#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_NTotCov	i_NVarCov	i_NVarRat	i_ORegAnno_bin	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
RBM44	375316	hgsc.bcm.edu	37	2	238726640	238726644	+	Frame_Shift_Del	DEL	ACATT	ACATT	-			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	ACATT	ACATT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr2:238726640_238726644delACATT	ENST00000409864.1	+	3	1335_1339	c.1081_1085delACATT	c.(1081-1086)acattafs	p.TL361fs	RBM44_ENST00000316997.4_Frame_Shift_Del_p.TL361fs|RBM44_ENST00000444524.2_Intron			Q6ZP01	RBM44_HUMAN	RNA binding motif protein 44	360						cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)	nucleotide binding (GO:0000166)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)			breast(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(7)|ovary(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	33		Breast(86;0.0042)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;3.74e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.3e-11)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000118)|Lung(119;0.0112)|LUSC - Lung squamous cell carcinoma(224;0.0266)		AAATCCTAGCACATTACCACAGGAT	0.332																																					p.360_362del		Atlas-Indel	.											.	RBM44	167	.	0			c.1080_1084del						PASS	.																																			SO:0001589	frameshift_variant	375316	exon3			.	AK097730	CCDS46554.1	2q37.3	2013-02-12			ENSG00000177483	ENSG00000177483		"""RNA binding motif (RRM) containing"""	24756	protein-coding gene	gene with protein product							Standard	NM_001080504		Approved	FLJ40411	uc002vxi.4	Q6ZP01	OTTHUMG00000152937	ENST00000409864.1:c.1081_1085delACATT	2.37:g.238726640_238726644delACATT	ENSP00000386727:p.Thr361fs	410.0	0.0	0		345.0	50.0	0.144928	NM_001080504	A0AUW3	Frame_Shift_Del	DEL	ENST00000409864.1	37	CCDS46554.1																																																																																			.	.	none		0.332	RBM44-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328733.2	NM_001080504	
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305783	39305784	+	In_Frame_Ins	INS	-	-	CTGGGGCGGCAGCAG			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr17:39305783_39305784insCTGGGGCGGCAGCAG	ENST00000343246.4	-	1	270_271	c.236_237insCTGCTGCCGCCCCAG	c.(235-237)tgc>tgCTGCTGCCGCCCCAGc	p.79_80insCCRPS		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].		C -> CCCRPS.		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)			tctggcagcagcaggggcggca	0.653																																					p.C79delinsCCCRPS		Atlas-Indel	.											KRTAP4-5,colon,carcinoma,-2,3	KRTAP4-5	34	3	0			c.237_238insCTGCTGCCGCCCCAG						PASS	.																																			SO:0001652	inframe_insertion	85289	exon1			.	AJ406937	CCDS32650.1	17q21.2	2013-06-25			ENSG00000198271	ENSG00000198271		"""Keratin associated proteins"""	18899	protein-coding gene	gene with protein product						11279113	Standard	NM_033188		Approved	KAP4.5	uc002hwb.3	Q9BYR2	OTTHUMG00000133638	ENST00000343246.4:c.236_237insCTGCTGCCGCCCCAG	17.37:g.39305783_39305784insCTGGGGCGGCAGCAG	ENSP00000340546:p.Cys79_Cys80insCysCysArgProSer	53.0	0.0	0		58.0	30.0	0.517241	NM_033188		In_Frame_Ins	INS	ENST00000343246.4	37	CCDS32650.1																																																																																			.	.	none		0.653	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1		
CHD8	57680	hgsc.bcm.edu	37	14	21884030	21884031	+	Frame_Shift_Ins	INS	-	-	T			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr14:21884030_21884031insT	ENST00000557364.1	-	6	2015_2016	c.1752_1753insA	c.(1750-1755)aaatatfs	p.Y585fs	CHD8_ENST00000399982.2_Frame_Shift_Ins_p.Y585fs|CHD8_ENST00000555962.1_Intron|CHD8_ENST00000430710.3_Frame_Shift_Ins_p.Y306fs			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	585					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|canonical Wnt signaling pathway (GO:0060070)|DNA duplex unwinding (GO:0032508)|in utero embryonic development (GO:0001701)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|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)|transcription, DNA-templated (GO:0006351)	MLL1 complex (GO:0071339)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(33)|ovary(6)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	85	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		TCCTCTGTATATTTTTTTCGCT	0.396																																					p.Y585fs		Pindel,Atlas-Indel	.											.	CHD8	339	.	0			c.1753_1754insA						PASS	.																																			SO:0001589	frameshift_variant	57680	exon5			.	AB046784	CCDS45081.1, CCDS53885.1	14q11.2	2008-02-05	2004-06-22	2004-06-23		ENSG00000100888			20153	protein-coding gene	gene with protein product		610528	"""helicase with SNF2 domain 1"""	HELSNF1		10997877	Standard	NM_020920		Approved	KIAA1564, DUPLIN	uc001war.2	Q9HCK8		ENST00000557364.1:c.1753dupA	14.37:g.21884037_21884037dupT	ENSP00000451601:p.Tyr585fs	0.0	0.0	.		22.0	22.0	1.000	NM_001170629	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Frame_Shift_Ins	INS	ENST00000557364.1	37	CCDS53885.1																																																																																			.	.	none		0.396	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920	
SMARCA2	6595	hgsc.bcm.edu	37	9	2039777	2039785	+	In_Frame_Del	DEL	CAGCAGCAG	CAGCAGCAG	-	rs376509101|rs145170448|rs62639301	byFrequency	TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	CAGCAGCAG	CAGCAGCAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr9:2039777_2039785delCAGCAGCAG	ENST00000382203.1	+	4	876_884	c.667_675delCAGCAGCAG	c.(667-675)cagcagcagdel	p.QQQ235del	RP11-264I13.2_ENST00000426860.1_RNA|SMARCA2_ENST00000382194.1_In_Frame_Del_p.QQQ235del|SMARCA2_ENST00000357248.2_In_Frame_Del_p.QQQ235del|SMARCA2_ENST00000349721.2_In_Frame_Del_p.QQQ235del|SMARCA2_ENST00000491574.1_3'UTR			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	235	Poly-Gln.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|chromatin remodeling (GO:0006338)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		gcagcagcaacagcagcagcagcagcagc	0.622																																					p.222_225del		Atlas-Indel	.											SMARCA2_ENST00000349721,NS,carcinoma,0,2	SMARCA2	313	2	0			c.666_674del						PASS	.																																			SO:0001651	inframe_deletion	6595	exon4			.	D26155	CCDS34977.1, CCDS34978.1, CCDS75807.1, CCDS75808.1	9p24.3	2008-11-11	2006-11-09		ENSG00000080503	ENSG00000080503			11098	protein-coding gene	gene with protein product		600014		SNF2L2		8012116	Standard	NM_003070		Approved	BAF190, hSNF2a, hBRM, Sth1p, SNF2LA, BRM, SNF2, SWI2	uc003zhc.3	P51531	OTTHUMG00000019445	ENST00000382203.1:c.667_675delCAGCAGCAG	9.37:g.2039786_2039794delCAGCAGCAG	ENSP00000371638:p.Gln235_Gln237del	100.0	0.0	0		93.0	13.0	0.139785	NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	In_Frame_Del	DEL	ENST00000382203.1	37	CCDS34977.1																																																																																			.	.	alt		0.622	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070	
RBM44	375316	hgsc.bcm.edu	37	2	238726642	238726647	+	In_Frame_Del	DEL	ATTACC	ATTACC	-	rs201162171		TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	ATTACC	ATTACC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr2:238726642_238726647delATTACC	ENST00000409864.1	+	3	1337_1342	c.1083_1088delATTACC	c.(1081-1089)acattacca>aca	p.LP362del	RBM44_ENST00000316997.4_In_Frame_Del_p.LP362del|RBM44_ENST00000444524.2_Intron			Q6ZP01	RBM44_HUMAN	RNA binding motif protein 44	361						cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)	nucleotide binding (GO:0000166)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)			breast(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(7)|ovary(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	33		Breast(86;0.0042)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;3.74e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.3e-11)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000118)|Lung(119;0.0112)|LUSC - Lung squamous cell carcinoma(224;0.0266)		ATCCTAGCACATTACCACAGGATAAA	0.33																																					p.361_363del		Pindel	.											.	RBM44	167	.	0			c.1082_1087del						PASS	.																																			SO:0001651	inframe_deletion	375316	exon3			.	AK097730	CCDS46554.1	2q37.3	2013-02-12			ENSG00000177483	ENSG00000177483		"""RNA binding motif (RRM) containing"""	24756	protein-coding gene	gene with protein product							Standard	NM_001080504		Approved	FLJ40411	uc002vxi.4	Q6ZP01	OTTHUMG00000152937	ENST00000409864.1:c.1083_1088delATTACC	2.37:g.238726642_238726647delATTACC	ENSP00000386727:p.Leu362_Pro363del	0.0	0.0	.		40.0	40.0	1.000	NM_001080504	A0AUW3	In_Frame_Del	DEL	ENST00000409864.1	37	CCDS46554.1																																																																																			.	.	none		0.330	RBM44-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328733.2	NM_001080504	
