C	A	rs376963957		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr13:25283889C>A	ENST00000381946.3	+	19	2853	c.2686C>A	c.(2686-2688)Cgc>Agc	p.R896S	ATP12A_ENST00000218548.6_Missense_Mutation_p.R902S			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	896					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		CTTTCTGCCCCGCACTCTCAT	0.532																																					p.R902S	Pancreas(156;1582 1935 18898 22665 26498)	Atlas-SNP	.											ATP12A,colon,carcinoma,-1,1	ATP12A	172	1	0			c.C2704A						scavenged	.						137.0	135.0	136.0					13																	25283889		2203	4300	6503	SO:0001583	missense	479	exon19			CTGCCCCGCACTC	L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"""ATPases / P-type"""	13816	protein-coding gene	gene with protein product	"""ATPase, Na+K+ transporting, alpha-1 polypeptide-like"", ""potassium-transporting ATPase alpha chain 2"", ""proton pump"", ""non-gastric H(+)/K(+) ATPase alpha subunit"", ""sodium/potassium ATPase, alpha polypeptide-like"""	182360	"""ATPase, Na+/K+ transporting, alpha polypeptide-like 1"""	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.2686C>A	13.37:g.25283889C>A	ENSP00000371372:p.Arg896Ser	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	220	3	0.0136364	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Missense_Mutation	SNP	ENST00000381946.3	37	CCDS31948.1	.	.	.	.	.	.	.	.	.	.	C	1.043	-0.678193	0.03378	.	.	ENSG00000075673	ENST00000218548;ENST00000381946	D;D	0.88586	-2.4;-2.4	6.03	-1.97	0.07503	ATPase, P-type cation-transporter, C-terminal (1);ATPase, P-type,  transmembrane domain (1);	1.216330	0.05322	N	0.526781	T	0.63331	0.2502	N	0.00788	-1.185	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.57335	-0.7829	10	0.14656	T	0.56	.	1.2614	0.02002	0.2377:0.1459:0.3545:0.2619	.	902;896	P54707-2;P54707	.;AT12A_HUMAN	S	902;896	ENSP00000218548:R902S;ENSP00000371372:R896S	ENSP00000218548:R902S	R	+	1	0	ATP12A	24181889	0.000000	0.05858	0.026000	0.17262	0.003000	0.03518	-0.317000	0.08060	-0.268000	0.09312	-1.104000	0.02111	CGC	.	.	alt		0.532	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676	