NSUN4	387338	hgsc.bcm.edu	37	1	46806573	46806654	+	Splice_Site	DEL	TCGATATAAGAAGAAATGGGTAAGGTCCGGCTGGGGGCGCAGGAGGGAAAAGTGAGGGTGGAAACTTCTCCAGTCTTTCCGT	TCGATATAAGAAGAAATGGGTAAGGTCCGGCTGGGGGCGCAGGAGGGAAAAGTGAGGGTGGAAACTTCTCCAGTCTTTCCGT	-	rs546723714|rs41293279		TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	TCGATATAAGAAGAAATGGGTAAGGTCCGGCTGGGGGCGCAGGAGGGAAAAGTGAGGGTGGAAACTTCTCCAGTCTTTCCGT	TCGATATAAGAAGAAATGGGTAAGGTCCGGCTGGGGGCGCAGGAGGGAAAAGTGAGGGTGGAAACTTCTCCAGTCTTTCCGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr1:46806573_46806654delTCGATATAAGAAGAAATGGGTAAGGTCCGGCTGGGGGCGCAGGAGGGAAAAGTGAGGGTGGAAACTTCTCCAGTCTTTCCGT	ENST00000474844.1	+	1	725_743	c.75_93delTCGATATAAGAAGAAATGGGTAAGGTCCGGCTGGGGGCGCAGGAGGGAAAAGTGAGGGTGGAAACTTCTCCAGTCTTTCCGT	c.(73-93)catcgatataagaagaaatgg>ca	p.HRYKKKW25fs	NSUN4_ENST00000536062.1_5'UTR|NSUN4_ENST00000537428.1_5'Flank	NM_199044.3	NP_950245.2	Q96CB9	NSUN4_HUMAN	NOP2/Sun domain family, member 4	25					rRNA methylation (GO:0031167)	mitochondrial large ribosomal subunit (GO:0005762)	methyltransferase activity (GO:0008168)|rRNA binding (GO:0019843)			endometrium(2)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)	8	Acute lymphoblastic leukemia(166;0.155)					CGCGGAGACATCGATATAAGAAGAAATGGGTAAGGTCCGGCTGGGGGCGCAGGAGGGAAAAGTGAGGGTGGAAACTTCTCCAGTCTTTCCGTTTCCCGGCCC	0.603											OREG0013456	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.25_31del		Pindel	.											.	NSUN4	26	.	0			c.74_93del						PASS	.																																			SO:0001630	splice_region_variant	387338	exon1			.	AK021577	CCDS534.1, CCDS57996.1	1p34	2012-02-24	2009-11-23		ENSG00000117481	ENSG00000117481		"""NOP2/Sun domain containing"""	31802	protein-coding gene	gene with protein product	"""sperm head and tail associated protein"""	615394	"""NOL1/NOP2/Sun domain family 4"", ""NOL1/NOP2/Sun domain family, member 4"""				Standard	NM_199044		Approved	MGC22960, SHTAP	uc001cpr.2	Q96CB9	OTTHUMG00000007808	ENST00000474844.1:c.93+1TCGATATAAGAAGAAATGGGTAAGGTCCGGCTGGGGGCGCAGGAGGGAAAAGTGAGGGTGGAAACTTCTCCAGTCTTTCCGT>-	1.37:g.46806573_46806654delTCGATATAAGAAGAAATGGGTAAGGTCCGGCTGGGGGCGCAGGAGGGAAAAGTGAGGGTGGAAACTTCTCCAGTCTTTCCGT		0.0	0.0	.	942	13.0	13.0	1.000	NM_199044	A8K6S6|B3KQ50|B4DHA4|Q5TDF7|Q96AN8|Q9HAJ8	Frame_Shift_Del	DEL	ENST00000474844.1	37	CCDS534.1																																																																																			.	.	none		0.603	NSUN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021427.1	NM_199044	Frame_Shift_Del
TEX2	55852	hgsc.bcm.edu	37	17	62290117	62290117	+	Silent	SNP	G	G	T			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr17:62290117G>T	ENST00000583097.1	-	2	1633	c.1461C>A	c.(1459-1461)ctC>ctA	p.L487L	TEX2_ENST00000258991.3_Silent_p.L487L|TEX2_ENST00000584379.1_Silent_p.L487L			Q8IWB9	TEX2_HUMAN	testis expressed 2	487					signal transduction (GO:0007165)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)				breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(8;1.33e-10)	READ - Rectum adenocarcinoma(1115;0.0689)		GGGGGAGGATGAGGTACACAT	0.512																																					p.L487L		Atlas-SNP	.											.	TEX2	89	.	0			c.C1461A						PASS	.						96.0	93.0	94.0					17																	62290117		2203	4300	6503	SO:0001819	synonymous_variant	55852	exon2			GAGGATGAGGTAC	AB051525	CCDS11658.1, CCDS74131.1	17q23.3	2007-03-13	2007-03-13			ENSG00000136478			30884	protein-coding gene	gene with protein product	"""transmembrane protein 96"""		"""testis expressed sequence 2"""			11214970	Standard	XM_005257507		Approved	HT008, TMEM96, KIAA1738	uc002jee.3	Q8IWB9		ENST00000583097.1:c.1461C>A	17.37:g.62290117G>T		119.0	0.0	0		146.0	44.0	0.30137	NM_018469	Q6AHZ5|Q8N3L0|Q9C0C5	Silent	SNP	ENST00000583097.1	37																																																																																				.	.	none		0.512	TEX2-003	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000443745.1	NM_018469	
PODNL1	79883	hgsc.bcm.edu	37	19	14043787	14043787	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr19:14043787G>A	ENST00000339560.5	-	8	1543	c.1270C>T	c.(1270-1272)Ccc>Tcc	p.P424S	PODNL1_ENST00000538517.2_Missense_Mutation_p.P333S|PODNL1_ENST00000254320.3_Missense_Mutation_p.P342S|PODNL1_ENST00000538371.2_Missense_Mutation_p.P422S	NM_024825.3	NP_079101.3	Q6PEZ8	PONL1_HUMAN	podocan-like 1	424	Leu-rich.					proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(19;5.26e-23)			AGGCCCATGGGCAGCCGGGTT	0.706																																					p.P424S		Atlas-SNP	.											.	PODNL1	27	.	0			c.C1270T						PASS	.						7.0	9.0	8.0					19																	14043787		2152	4212	6364	SO:0001583	missense	79883	exon8			CCATGGGCAGCCG	AK027100	CCDS12300.1, CCDS54225.1, CCDS54226.1	19p13.12	2008-02-05							26275	protein-coding gene	gene with protein product						12477932	Standard	NM_024825		Approved	FLJ23447, SLRR5B	uc010xnj.2	Q6PEZ8		ENST00000339560.5:c.1270C>T	19.37:g.14043787G>A	ENSP00000345175:p.Pro424Ser	19.0	0.0	0		39.0	14.0	0.358974	NM_024825	B7Z564|Q9H5G9	Missense_Mutation	SNP	ENST00000339560.5	37	CCDS12300.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.948115	0.73787	.	.	ENSG00000132000	ENST00000538371;ENST00000538517;ENST00000339560;ENST00000545071;ENST00000254320	T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16	4.89	4.89	0.63831	.	0.000000	0.48286	D	0.000183	D	0.87553	0.6206	M	0.79475	2.455	0.44555	D	0.997517	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;1.0;1.0	D	0.88485	0.3071	10	0.54805	T	0.06	.	14.9488	0.71054	0.0:0.0:1.0:0.0	.	422;342;333;424	F5H7F9;B7Z3M0;G3V1J6;Q6PEZ8	.;.;.;PONL1_HUMAN	S	422;333;424;274;342	ENSP00000442553:P422S;ENSP00000440080:P333S;ENSP00000345175:P424S;ENSP00000254320:P342S	ENSP00000254320:P342S	P	-	1	0	PODNL1	13904787	1.000000	0.71417	0.995000	0.50966	0.372000	0.29890	8.738000	0.91569	2.271000	0.75665	0.453000	0.30009	CCC	.	.	none		0.706	PODNL1-003	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457967.1	NM_024825	
AMOTL1	154810	hgsc.bcm.edu	37	11	94602519	94602519	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr11:94602519G>A	ENST00000433060.2	+	12	2786	c.2645G>A	c.(2644-2646)aGt>aAt	p.S882N	AMOTL1_ENST00000317829.8_Missense_Mutation_p.S832N|AMOTL1_ENST00000317837.9_Missense_Mutation_p.S469N	NM_130847.2	NP_570899.1	Q8IY63	AMOL1_HUMAN	angiomotin like 1	882					establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|hippo signaling (GO:0035329)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|tight junction (GO:0005923)	identical protein binding (GO:0042802)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	36		Acute lymphoblastic leukemia(157;2.38e-05)|all_hematologic(158;0.00824)				ACTGACAAGAGTGCCGAGCTC	0.652																																					p.S882N		Atlas-SNP	.											.	AMOTL1	95	.	0			c.G2645A						PASS	.						36.0	46.0	43.0					11																	94602519		2173	4278	6451	SO:0001583	missense	154810	exon12			ACAAGAGTGCCGA	AF453742	CCDS44712.1, CCDS73368.1	11q21	2008-07-18				ENSG00000166025			17811	protein-coding gene	gene with protein product	"""junction-enriched and associated protein"""	614657				11733531	Standard	XM_005273798		Approved	JEAP	uc001pfb.3	Q8IY63		ENST00000433060.2:c.2645G>A	11.37:g.94602519G>A	ENSP00000387739:p.Ser882Asn	103.0	0.0	0		87.0	25.0	0.287356	NM_130847	Q63HK7|Q8NDN0|Q8TEN8|Q8WXD1|Q96CM5	Missense_Mutation	SNP	ENST00000433060.2	37	CCDS44712.1	.	.	.	.	.	.	.	.	.	.	G	13.27	2.187928	0.38609	.	.	ENSG00000166025	ENST00000317829;ENST00000317837;ENST00000433060	T;T;T	0.19669	2.15;2.34;2.13	5.48	4.56	0.56223	.	0.181464	0.49916	D	0.000126	T	0.20618	0.0496	L	0.54323	1.7	0.21020	N	0.999801	B;B	0.11235	0.004;0.001	B;B	0.13407	0.009;0.004	T	0.16012	-1.0417	10	0.20046	T	0.44	-6.9791	12.7542	0.57325	0.0:0.1248:0.7455:0.1297	.	832;882	Q8IY63-2;Q8IY63	.;AMOL1_HUMAN	N	832;469;882	ENSP00000320968:S832N;ENSP00000323474:S469N;ENSP00000387739:S882N	ENSP00000320968:S832N	S	+	2	0	AMOTL1	94242167	1.000000	0.71417	0.483000	0.27378	0.247000	0.25773	6.087000	0.71362	1.299000	0.44798	0.561000	0.74099	AGT	.	.	none		0.652	AMOTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396474.3	NM_130847	
SLC7A2	6542	hgsc.bcm.edu	37	8	17409482	17409482	+	Missense_Mutation	SNP	G	G	A	rs139867348		TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr8:17409482G>A	ENST00000494857.1	+	7	1260	c.1042G>A	c.(1042-1044)Gcc>Acc	p.A348T	SLC7A2_ENST00000522656.1_Missense_Mutation_p.A348T|SLC7A2_ENST00000398090.3_Missense_Mutation_p.A388T|SLC7A2_ENST00000470360.1_Missense_Mutation_p.A388T|SLC7A2_ENST00000004531.10_Missense_Mutation_p.A388T	NM_001008539.3	NP_001008539.3	P52569	CTR2_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	348					amino acid transport (GO:0006865)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|macrophage activation (GO:0042116)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide production involved in inflammatory response (GO:0002537)|regulation of inflammatory response (GO:0050727)|regulation of macrophage activation (GO:0043030)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	basic amino acid transmembrane transporter activity (GO:0015174)|high-affinity arginine transmembrane transporter activity (GO:0005289)|L-lysine transmembrane transporter activity (GO:0015189)|L-ornithine transmembrane transporter activity (GO:0000064)	p.A348T(1)|p.A388T(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(4)|lung(8)|ovary(2)|skin(1)|stomach(1)	25				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	L-Lysine(DB00123)|L-Ornithine(DB00129)	TTCTCTCTGCGCCTTGTCAAC	0.478																																					p.A388T		Atlas-SNP	.											SLC7A2_ENST00000470360,NS,carcinoma,0,4	SLC7A2	157	4	2	Substitution - Missense(2)	endometrium(2)	c.G1162A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA	1,4405	2.1+/-5.4	0,1,2202	80.0	80.0	80.0		1042,1162,1162	5.3	1.0	8	dbSNP_134	80	0,8600		0,0,4300	no	missense,missense,missense	SLC7A2	NM_001008539.3,NM_001164771.1,NM_003046.5	58,58,58	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging	348/659,388/699,388/698	17409482	1,13005	2203	4300	6503	SO:0001583	missense	6542	exon6			CTCTGCGCCTTGT	D29990	CCDS6002.2, CCDS34852.1, CCDS55203.1	8p22	2013-05-22			ENSG00000003989	ENSG00000003989		"""Solute carriers"""	11060	protein-coding gene	gene with protein product		601872		ATRC2		8954799	Standard	NM_001164771		Approved	CAT-2, HCAT2	uc011kye.2	P52569	OTTHUMG00000130819	ENST00000494857.1:c.1042G>A	8.37:g.17409482G>A	ENSP00000419140:p.Ala348Thr	149.0	0.0	0		134.0	41.0	0.30597	NM_001164771	B7ZL54|O15291|O15292|Q14CQ6|Q6NSZ7|Q86TC6	Missense_Mutation	SNP	ENST00000494857.1	37	CCDS34852.1	.	.	.	.	.	.	.	.	.	.	G	31	5.064440	0.93898	2.27E-4	0.0	ENSG00000003989	ENST00000494857;ENST00000522656;ENST00000470360;ENST00000004531;ENST00000398090	D;D;D;D;D	0.90444	-2.67;-2.67;-2.67;-2.67;-2.67	5.26	5.26	0.73747	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	D	0.95465	0.8527	M	0.79258	2.445	0.80722	D	1	D;D;D	0.89917	0.992;1.0;1.0	P;D;D	0.91635	0.761;0.989;0.999	D	0.95700	0.8748	10	0.87932	D	0	.	19.2416	0.93887	0.0:0.0:1.0:0.0	.	388;388;348	P52569-3;P52569-2;P52569	.;.;CTR2_HUMAN	T	348;348;388;388;388	ENSP00000419140:A348T;ENSP00000430464:A348T;ENSP00000419873:A388T;ENSP00000004531:A388T;ENSP00000381164:A388T	ENSP00000004531:A388T	A	+	1	0	SLC7A2	17453860	1.000000	0.71417	0.994000	0.49952	0.926000	0.56050	9.869000	0.99810	2.621000	0.88768	0.655000	0.94253	GCC	G|1.000;A|0.000	0.000	weak		0.478	SLC7A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253367.3	NM_003046	
ZNF706	51123	hgsc.bcm.edu	37	8	102212299	102212299	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr8:102212299G>T	ENST00000520347.1	-	3	3118	c.162C>A	c.(160-162)ttC>ttA	p.F54L	ZNF706_ENST00000518336.1_Missense_Mutation_p.F54L|ZNF706_ENST00000519882.1_Missense_Mutation_p.F54L|ZNF706_ENST00000517844.1_Missense_Mutation_p.F54L|ZNF706_ENST00000520984.1_Missense_Mutation_p.F54L|ZNF706_ENST00000311212.4_Missense_Mutation_p.F54L|ZNF706_ENST00000521272.1_Missense_Mutation_p.F54L|ZNF706_ENST00000519744.1_Intron			Q9Y5V0	ZN706_HUMAN	zinc finger protein 706	54							metal ion binding (GO:0046872)			large_intestine(1)|ovary(2)	3	all_cancers(14;3.3e-07)|all_epithelial(15;3.47e-09)|Lung NSC(17;3.44e-05)|all_lung(17;0.000117)		Epithelial(11;8.57e-11)|all cancers(13;1.43e-08)|OV - Ovarian serous cystadenocarcinoma(57;1.43e-05)			AGTGCTGCTTGAAGGTCTTAG	0.368																																					p.F54L		Atlas-SNP	.											.	ZNF706	12	.	0			c.C162A						PASS	.						163.0	147.0	152.0					8																	102212299		2203	4300	6503	SO:0001583	missense	51123	exon4			CTGCTTGAAGGTC	AF125099	CCDS6291.1	8q22.3	2005-09-22				ENSG00000120963			24992	protein-coding gene	gene with protein product						11042152	Standard	NM_001042510		Approved	HSPC038	uc031tbv.1	Q9Y5V0		ENST00000520347.1:c.162C>A	8.37:g.102212299G>T	ENSP00000430823:p.Phe54Leu	130.0	0.0	0		110.0	5.0	0.0454545	NM_001042510	A8K362	Missense_Mutation	SNP	ENST00000520347.1	37	CCDS6291.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	26.3|26.3	4.728806|4.728806	0.89390|0.89390	.|.	.|.	ENSG00000120963|ENSG00000120963	ENST00000520984;ENST00000311212;ENST00000517844;ENST00000520347;ENST00000519882;ENST00000521272;ENST00000518336|ENST00000519103	.|.	.|.	.|.	5.87|5.87	5.0|5.0	0.66597|0.66597	Zinc finger, C2H2-like (1);|.	0.044791|.	0.85682|.	D|.	0.000000|.	T|.	0.70824|.	0.3268|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	P|.	0.40534|.	0.72|.	P|.	0.48704|.	0.587|.	T|.	0.70260|.	-0.4921|.	8|.	0.28530|.	T|.	0.3|.	.|.	15.045|15.045	0.71822|0.71822	0.0678:0.0:0.9321:0.0|0.0678:0.0:0.9321:0.0	.|.	54|.	Q9Y5V0|.	ZN706_HUMAN|.	L|X	54|35	.|.	ENSP00000311768:F54L|.	F|S	-|-	3|2	2|0	ZNF706|ZNF706	102281475|102281475	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	3.646000|3.646000	0.54396|0.54396	1.500000|1.500000	0.48636|0.48636	0.655000|0.655000	0.94253|0.94253	TTC|TCA	.	.	none		0.368	ZNF706-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380477.1	NM_016096	
ENC1	8507	hgsc.bcm.edu	37	5	73930903	73930903	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr5:73930903T>C	ENST00000302351.4	-	2	2538	c.1408A>G	c.(1408-1410)Aac>Gac	p.N470D	ENC1_ENST00000510316.1_Missense_Mutation_p.N397D|ENC1_ENST00000509284.1_5'Flank|ENC1_ENST00000537006.1_Missense_Mutation_p.N470D	NM_003633.3	NP_003624.1	O14682	ENC1_HUMAN	ectodermal-neural cortex 1 (with BTB domain)	470					multicellular organismal development (GO:0007275)|negative regulation of translation (GO:0017148)|nervous system development (GO:0007399)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	20		all_lung(232;0.0154)|Lung NSC(167;0.0331)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;1.45e-59)		GTCCACCTGTTTTCACACTGA	0.507																																					p.N470D		Atlas-SNP	.											.	ENC1	56	.	0			c.A1408G						PASS	.						50.0	56.0	54.0					5																	73930903		2203	4300	6503	SO:0001583	missense	8507	exon2			ACCTGTTTTCACA	AF059611	CCDS4021.1, CCDS58958.1	5q13	2013-01-30	2013-01-30		ENSG00000171617	ENSG00000171617		"""Kelch-like"", ""BTB/POZ domain containing"""	3345	protein-coding gene	gene with protein product	"""kelch-like family member 37"""	605173	"""ectodermal-neural cortex 1 (with BTB-like domain)"""	NRPB		9305847, 9566959	Standard	NM_003633		Approved	PIG10, ENC-1, TP53I10, KLHL37	uc003kdc.5	O14682	OTTHUMG00000102059	ENST00000302351.4:c.1408A>G	5.37:g.73930903T>C	ENSP00000306356:p.Asn470Asp	61.0	0.0	0		59.0	21.0	0.355932	NM_003633	B4DHJ1|E9PFU0|O75464|Q9UPG9	Missense_Mutation	SNP	ENST00000302351.4	37	CCDS4021.1	.	.	.	.	.	.	.	.	.	.	T	15.43	2.830609	0.50845	.	.	ENSG00000171617	ENST00000302351;ENST00000510316;ENST00000537006	T;T;T	0.66638	-0.22;-0.22;-0.22	5.89	5.89	0.94794	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.58850	0.2151	L	0.33668	1.02	0.80722	D	1	B	0.12013	0.005	B	0.11329	0.006	T	0.55159	-0.8184	10	0.54805	T	0.06	.	16.3123	0.82883	0.0:0.0:0.0:1.0	.	470	O14682	ENC1_HUMAN	D	470;397;470	ENSP00000306356:N470D;ENSP00000423804:N397D;ENSP00000446289:N470D	ENSP00000306356:N470D	N	-	1	0	ENC1	73966659	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.040000	0.89188	2.254000	0.74563	0.459000	0.35465	AAC	.	.	none		0.507	ENC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219862.2	NM_003633	
SLC4A1	6521	hgsc.bcm.edu	37	17	42336903	42336903	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr17:42336903T>C	ENST00000262418.6	-	8	811	c.656A>G	c.(655-657)aAg>aGg	p.K219R	AC003043.1_ENST00000597382.1_Intron|SLC4A1_ENST00000471005.1_5'Flank	NM_000342.3	NP_000333.1	P02730	B3AT_HUMAN	solute carrier family 4 (anion exchanger), member 1 (Diego blood group)	219	Globular.				anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|cellular ion homeostasis (GO:0006873)|chloride transport (GO:0006821)|ion transport (GO:0006811)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|cortical cytoskeleton (GO:0030863)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	anion transmembrane transporter activity (GO:0008509)|anion:anion antiporter activity (GO:0015301)|ankyrin binding (GO:0030506)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	40		Breast(137;0.014)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.115)		CGGGGGAATCTTTTCCAGAAT	0.597																																					p.K219R		Atlas-SNP	.											.	SLC4A1	104	.	0			c.A656G						PASS	.						95.0	88.0	90.0					17																	42336903		2203	4300	6503	SO:0001583	missense	6521	exon8			GGAATCTTTTCCA		CCDS11481.1	17q21.31	2014-07-19	2014-01-02		ENSG00000004939	ENSG00000004939		"""CD molecules"", ""Blood group antigens"", ""Solute carriers"""	11027	protein-coding gene	gene with protein product	"""Froese blood group"", ""Swann blood group"", ""Wright blood group"""	109270	"""Waldner blood group"", ""erythrocyte membrane protein band 3"", ""Diego blood group"", ""solute carrier family 4, anion exchanger, member 1 (erythrocyte membrane protein band 3, Diego blood group)"", ""solute carrier family 4 (anion exchanger), member 1"""	EPB3, AE1, DI, WD		8434259	Standard	NM_000342		Approved	RTA1A, CD233, FR, SW, WR	uc002igf.4	P02730	OTTHUMG00000156843	ENST00000262418.6:c.656A>G	17.37:g.42336903T>C	ENSP00000262418:p.Lys219Arg	74.0	0.0	0		95.0	4.0	0.0421053	NM_000342	G4V2I6|P78487|Q1ZZ45|Q4KKW9|Q4VB84|Q9UCY7|Q9UDJ1	Missense_Mutation	SNP	ENST00000262418.6	37	CCDS11481.1	.	.	.	.	.	.	.	.	.	.	t	6.620	0.482756	0.12581	.	.	ENSG00000004939	ENST00000262418	T	0.69435	-0.4	5.34	1.89	0.25635	Bicarbonate transporter, cytoplasmic (2);Phosphotransferase/anion transporter (1);	0.483231	0.23159	N	0.051267	T	0.61035	0.2315	M	0.65975	2.015	0.39099	D	0.961257	B;B	0.20671	0.008;0.047	B;B	0.28916	0.012;0.096	T	0.52147	-0.8614	10	0.31617	T	0.26	.	6.9872	0.24735	0.0:0.0962:0.1395:0.7643	.	219;219	E2RVJ0;P02730	.;B3AT_HUMAN	R	219	ENSP00000262418:K219R	ENSP00000262418:K219R	K	-	2	0	SLC4A1	39692429	1.000000	0.71417	0.817000	0.32601	0.144000	0.21451	2.477000	0.45180	0.048000	0.15891	-0.666000	0.03841	AAG	.	.	none		0.597	SLC4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346194.1	NM_000342	
ABI3BP	25890	hgsc.bcm.edu	37	3	100497214	100497214	+	Missense_Mutation	SNP	C	C	T	rs564595054	byFrequency	TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr3:100497214C>T	ENST00000284322.5	-	26	2223	c.2114G>A	c.(2113-2115)cGc>cAc	p.R705H	ABI3BP_ENST00000383691.4_Missense_Mutation_p.R659H|ABI3BP_ENST00000471714.1_Missense_Mutation_p.R1407H	NM_015429.3	NP_056244.2	Q7Z7G0	TARSH_HUMAN	ABI family, member 3 (NESH) binding protein	705	Pro-rich.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular space (GO:0005615)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)			central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	50						GGGTGGGCGGCGAGTCCCTGG	0.403													C|||	2	0.000399361	0.0008	0.0	5008	,	,		12839	0.0		0.0	False		,,,				2504	0.001				p.R705H		Atlas-SNP	.											ABI3BP_ENST00000383691,colon,carcinoma,-1,2	ABI3BP	305	2	0			c.G2114A						scavenged	.						95.0	94.0	94.0					3																	100497214		1866	4097	5963	SO:0001583	missense	25890	exon26			GGGCGGCGAGTCC	AB056106	CCDS46880.1	3q12.2	2013-02-11	2008-09-12		ENSG00000154175	ENSG00000154175		"""Fibronectin type III domain containing"""	17265	protein-coding gene	gene with protein product	"""target of Nesh-SH3"""	606279				11501947	Standard	NM_015429		Approved	NESHBP, DKFZP586L2024, TARSH	uc003dun.3	Q7Z7G0	OTTHUMG00000159094	ENST00000284322.5:c.2114G>A	3.37:g.100497214C>T	ENSP00000284322:p.Arg705His	57.0	0.0	0		52.0	3.0	0.0576923	NM_015429	B3KSL4|Q6ZW20|Q6ZW22|Q9C082|Q9UFI6	Missense_Mutation	SNP	ENST00000284322.5	37	CCDS46880.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.38|12.38	1.919848|1.919848	0.33908|0.33908	.|.	.|.	ENSG00000154175|ENSG00000154175	ENST00000495591|ENST00000471714;ENST00000284322;ENST00000383692;ENST00000429331;ENST00000383691;ENST00000486770	.|T;T;T	.|0.23147	.|2.28;1.96;1.92	5.79|5.79	1.33|1.33	0.21861|0.21861	.|.	.|0.493767	.|0.20611	.|N	.|0.088971	T|T	0.14270|0.14270	0.0345|0.0345	L|L	0.43152|0.43152	1.355|1.355	0.09310|0.09310	N|N	1|1	.|B;B;P;B	.|0.35456	.|0.037;0.027;0.502;0.01	.|B;B;B;B	.|0.22753	.|0.006;0.007;0.041;0.004	T|T	0.13575|0.13575	-1.0504|-1.0504	5|10	.|0.41790	.|T	.|0.15	-1.1719|-1.1719	4.1604|4.1604	0.10280|0.10280	0.0:0.3549:0.3169:0.3282|0.0:0.3549:0.3169:0.3282	.|.	.|659;705;1407;414	.|B4DSV9;Q7Z7G0;D3YTG3;D3YTD6	.|.;TARSH_HUMAN;.;.	T|H	761|1407;705;414;116;659;117	.|ENSP00000420524:R1407H;ENSP00000284322:R705H;ENSP00000373189:R659H	.|ENSP00000284322:R705H	A|R	-|-	1|2	0|0	ABI3BP|ABI3BP	101979904|101979904	0.123000|0.123000	0.22298|0.22298	0.538000|0.538000	0.28064|0.28064	0.889000|0.889000	0.51656|0.51656	-0.086000|-0.086000	0.11233|0.11233	0.812000|0.812000	0.34326|0.34326	0.462000|0.462000	0.41574|0.41574	GCC|CGC	.	.	none		0.403	ABI3BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353260.1		
CADM3	57863	hgsc.bcm.edu	37	1	159166170	159166170	+	Missense_Mutation	SNP	G	G	C			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr1:159166170G>C	ENST00000368125.4	+	6	865	c.708G>C	c.(706-708)atG>atC	p.M236I	CADM3_ENST00000368124.4_Missense_Mutation_p.M270I|CTA-134P22.2_ENST00000415675.2_RNA	NM_001127173.1	NP_001120645.1	Q8N126	CADM3_HUMAN	cell adhesion molecule 3	236	Ig-like C2-type 2.				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)					CAACTGCGATGATTAGGCCAG	0.517											OREG0013913	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.M270I		Atlas-SNP	.											.	CADM3	118	.	0			c.G810C						PASS	.						206.0	142.0	164.0					1																	159166170		2203	4300	6503	SO:0001583	missense	57863	exon7			TGCGATGATTAGG	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.708G>C	1.37:g.159166170G>C	ENSP00000357107:p.Met236Ile	109.0	0.0	0	1799	86.0	22.0	0.255814	NM_021189	Q8IZQ9|Q9NVJ5|Q9UJP1	Missense_Mutation	SNP	ENST00000368125.4	37	CCDS44251.1	.	.	.	.	.	.	.	.	.	.	G	11.19	1.565133	0.27915	.	.	ENSG00000162706	ENST00000368124;ENST00000368125;ENST00000416746	T;T;T	0.52295	2.56;2.56;0.67	4.78	4.78	0.61160	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.755390	0.12781	N	0.439679	T	0.19846	0.0477	N	0.11927	0.2	0.30714	N	0.748991	B;B;B	0.22211	0.001;0.066;0.011	B;B;B	0.32393	0.004;0.145;0.014	T	0.20207	-1.0282	10	0.48119	T	0.1	.	13.1756	0.59624	0.0:0.0:1.0:0.0	.	190;236;270	Q8N126-3;Q8N126;Q8N126-2	.;CADM3_HUMAN;.	I	270;236;190	ENSP00000357106:M270I;ENSP00000357107:M236I;ENSP00000387802:M190I	ENSP00000357106:M270I	M	+	3	0	CADM3	157432794	0.998000	0.40836	0.525000	0.27900	0.306000	0.27790	2.465000	0.45075	2.470000	0.83445	0.655000	0.94253	ATG	.	.	none		0.517	CADM3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090330.1	NM_021189	
CENPJ	55835	hgsc.bcm.edu	37	13	25479846	25479846	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr13:25479846A>G	ENST00000381884.4	-	7	2515	c.2330T>C	c.(2329-2331)gTg>gCg	p.V777A	CENPJ_ENST00000545981.1_Missense_Mutation_p.V777A	NM_018451.4	NP_060921.3	Q9HC77	CENPJ_HUMAN	centromere protein J	777					cell division (GO:0051301)|centriole replication (GO:0007099)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|microtubule polymerization (GO:0046785)|mitotic cell cycle (GO:0000278)|regulation of centriole replication (GO:0046599)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|gamma-tubulin small complex (GO:0008275)|microtubule (GO:0005874)	protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|tubulin binding (GO:0015631)			endometrium(5)|kidney(4)|large_intestine(14)|lung(13)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.00793)|Epithelial(112;0.0411)|OV - Ovarian serous cystadenocarcinoma(117;0.139)		GGGCTCAGACACTTTATGTTT	0.393																																					p.V777A		Atlas-SNP	.											.	CENPJ	116	.	0			c.T2330C						PASS	.						175.0	167.0	170.0					13																	25479846		2203	4300	6503	SO:0001583	missense	55835	exon7			TCAGACACTTTAT	AF139625	CCDS9310.1	13q12.12	2013-11-05			ENSG00000151849	ENSG00000151849			17272	protein-coding gene	gene with protein product	"""centrosomal P4.1-associated protein"""	609279	"""microcephaly, primary autosomal recessive 6"""	MCPH6		11003675, 22699936	Standard	NM_018451		Approved	CPAP, BM032, LAP, LIP1, Sas-4, SASS4, SCKL4	uc001upt.5	Q9HC77	OTTHUMG00000016595	ENST00000381884.4:c.2330T>C	13.37:g.25479846A>G	ENSP00000371308:p.Val777Ala	94.0	0.0	0		50.0	23.0	0.46	NM_018451	Q2KHM6|Q5JPD5|Q5T6R5|Q96KS5|Q9C067	Missense_Mutation	SNP	ENST00000381884.4	37	CCDS9310.1	.	.	.	.	.	.	.	.	.	.	A	0.113	-1.135609	0.01742	.	.	ENSG00000151849	ENST00000381884;ENST00000545981;ENST00000445729	T;T	0.35236	1.32;1.91	5.53	-11.1	0.00147	.	0.821166	0.10737	N	0.639900	T	0.12944	0.0314	L	0.35288	1.05	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33701	-0.9858	10	0.07482	T	0.82	.	0.2461	0.00199	0.2284:0.2381:0.2221:0.3114	.	777	Q9HC77	CENPJ_HUMAN	A	777	ENSP00000371308:V777A;ENSP00000441090:V777A	ENSP00000371308:V777A	V	-	2	0	CENPJ	24377846	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.506000	0.06359	-2.029000	0.00930	-2.802000	0.00113	GTG	.	.	none		0.393	CENPJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044209.1	NM_018451	
TENM2	57451	hgsc.bcm.edu	37	5	167645245	167645245	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr5:167645245C>T	ENST00000518659.1	+	23	4388	c.4349C>T	c.(4348-4350)gCg>gTg	p.A1450V	TENM2_ENST00000520394.1_Missense_Mutation_p.A1211V|TENM2_ENST00000545108.1_Missense_Mutation_p.A1449V|TENM2_ENST00000403607.2_Missense_Mutation_p.A1274V|TENM2_ENST00000519204.1_Missense_Mutation_p.A1329V	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	1450					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)										AGCATCATTGCGGGACGCCCC	0.502																																					p.A1441V		Atlas-SNP	.											ODZ2_ENST00000519204,NS,carcinoma,-1,3	.	.	3	0			c.C4322T						PASS	.						209.0	215.0	213.0					5																	167645245		2180	4278	6458	SO:0001583	missense	57451	exon23			TCATTGCGGGACG	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"""odz, odd Oz/ten-m homolog 2 (Drosophila)"""	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.4349C>T	5.37:g.167645245C>T	ENSP00000429430:p.Ala1450Val	110.0	0.0	0		102.0	28.0	0.27451	NM_001122679	Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	37		.	.	.	.	.	.	.	.	.	.	C	22.2	4.263444	0.80358	.	.	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	D;D;D;D;D	0.90563	-2.69;-2.69;-2.69;-2.69;-2.69	5.71	5.71	0.89125	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	D	0.95743	0.8615	M	0.80183	2.485	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.987	D	0.95724	0.8769	10	0.87932	D	0	.	19.8677	0.96824	0.0:1.0:0.0:0.0	.	1449;1450;1211	F5H2D1;Q9NT68;F8VNQ3	.;TEN2_HUMAN;.	V	1450;1449;1329;1211;1274	ENSP00000429430:A1450V;ENSP00000438635:A1449V;ENSP00000428964:A1329V;ENSP00000427874:A1211V;ENSP00000384905:A1274V	ENSP00000384905:A1274V	A	+	2	0	ODZ2	167577823	1.000000	0.71417	0.982000	0.44146	0.989000	0.77384	6.089000	0.71384	2.709000	0.92574	0.655000	0.94253	GCG	.	.	none		0.502	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679	
LRP8	7804	hgsc.bcm.edu	37	1	53755315	53755315	+	Missense_Mutation	SNP	G	G	C			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr1:53755315G>C	ENST00000306052.6	-	3	392	c.291C>G	c.(289-291)caC>caG	p.H97Q	LRP8_ENST00000371454.2_Missense_Mutation_p.H97Q|RP4-784A16.2_ENST00000421637.1_RNA|LRP8_ENST00000347547.2_Missense_Mutation_p.H97Q|LRP8_ENST00000354412.3_Missense_Mutation_p.H97Q|LRP8_ENST00000465675.1_5'UTR|RP4-784A16.3_ENST00000450469.1_RNA	NM_004631.4	NP_004622.2	Q14114	LRP8_HUMAN	low density lipoprotein receptor-related protein 8, apolipoprotein e receptor	97	LDL-receptor class A 2. {ECO:0000255|PROSITE-ProRule:PRU00124}.				ammon gyrus development (GO:0021541)|blood coagulation (GO:0007596)|cellular response to cholesterol (GO:0071397)|cellular response to growth factor stimulus (GO:0071363)|cytokine-mediated signaling pathway (GO:0019221)|endocytosis (GO:0006897)|layer formation in cerebral cortex (GO:0021819)|lipid metabolic process (GO:0006629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phototransduction, visible light (GO:0007603)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendrite development (GO:1900006)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|proteolysis (GO:0006508)|receptor-mediated endocytosis (GO:0006898)|reelin-mediated signaling pathway (GO:0038026)|regulation of synaptic transmission (GO:0050804)|response to drug (GO:0042493)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)	caveola (GO:0005901)|dendrite (GO:0030425)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|high-density lipoprotein particle binding (GO:0008035)|reelin receptor activity (GO:0038025)|transmembrane signaling receptor activity (GO:0004888)|very-low-density lipoprotein particle receptor activity (GO:0030229)			endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(2)|skin(1)	21						CGTGGATGCAGTGGCCGTTGT	0.612																																					p.H97Q		Atlas-SNP	.											.	LRP8	58	.	0			c.C291G						PASS	.						103.0	73.0	83.0					1																	53755315		2203	4300	6503	SO:0001583	missense	7804	exon3			GATGCAGTGGCCG	D50678	CCDS578.1, CCDS579.1, CCDS580.1, CCDS30720.1	1p32.3	2013-05-29			ENSG00000157193	ENSG00000157193		"""Low density lipoprotein receptors"""	6700	protein-coding gene	gene with protein product		602600				8626535, 9079678	Standard	NM_004631		Approved	APOER2, MCI1, LRP-8, HSZ75190	uc001cvi.2	Q14114	OTTHUMG00000008924	ENST00000306052.6:c.291C>G	1.37:g.53755315G>C	ENSP00000303634:p.His97Gln	35.0	0.0	0		40.0	9.0	0.225	NM_004631	B1AMT6|B1AMT7|B1AMT8|O14968|Q86V27|Q99876|Q9BR78	Missense_Mutation	SNP	ENST00000306052.6	37	CCDS578.1	.	.	.	.	.	.	.	.	.	.	G	15.42	2.827526	0.50845	.	.	ENSG00000157193	ENST00000306052;ENST00000371454;ENST00000354412;ENST00000347547	D;D;D;D	0.94897	-3.55;-3.55;-3.55;-3.55	5.33	5.33	0.75918	.	.	.	.	.	D	0.90232	0.6946	N	0.16266	0.395	0.22280	N	0.999238	B;B;B;B	0.34372	0.028;0.451;0.259;0.049	B;B;B;B	0.43701	0.034;0.225;0.428;0.055	T	0.79593	-0.1739	9	0.09843	T	0.71	.	11.9452	0.52924	0.0826:0.0:0.9174:0.0	.	97;97;97;97	Q14114-2;Q14114-4;Q14114-3;Q14114	.;.;.;LRP8_HUMAN	Q	97	ENSP00000303634:H97Q;ENSP00000360509:H97Q;ENSP00000346391:H97Q;ENSP00000334522:H97Q	ENSP00000303634:H97Q	H	-	3	2	LRP8	53527903	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	1.925000	0.40074	2.778000	0.95560	0.655000	0.94253	CAC	.	.	none		0.612	LRP8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000024699.1	NM_004631	
TBCE	6905	hgsc.bcm.edu	37	1	235590506	235590506	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr1:235590506T>C	ENST00000366601.3	+	6	688	c.512T>C	c.(511-513)gTg>gCg	p.V171A	TBCE_ENST00000472011.1_3'UTR|RP11-293G6__A.2_ENST00000430613.2_RNA|TBCE_ENST00000543662.1_Missense_Mutation_p.V171A|TBCE_ENST00000406207.1_Missense_Mutation_p.V171A			Q15813	TBCE_HUMAN	tubulin folding cofactor E	171					'de novo' posttranslational protein folding (GO:0051084)|adult locomotory behavior (GO:0008344)|cellular protein metabolic process (GO:0044267)|developmental growth (GO:0048589)|microtubule cytoskeleton organization (GO:0000226)|muscle atrophy (GO:0014889)|peripheral nervous system neuron axonogenesis (GO:0048936)|post-chaperonin tubulin folding pathway (GO:0007023)|post-embryonic development (GO:0009791)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	chaperone binding (GO:0051087)			NS(1)|endometrium(2)|large_intestine(3)|lung(6)|prostate(1)|skin(1)	14	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00192)|Prostate(94;0.0294)|all_epithelial(177;0.155)|Lung SC(1967;0.238)	OV - Ovarian serous cystadenocarcinoma(106;2.56e-05)			TGGGATGAAGTGATACACATT	0.363																																					p.V171A		Atlas-SNP	.											.	TBCE	40	.	0			c.T512C						PASS	.						140.0	133.0	135.0					1																	235590506		2203	4300	6503	SO:0001583	missense	6905	exon6			ATGAAGTGATACA	U61232	CCDS1605.1, CCDS73052.1	1q42.3	2014-02-04	2006-11-21		ENSG00000116957	ENSG00000116957			11582	protein-coding gene	gene with protein product		604934	"""tubulin-specific chaperone e"", ""Kenny-Caffey syndrome"", ""hypoparathyroidism, growth and mental retardation, and dysmorphism"""	KCS, HRD		8706133, 9806825, 12389028	Standard	NM_001079515		Approved	KCS1, pac2	uc001hxa.1	Q15813	OTTHUMG00000039987	ENST00000366601.3:c.512T>C	1.37:g.235590506T>C	ENSP00000355560:p.Val171Ala	69.0	0.0	0		80.0	28.0	0.35	NM_003193	A8K8C2|B7Z3P1	Missense_Mutation	SNP	ENST00000366601.3	37	CCDS1605.1	.	.	.	.	.	.	.	.	.	.	T	17.11	3.304959	0.60305	.	.	ENSG00000116957	ENST00000366601;ENST00000406207;ENST00000543662	T;T;T	0.39229	1.09;1.09;1.09	5.43	5.43	0.79202	.	0.061993	0.64402	D	0.000005	T	0.65450	0.2692	M	0.83483	2.645	0.58432	D	0.999999	D;D;D	0.69078	0.997;0.97;0.991	D;P;P	0.65773	0.938;0.539;0.905	T	0.71148	-0.4677	10	0.72032	D	0.01	-16.6054	14.0172	0.64531	0.0:0.0:0.0:1.0	.	171;171;171	B7Z3P1;A8K8C2;Q15813	.;.;TBCE_HUMAN	A	171	ENSP00000355560:V171A;ENSP00000384571:V171A;ENSP00000439170:V171A	ENSP00000355560:V171A	V	+	2	0	TBCE	233657129	0.999000	0.42202	0.949000	0.38748	0.473000	0.32948	4.558000	0.60789	2.189000	0.69895	0.443000	0.29094	GTG	.	.	none		0.363	TBCE-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000096458.3	NM_003193	
CHTF18	63922	hgsc.bcm.edu	37	16	841239	841239	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr16:841239C>T	ENST00000262315.9	+	8	1036	c.973C>T	c.(973-975)Ccc>Tcc	p.P325S	CHTF18_ENST00000491530.1_3'UTR|CHTF18_ENST00000455171.2_Missense_Mutation_p.P353S|RPUSD1_ENST00000007264.2_5'Flank|CHTF18_ENST00000317063.6_Missense_Mutation_p.P520S|RPUSD1_ENST00000567114.1_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)	325					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)				TTCCCGGAAGCCCAGGCCCAG	0.647																																					p.P325S		Atlas-SNP	.											.	CHTF18	52	.	0			c.C973T						PASS	.						19.0	24.0	22.0					16																	841239		2062	4183	6245	SO:0001583	missense	63922	exon8			CGGAAGCCCAGGC	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.973C>T	16.37:g.841239C>T	ENSP00000262315:p.Pro325Ser	31.0	0.0	0		55.0	29.0	0.527273	NM_022092	B7ZBA2|D3DU68|Q7Z6Y4|Q7Z6Y6|Q9BR83|Q9BRG5|Q9H7K3	Missense_Mutation	SNP	ENST00000262315.9	37	CCDS45371.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.52|10.52	1.373536|1.373536	0.24857|0.24857	.|.	.|.	ENSG00000127586|ENSG00000127586	ENST00000426047|ENST00000317063;ENST00000455171;ENST00000262315	.|T;T;T	.|0.10573	.|2.86;2.9;2.88	4.85|4.85	0.255|0.255	0.15561|0.15561	.|.	.|0.459860	.|0.21606	.|N	.|0.071879	T|T	0.09730|0.09730	0.0239|0.0239	M|M	0.74647|0.74647	2.275|2.275	0.35423|0.35423	D|D	0.79339|0.79339	.|B;B	.|0.32467	.|0.372;0.139	.|B;B	.|0.29942	.|0.109;0.017	T|T	0.13282|0.13282	-1.0515|-1.0515	5|10	.|0.25106	.|T	.|0.35	-14.7794|-14.7794	2.5691|2.5691	0.04790|0.04790	0.1507:0.5277:0.1468:0.1748|0.1507:0.5277:0.1468:0.1748	.|.	.|353;325	.|Q8WVB6-2;Q8WVB6	.|.;CTF18_HUMAN	V|S	220|520;353;325	.|ENSP00000313029:P520S;ENSP00000406252:P353S;ENSP00000262315:P325S	.|ENSP00000262315:P325S	A|P	+|+	2|1	0|0	CHTF18|CHTF18	781240|781240	0.863000|0.863000	0.29885|0.29885	0.995000|0.995000	0.50966|0.50966	0.896000|0.896000	0.52359|0.52359	0.552000|0.552000	0.23376|0.23376	0.190000|0.190000	0.20209|0.20209	0.579000|0.579000	0.79373|0.79373	GCC|CCC	.	.	none		0.647	CHTF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109061.3	NM_022092	
DYRK1A	1859	hgsc.bcm.edu	37	21	38862627	38862627	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr21:38862627C>T	ENST00000398960.2	+	6	890	c.815C>T	c.(814-816)gCa>gTa	p.A272V	DYRK1A_ENST00000338785.3_Missense_Mutation_p.A272V|DYRK1A_ENST00000321219.8_Missense_Mutation_p.A272V|DYRK1A_ENST00000451934.1_Missense_Mutation_p.A272V|DYRK1A_ENST00000339659.4_Missense_Mutation_p.A263V|DYRK1A_ENST00000455387.2_Missense_Mutation_p.A44V|DYRK1A_ENST00000398956.2_Missense_Mutation_p.A272V	NM_001396.3|NM_130438.2	NP_001387.2|NP_569122.1	Q13627	DYR1A_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A	272	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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						ATGTGCACTGCACTGCTTTTC	0.428																																					p.A272V	Melanoma(114;464 1602 31203 43785 45765)	Atlas-SNP	.											.	DYRK1A	85	.	0			c.C815T						PASS	.						107.0	97.0	100.0					21																	38862627		2203	4300	6503	SO:0001583	missense	1859	exon6			GCACTGCACTGCT	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.815C>T	21.37:g.38862627C>T	ENSP00000381932:p.Ala272Val	148.0	0.0	0		142.0	36.0	0.253521	NM_001396	O60769|Q92582|Q92810|Q9UNM5	Missense_Mutation	SNP	ENST00000398960.2	37	CCDS42925.1	.	.	.	.	.	.	.	.	.	.	C	36	5.715261	0.96830	.	.	ENSG00000157540	ENST00000338785;ENST00000339659;ENST00000321219;ENST00000451934;ENST00000398960;ENST00000398956;ENST00000455387	T;T;T;T;T;T;T	0.31510	1.49;1.49;1.49;1.49;1.49;1.49;1.49	5.91	5.91	0.95273	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.56558	0.1993	M	0.64997	1.995	0.80722	D	1	D;D;D;D;D	0.89917	0.988;0.988;1.0;1.0;0.988	P;P;D;D;P	0.79108	0.683;0.683;0.992;0.968;0.761	T	0.55289	-0.8164	10	0.87932	D	0	.	20.2989	0.98608	0.0:1.0:0.0:0.0	.	272;272;272;263;272	Q13627-3;Q13627-4;Q13627;Q13627-2;Q13627-5	.;.;DYR1A_HUMAN;.;.	V	272;263;272;272;272;272;44	ENSP00000342690:A272V;ENSP00000340373:A263V;ENSP00000319032:A272V;ENSP00000416089:A272V;ENSP00000381932:A272V;ENSP00000381929:A272V;ENSP00000407854:A44V	ENSP00000319032:A272V	A	+	2	0	DYRK1A	37784497	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.741000	0.84997	2.794000	0.96219	0.573000	0.79308	GCA	.	.	none		0.428	DYRK1A-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194804.1	NM_001396	
POU2F2	5452	hgsc.bcm.edu	37	19	42600030	42600030	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr19:42600030T>C	ENST00000526816.2	-	9	730	c.715A>G	c.(715-717)Acg>Gcg	p.T239A	POU2F2_ENST00000389341.5_Missense_Mutation_p.T223A|POU2F2_ENST00000560558.1_Missense_Mutation_p.T184A|POU2F2_ENST00000560398.1_Missense_Mutation_p.T245A|POU2F2_ENST00000529952.1_Missense_Mutation_p.T239A|POU2F2_ENST00000342301.4_Missense_Mutation_p.T239A|POU2F2_ENST00000529067.1_Missense_Mutation_p.T223A|POU2F2_ENST00000533720.1_Missense_Mutation_p.T223A			P09086	PO2F2_HUMAN	POU class 2 homeobox 2	239	POU-specific. {ECO:0000255|PROSITE- ProRule:PRU00530}.				cell maturation (GO:0048469)|humoral immune response (GO:0006959)|immunoglobulin secretion involved in immune response (GO:0002380)|mature B cell differentiation (GO:0002335)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(5)|lung(4)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Prostate(69;0.059)			Dolutegravir(DB08930)	GAAATGGTCGTCTGGCTGAAG	0.627																																					p.T239A		Atlas-SNP	.											POU2F2_ENST00000292077,NS,lymphoid_neoplasm,0,8	POU2F2	106	8	0			c.A715G						PASS	.						119.0	118.0	118.0					19																	42600030		2203	4300	6503	SO:0001583	missense	5452	exon9			TGGTCGTCTGGCT		CCDS33035.1, CCDS56094.1, CCDS56095.1, CCDS58665.1	19q13.2	2011-06-20	2007-07-13					"""Homeoboxes / POU class"""	9213	protein-coding gene	gene with protein product		164176	"""POU domain class 2, transcription factor 2"""	OTF2			Standard	NM_001207026		Approved	OCT2	uc002osp.3	P09086		ENST00000526816.2:c.715A>G	19.37:g.42600030T>C	ENSP00000431603:p.Thr239Ala	73.0	0.0	0		94.0	29.0	0.308511	NM_001207025	Q16648|Q7M4M8|Q9BRS4	Missense_Mutation	SNP	ENST00000526816.2	37	CCDS56095.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.957613	0.73902	.	.	ENSG00000028277	ENST00000389341;ENST00000342301;ENST00000292077;ENST00000533720;ENST00000526816;ENST00000529067;ENST00000529952	D;D;D;D;D	0.85861	-2.04;-2.04;-2.04;-2.04;-2.04	4.38	2.18	0.27775	POU-specific (4);Lambda repressor-like, DNA-binding (2);POU (1);	0.247967	0.39834	N	0.001250	D	0.91492	0.7314	M	0.88310	2.945	0.52501	D	0.999956	D;P;B	0.76494	0.999;0.953;0.262	D;D;B	0.79784	0.993;0.938;0.37	D	0.89325	0.3643	10	0.87932	D	0	.	6.8485	0.24003	0.15:0.0:0.1568:0.6932	.	223;239;223	P09086-4;P09086;P09086-3	.;PO2F2_HUMAN;.	A	223;239;239;223;238;223;239	ENSP00000373992:T223A;ENSP00000339369:T239A;ENSP00000437221:T223A;ENSP00000437224:T223A;ENSP00000436988:T239A	ENSP00000292077:T239A	T	-	1	0	POU2F2	47291870	1.000000	0.71417	0.972000	0.41901	0.994000	0.84299	7.819000	0.86621	0.269000	0.21961	0.454000	0.30748	ACG	.	.	none		0.627	POU2F2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387329.3		
TEK	7010	hgsc.bcm.edu	37	9	27204915	27204915	+	Missense_Mutation	SNP	C	C	T	rs561507573		TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr9:27204915C>T	ENST00000380036.4	+	14	2658	c.2216C>T	c.(2215-2217)gCg>gTg	p.A739V	TEK_ENST00000406359.4_Missense_Mutation_p.A696V|TEK_ENST00000519097.1_Missense_Mutation_p.A592V	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	739					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|definitive hemopoiesis (GO:0060216)|endochondral ossification (GO:0001958)|endothelial cell proliferation (GO:0001935)|glomerulus vasculature development (GO:0072012)|heart development (GO:0007507)|heart trabecula formation (GO:0060347)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of inflammatory response (GO:0050728)|organ regeneration (GO:0031100)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of endothelial cell apoptotic process (GO:2000351)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of vascular permeability (GO:0043114)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)|Tie signaling pathway (GO:0048014)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(3)|kidney(1)|lung(2)|ovary(3)|skin(3)	15		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)	Ponatinib(DB08901)|Regorafenib(DB08896)|Vandetanib(DB05294)	ACAGCACCAGCGGACCTCGGA	0.507													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18299	0.0		0.0	False		,,,				2504	0.0				p.A739V		Atlas-SNP	.											.	TEK	250	.	0			c.C2216T						PASS	.						131.0	120.0	124.0					9																	27204915		2203	4300	6503	SO:0001583	missense	7010	exon14			CACCAGCGGACCT	L06139	CCDS6519.1, CCDS75825.1	9p21	2013-02-11	2008-07-31		ENSG00000120156	ENSG00000120156		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	11724	protein-coding gene	gene with protein product		600221	"""venous malformations, multiple cutaneous and mucosal"""	VMCM		1312667, 7833915	Standard	XM_005251561		Approved	TIE2, TIE-2, VMCM1, CD202b	uc003zqi.4	Q02763	OTTHUMG00000019712	ENST00000380036.4:c.2216C>T	9.37:g.27204915C>T	ENSP00000369375:p.Ala739Val	65.0	0.0	0		57.0	17.0	0.298246	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Missense_Mutation	SNP	ENST00000380036.4	37	CCDS6519.1	.	.	.	.	.	.	.	.	.	.	C	10.56	1.385178	0.25031	.	.	ENSG00000120156	ENST00000519097;ENST00000380036;ENST00000406359	T;T;T	0.74632	-0.83;-0.85;-0.86	6.02	0.534	0.17127	Fibronectin, type III (1);	1.391580	0.04700	N	0.415659	T	0.56046	0.1959	N	0.24115	0.695	0.09310	N	1	B;B;B;B	0.24426	0.0;0.054;0.0;0.103	B;B;B;B	0.20577	0.0;0.03;0.0;0.01	T	0.38265	-0.9669	10	0.27082	T	0.32	.	1.3342	0.02141	0.4257:0.2524:0.1303:0.1916	.	592;772;696;739	E7EWI2;Q59HG2;B4DHD3;Q02763	.;.;.;TIE2_HUMAN	V	592;739;696	ENSP00000430686:A592V;ENSP00000369375:A739V;ENSP00000383977:A696V	ENSP00000369375:A739V	A	+	2	0	TEK	27194915	0.000000	0.05858	0.000000	0.03702	0.057000	0.15508	-0.246000	0.08878	0.351000	0.24027	-0.311000	0.09066	GCG	.	.	none		0.507	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3		
HDAC2	3066	hgsc.bcm.edu	37	6	114262912	114262912	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr6:114262912T>G	ENST00000519065.1	-	13	1772	c.1396A>C	c.(1396-1398)Aaa>Caa	p.K466Q	HDAC2_ENST00000368632.2_Missense_Mutation_p.K436Q|HDAC2_ENST00000398283.2_Missense_Mutation_p.K560Q|HDAC2_ENST00000519108.1_Missense_Mutation_p.K436Q			Q92769	HDAC2_HUMAN	histone deacetylase 2	466					ATP-dependent chromatin remodeling (GO:0043044)|blood coagulation (GO:0007596)|cardiac muscle cell development (GO:0055013)|chromatin remodeling (GO:0006338)|circadian regulation of gene expression (GO:0032922)|dendrite development (GO:0016358)|embryonic digit morphogenesis (GO:0042733)|epidermal cell differentiation (GO:0009913)|eyelid development in camera-type eye (GO:0061029)|fungiform papilla formation (GO:0061198)|hair follicle placode formation (GO:0060789)|hippocampus development (GO:0021766)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|maintenance of chromatin silencing (GO:0006344)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of cell cycle (GO:0045786)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of neuron projection development (GO:0010977)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell proliferation (GO:0008284)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of proteolysis (GO:0045862)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of protein deacetylation (GO:0090311)|regulation of protein kinase B signaling (GO:0051896)|regulation of sarcomere organization (GO:0060297)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|heterochromatin (GO:0000792)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)|replication fork (GO:0005657)|Sin3 complex (GO:0016580)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|deacetylase activity (GO:0019213)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|poly(A) RNA binding (GO:0044822)|protein deacetylase activity (GO:0033558)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			biliary_tract(1)|central_nervous_system(5)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)|skin(2)	27		all_cancers(87;0.000629)|all_epithelial(87;0.00274)|Colorectal(196;0.0317)|all_lung(197;0.24)		all cancers(137;0.00318)|OV - Ovarian serous cystadenocarcinoma(136;0.00569)|Epithelial(106;0.0112)|GBM - Glioblastoma multiforme(226;0.0832)	Aminophylline(DB01223)|Lovastatin(DB00227)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Valproic Acid(DB00313)|Vorinostat(DB02546)	TCCTTGGATTTATCTTCTTCC	0.234																																					p.K466Q		Atlas-SNP	.											.	HDAC2	102	.	0			c.A1396C						PASS	.						64.0	62.0	63.0					6																	114262912		1805	4060	5865	SO:0001583	missense	3066	exon13			TGGATTTATCTTC	U31814	CCDS43493.1, CCDS43493.2	6q21	2008-08-29			ENSG00000196591	ENSG00000196591			4853	protein-coding gene	gene with protein product		605164				9782097	Standard	NM_001527		Approved	RPD3, YAF1	uc003pwd.2	Q92769	OTTHUMG00000015411	ENST00000519065.1:c.1396A>C	6.37:g.114262912T>G	ENSP00000430432:p.Lys466Gln	95.0	0.0	0		76.0	20.0	0.263158	NM_001527	B3KRS5|B4DL58|E1P561|Q5SRI8|Q5SZ86|Q8NEH4	Missense_Mutation	SNP	ENST00000519065.1	37	CCDS43493.2	.	.	.	.	.	.	.	.	.	.	T	17.37	3.372576	0.61624	.	.	ENSG00000196591	ENST00000519065;ENST00000398283;ENST00000519108;ENST00000368632	T;T;T;T	0.75260	-0.87;-0.92;-0.87;-0.87	5.76	5.76	0.90799	.	0.075114	0.56097	D	0.000037	T	0.62575	0.2439	L	0.40543	1.245	0.48696	D	0.999691	D;B	0.57899	0.981;0.137	P;B	0.49637	0.617;0.019	T	0.61540	-0.7042	10	0.21014	T	0.42	-36.1428	14.6077	0.68493	0.0:0.0:0.0:1.0	.	436;466	B3KRS5;Q92769	.;HDAC2_HUMAN	Q	466;560;436;436	ENSP00000430432:K466Q;ENSP00000381331:K560Q;ENSP00000430008:K436Q;ENSP00000357621:K436Q	ENSP00000357621:K436Q	K	-	1	0	HDAC2	114369605	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	4.297000	0.59061	2.323000	0.78572	0.528000	0.53228	AAA	.	.	none		0.234	HDAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041909.2		
CARS2	79587	hgsc.bcm.edu	37	13	111340323	111340323	+	Missense_Mutation	SNP	C	C	A			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr13:111340323C>A	ENST00000257347.4	-	4	499	c.436G>T	c.(436-438)Gac>Tac	p.D146Y	CARS2_ENST00000535398.1_5'UTR	NM_024537.2	NP_078813.1	Q9HA77	SYCM_HUMAN	cysteinyl-tRNA synthetase 2, mitochondrial (putative)	146					cysteinyl-tRNA aminoacylation (GO:0006423)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|cysteine-tRNA ligase activity (GO:0004817)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|prostate(4)|skin(1)	13	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.163)		L-Cysteine(DB00151)	TGCTTGAAGTCTTCCTCATAA	0.532																																					p.D146Y		Atlas-SNP	.											.	CARS2	37	.	0			c.G436T						PASS	.						79.0	69.0	72.0					13																	111340323		2203	4300	6503	SO:0001583	missense	79587	exon4			TGAAGTCTTCCTC	BC007220	CCDS9514.1	13q34	2011-07-01	2007-02-22		ENSG00000134905	ENSG00000134905	6.1.1.16	"""Aminoacyl tRNA synthetases / Class I"""	25695	protein-coding gene	gene with protein product	"""cysteine tRNA ligase 2, mitochondrial (putative)"""	612800				15779907	Standard	NM_024537		Approved	FLJ12118	uc001vrd.2	Q9HA77	OTTHUMG00000017347	ENST00000257347.4:c.436G>T	13.37:g.111340323C>A	ENSP00000257347:p.Asp146Tyr	90.0	0.0	0		55.0	16.0	0.290909	NM_024537	Q8NI84|Q96IV4	Missense_Mutation	SNP	ENST00000257347.4	37	CCDS9514.1	.	.	.	.	.	.	.	.	.	.	C	12.70	2.015505	0.35511	.	.	ENSG00000134905	ENST00000257347;ENST00000542709	T	0.31247	1.5	4.71	3.86	0.44501	Rossmann-like alpha/beta/alpha sandwich fold (1);	0.322809	0.31834	N	0.006995	T	0.44808	0.1311	L	0.51914	1.62	0.39637	D	0.970261	D	0.55385	0.971	P	0.62491	0.903	T	0.41342	-0.9514	10	0.49607	T	0.09	-3.3731	12.2493	0.54589	0.0:0.9143:0.0:0.0857	.	146	Q9HA77	SYCM_HUMAN	Y	146;137	ENSP00000257347:D146Y	ENSP00000257347:D146Y	D	-	1	0	CARS2	110138324	1.000000	0.71417	0.749000	0.31150	0.586000	0.36452	4.335000	0.59298	1.086000	0.41228	0.557000	0.71058	GAC	.	.	none		0.532	CARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045772.3	NM_024537	
RAP1GAP	5909	hgsc.bcm.edu	37	1	21928279	21928279	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr1:21928279G>A	ENST00000374765.4	-	20	1750	c.1550C>T	c.(1549-1551)cCg>cTg	p.P517L	RAP1GAP_ENST00000290101.4_Missense_Mutation_p.P581L|RAP1GAP_ENST00000374761.2_Missense_Mutation_p.P548L|RAP1GAP_ENST00000374763.2_Missense_Mutation_p.P602L|RAP1GAP_ENST00000542643.2_Missense_Mutation_p.P543L	NM_002885.2	NP_002876.2	P47736	RPGP1_HUMAN	RAP1 GTPase activating protein	517					GTP catabolic process (GO:0006184)|positive regulation of Rap GTPase activity (GO:0032854)|regulation of Ras GTPase activity (GO:0032318)|signal transduction (GO:0007165)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|protein homodimerization activity (GO:0042803)|Rap GTPase activator activity (GO:0046582)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	17		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.000861)|all_lung(284;0.000901)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;2.3e-26)|COAD - Colon adenocarcinoma(152;1.59e-05)|GBM - Glioblastoma multiforme(114;2.7e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000354)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00862)|READ - Rectum adenocarcinoma(331;0.0625)|Lung(427;0.146)		CTGACCAGCCGGAGGGCTCTC	0.672																																					p.P581L		Atlas-SNP	.											.	RAP1GAP	119	.	0			c.C1742T						PASS	.						45.0	43.0	43.0					1																	21928279		2203	4300	6503	SO:0001583	missense	5909	exon20			CCAGCCGGAGGGC	BC054490	CCDS218.1, CCDS53276.1, CCDS53277.1	1p36.1-p35	2009-09-14	2006-04-12	2006-04-12	ENSG00000076864	ENSG00000076864			9858	protein-coding gene	gene with protein product		600278	"""RAP1, GTPase activating protein 1"""	RAP1GA1		1904317	Standard	NM_001145657		Approved	KIAA0474, RAP1GAP1, RAP1GAPII	uc001bew.3	P47736	OTTHUMG00000007513	ENST00000374765.4:c.1550C>T	1.37:g.21928279G>A	ENSP00000363897:p.Pro517Leu	31.0	0.0	0		28.0	6.0	0.214286	NM_001145658	J3QSS6|O75062|Q5T3S9|Q5T3T4|Q7Z5S8|Q9UQ51	Missense_Mutation	SNP	ENST00000374765.4	37	CCDS218.1	.	.	.	.	.	.	.	.	.	.	g	22.3	4.275461	0.80580	.	.	ENSG00000076864	ENST00000290101;ENST00000374761;ENST00000542643;ENST00000374765;ENST00000374763;ENST00000374758	D;D;D;D	0.89050	-2.43;-2.43;-2.46;-2.42	4.72	4.72	0.59763	.	0.411353	0.23279	N	0.049923	D	0.84875	0.5569	L	0.39633	1.23	0.52501	D	0.999951	D;P;B;P	0.54397	0.966;0.913;0.041;0.913	B;B;B;B	0.43018	0.405;0.121;0.006;0.121	D	0.84295	0.0502	10	0.32370	T	0.25	-7.3773	15.211	0.73225	0.0:0.0:1.0:0.0	.	543;517;547;517	P47736-2;P47736;P47736-3;Q7Z5S8	.;RPGP1_HUMAN;.;.	L	581;548;543;517;547;602	ENSP00000290101:P581L;ENSP00000363893:P548L;ENSP00000441661:P543L;ENSP00000363897:P517L	ENSP00000290101:P581L	P	-	2	0	RAP1GAP	21800866	1.000000	0.71417	0.984000	0.44739	0.994000	0.84299	7.049000	0.76613	2.452000	0.82932	0.556000	0.70494	CCG	.	.	none		0.672	RAP1GAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019759.2	NM_002885	
COL21A1	81578	hgsc.bcm.edu	37	6	56006741	56006741	+	Missense_Mutation	SNP	G	G	T	rs575546564		TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr6:56006741G>T	ENST00000244728.5	-	11	1872	c.1475C>A	c.(1474-1476)tCt>tAt	p.S492Y	COL21A1_ENST00000535941.1_Missense_Mutation_p.S492Y|COL21A1_ENST00000370819.1_Missense_Mutation_p.S489Y	NM_030820.3	NP_110447.2	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1	492	Collagen-like 1.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(1)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|prostate(2)	41	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)			TATTCCTGGAGATCCTGGAAC	0.274																																					p.S492Y		Atlas-SNP	.											.	COL21A1	201	.	0			c.C1475A						PASS	.						46.0	45.0	46.0					6																	56006741		911	2069	2980	SO:0001583	missense	81578	exon11			CCTGGAGATCCTG	AF330693	CCDS55025.1	6p12.3-p11.2	2013-01-16			ENSG00000124749	ENSG00000124749		"""Collagens"""	17025	protein-coding gene	gene with protein product		610002				11566190	Standard	XR_241922		Approved		uc003pcs.3	Q96P44	OTTHUMG00000014907	ENST00000244728.5:c.1475C>A	6.37:g.56006741G>T	ENSP00000244728:p.Ser492Tyr	155.0	0.0	0		125.0	27.0	0.216	NM_030820	A6NIX5|B2R8J9|Q49A51|Q71RF4|Q8WXV8|Q9H0V3	Missense_Mutation	SNP	ENST00000244728.5	37	CCDS55025.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.876|8.876	0.950487|0.950487	0.18431|0.18431	.|.	.|.	ENSG00000124749|ENSG00000124749	ENST00000456983|ENST00000244728;ENST00000370819;ENST00000535941;ENST00000370811	.|D;D;D	.|0.92858	.|-3.12;-3.12;-3.12	5.27|5.27	4.39|4.39	0.52855|0.52855	.|.	.|0.116551	.|0.37715	.|N	.|0.001980	D|D	0.91192|0.91192	0.7225|0.7225	M|M	0.64170|0.64170	1.965|1.965	0.58432|0.58432	D|D	0.999996|0.999996	.|P;D	.|0.57257	.|0.955;0.979	.|P;P	.|0.55222	.|0.566;0.771	D|D	0.91203|0.91203	0.4993|0.4993	5|10	.|0.59425	.|D	.|0.04	.|.	9.1386|9.1386	0.36890|0.36890	0.0978:0.0:0.9022:0.0|0.0978:0.0:0.9022:0.0	.|.	.|489;492	.|Q96P44-3;Q96P44	.|.;COLA1_HUMAN	I|Y	56|492;489;492;489	.|ENSP00000244728:S492Y;ENSP00000359855:S489Y;ENSP00000444384:S492Y	.|ENSP00000244728:S492Y	L|S	-|-	1|2	0|0	COL21A1|COL21A1	56114700|56114700	0.981000|0.981000	0.34729|0.34729	0.814000|0.814000	0.32528|0.32528	0.926000|0.926000	0.56050|0.56050	3.065000|3.065000	0.49994|0.49994	2.624000|2.624000	0.88883|0.88883	0.655000|0.655000	0.94253|0.94253	CTC|TCT	.	.	none		0.274	COL21A1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041004.2		
ABCC9	10060	hgsc.bcm.edu	37	12	21998615	21998615	+	Silent	SNP	C	C	T			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr12:21998615C>T	ENST00000261201.4	-	24	3017	c.3018G>A	c.(3016-3018)tcG>tcA	p.S1006S	RP11-729I10.2_ENST00000539874.1_RNA|ABCC9_ENST00000261200.4_Silent_p.S1006S|ABCC9_ENST00000345162.2_Silent_p.S970S	NM_005691.2	NP_005682.2	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 9	1006	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				defense response to virus (GO:0051607)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	ATP-sensitive potassium channel complex (GO:0008282)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcomere (GO:0030017)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium channel activity (GO:0005267)|potassium channel regulator activity (GO:0015459)|sulfonylurea receptor activity (GO:0008281)|transporter activity (GO:0005215)			NS(2)|breast(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|lung(56)|ovary(4)|pancreas(1)|prostate(4)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(5)	118					Adenosine triphosphate(DB00171)|Glyburide(DB01016)	CTACAATGACCGAATGCTTCA	0.433																																					p.S1006S		Atlas-SNP	.											ABCC9,colon,carcinoma,-1,1	ABCC9	411	1	0			c.G3018A						PASS	.						118.0	103.0	108.0					12																	21998615		2203	4300	6503	SO:0001819	synonymous_variant	10060	exon24			AATGACCGAATGC	AF061323	CCDS8693.1, CCDS8694.1	12p12.1	2014-09-17			ENSG00000069431	ENSG00000069431		"""ATP binding cassette transporters / subfamily C"""	60	protein-coding gene	gene with protein product	"""sulfonylurea receptor 2"""	601439				9457174, 15034580	Standard	NM_020297		Approved	SUR2, CMD1O	uc001rfh.3	O60706	OTTHUMG00000169094	ENST00000261201.4:c.3018G>A	12.37:g.21998615C>T		81.0	0.0	0		47.0	17.0	0.361702	NM_005691	O60707	Silent	SNP	ENST00000261201.4	37	CCDS8694.1																																																																																			.	.	none		0.433	ABCC9-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402230.1	NM_005691	
FNTA	2339	hgsc.bcm.edu	37	8	42940407	42940407	+	Silent	SNP	A	A	T			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr8:42940407A>T	ENST00000302279.3	+	9	1316	c.1122A>T	c.(1120-1122)ccA>ccT	p.P374P	FNTA_ENST00000529687.1_Silent_p.P223P|FNTA_ENST00000342116.4_Silent_p.P307P	NM_002027.2	NP_002018.1	P49354	FNTA_HUMAN	farnesyltransferase, CAAX box, alpha	374					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|phototransduction, visible light (GO:0007603)|positive regulation of deacetylase activity (GO:0090045)|positive regulation of tubulin deacetylation (GO:0090044)|protein farnesylation (GO:0018343)|protein geranylgeranylation (GO:0018344)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|transforming growth factor beta receptor signaling pathway (GO:0007179)	CAAX-protein geranylgeranyltransferase complex (GO:0005953)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule associated complex (GO:0005875)|protein farnesyltransferase complex (GO:0005965)	alpha-tubulin binding (GO:0043014)|CAAX-protein geranylgeranyltransferase activity (GO:0004662)|microtubule binding (GO:0008017)|protein farnesyltransferase activity (GO:0004660)|protein geranylgeranyltransferase activity (GO:0004661)			cervix(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(8)|ovary(1)|prostate(1)|urinary_tract(1)	16	Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184)	all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17)			ATGACTCACCAACAAATGTAC	0.393																																					p.P374P		Atlas-SNP	.											.	FNTA	34	.	0			c.A1122T						PASS	.						99.0	85.0	90.0					8																	42940407		2203	4300	6503	SO:0001819	synonymous_variant	2339	exon9			CTCACCAACAAAT	L10413	CCDS6140.1	8p11.21	2011-06-27			ENSG00000168522	ENSG00000168522		"""Prenyltransferase alpha subunit repeat containing"""	3782	protein-coding gene	gene with protein product	"""protein prenyltransferase alpha subunit repeat containing 2"""	134635				8276393	Standard	NR_033698		Approved	FPTA, PGGT1A, PTAR2	uc003xps.3	P49354	OTTHUMG00000165279	ENST00000302279.3:c.1122A>T	8.37:g.42940407A>T		379.0	0.0	0		343.0	97.0	0.282799	NM_002027	A6NJW0|Q53XJ9|Q9UDC1	Silent	SNP	ENST00000302279.3	37	CCDS6140.1																																																																																			.	.	none		0.393	FNTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383178.1	NM_002027	
BBS1	582	hgsc.bcm.edu	37	11	66294208	66294208	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr11:66294208G>T	ENST00000318312.7	+	13	1320	c.1269G>T	c.(1267-1269)atG>atT	p.M423I	BBS1_ENST00000393994.2_Missense_Mutation_p.M294I|CTD-3074O7.11_ENST00000419755.3_Missense_Mutation_p.M460I|BBS1_ENST00000529766.1_3'UTR|ZDHHC24_ENST00000526986.1_Intron|BBS1_ENST00000455748.2_Missense_Mutation_p.M326I	NM_024649.4	NP_078925.3	Q8NFJ9	BBS1_HUMAN	Bardet-Biedl syndrome 1	423					cilium assembly (GO:0042384)|Golgi to plasma membrane protein transport (GO:0043001)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	BBSome (GO:0034464)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	patched binding (GO:0005113)|RNA polymerase II repressing transcription factor binding (GO:0001103)|smoothened binding (GO:0005119)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)|skin(2)|stomach(2)|urinary_tract(1)	28						CCCAGGCCATGAAACTCAATG	0.587									Bardet-Biedl syndrome																												p.M423I	GBM(152;173 2612 9770 10137)	Atlas-SNP	.											.	BBS1	58	.	0			c.G1269T						PASS	.						159.0	151.0	153.0					11																	66294208		2200	4295	6495	SO:0001583	missense	582	exon13	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	GGCCATGAAACTC	AF503941	CCDS8142.1	11q13	2013-01-08			ENSG00000174483	ENSG00000174483			966	protein-coding gene	gene with protein product		209901				9039982, 12567324	Standard	NM_024649		Approved	FLJ23590	uc001oij.1	Q8NFJ9	OTTHUMG00000167110	ENST00000318312.7:c.1269G>T	11.37:g.66294208G>T	ENSP00000317469:p.Met423Ile	118.0	0.0	0		125.0	23.0	0.184	NM_024649	Q32MM9|Q32MN0|Q96SN4	Missense_Mutation	SNP	ENST00000318312.7	37	CCDS8142.1	.	.	.	.	.	.	.	.	.	.	G	0.378	-0.930525	0.02359	.	.	ENSG00000256349;ENSG00000174483;ENSG00000174483;ENSG00000174483	ENST00000419755;ENST00000318312;ENST00000455748;ENST00000393994	D;D;D;D	0.96300	-3.89;-3.97;-3.8;-3.7	4.69	-2.72	0.05968	.	.	.	.	.	T	0.78604	0.4309	N	0.00525	-1.395	0.09310	N	1	B;B;B;B;B;B	0.06786	0.0;0.001;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.06405	0.0;0.002;0.0;0.001;0.0;0.001	T	0.75838	-0.3176	9	0.07175	T	0.84	.	0.5633	0.00683	0.354:0.1232:0.2725:0.2503	.	98;326;294;311;423;460	B4DH75;E7EQH1;Q32MM9;Q4G0L2;Q8NFJ9;Q8NFJ9-2	.;.;.;.;BBS1_HUMAN;.	I	460;423;326;294	ENSP00000398526:M460I;ENSP00000317469:M423I;ENSP00000405764:M326I;ENSP00000377563:M294I	ENSP00000317469:M423I	M	+	3	0	BBS1;CTD-3074O7.11	66050784	0.001000	0.12720	0.002000	0.10522	0.787000	0.44495	-0.617000	0.05584	-0.634000	0.05538	-0.150000	0.13652	ATG	.	.	none		0.587	BBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393235.2		
SPHKAP	80309	hgsc.bcm.edu	37	2	228881444	228881444	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr2:228881444C>T	ENST00000392056.3	-	7	4172	c.4126G>A	c.(4126-4128)Gtt>Att	p.V1376I	SPHKAP_ENST00000344657.5_Missense_Mutation_p.V1376I	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	1376						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)			NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		CATTCGGTAACAGAGTCTTTC	0.473																																					p.V1376I		Atlas-SNP	.											.	SPHKAP	750	.	0			c.G4126A						PASS	.						75.0	77.0	76.0					2																	228881444		2203	4300	6503	SO:0001583	missense	80309	exon7			CGGTAACAGAGTC		CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"""A-kinase anchor proteins"""	30619	protein-coding gene	gene with protein product	"""sphingosine kinase type 1-interacting protein"""	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.4126G>A	2.37:g.228881444C>T	ENSP00000375909:p.Val1376Ile	103.0	0.0	0		80.0	19.0	0.2375	NM_030623	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	37	CCDS46537.1	.	.	.	.	.	.	.	.	.	.	C	8.953	0.968624	0.18659	.	.	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.13089	2.62;2.62	5.14	0.496	0.16896	.	1.516350	0.03499	N	0.217772	T	0.05135	0.0137	N	0.02315	-0.6	0.09310	N	1	B;B;B	0.15141	0.002;0.002;0.012	B;B;B	0.15484	0.001;0.004;0.013	T	0.31998	-0.9923	10	0.18276	T	0.48	.	2.5383	0.04719	0.0973:0.3926:0.2658:0.2443	.	407;1376;1376	B3KR30;Q2M3C7;Q2M3C7-2	.;SPKAP_HUMAN;.	I	1376	ENSP00000375909:V1376I;ENSP00000339886:V1376I	ENSP00000339886:V1376I	V	-	1	0	SPHKAP	228589688	0.000000	0.05858	0.000000	0.03702	0.144000	0.21451	-0.174000	0.09839	-0.056000	0.13221	0.655000	0.94253	GTT	.	.	none		0.473	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623	
TRIM66	9866	hgsc.bcm.edu	37	11	8646767	8646767	+	Silent	SNP	G	G	A			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr11:8646767G>A	ENST00000299550.6	-	11	2078	c.1884C>T	c.(1882-1884)acC>acT	p.T628T	TRIM66_ENST00000402157.2_Silent_p.T626T	NM_014818.1	NP_055633.1	O15016	TRI66_HUMAN	tripartite motif containing 66	628						aggresome (GO:0016235)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|kidney(1)|lung(1)|skin(2)	9						TGCTCAGCGAGGTGGAGTGCT	0.572																																					p.T628T		Atlas-SNP	.											.	TRIM66	45	.	0			c.C1884T						PASS	.						8.0	9.0	9.0					11																	8646767		692	1590	2282	SO:0001819	synonymous_variant	9866	exon11			CAGCGAGGTGGAG	AB002296		11p15.4	2013-01-28	2011-01-25		ENSG00000166436	ENSG00000166436		"""Tripartite motif containing / Tripartite motif containing"", ""Zinc fingers, PHD-type"""	29005	protein-coding gene	gene with protein product		612000	"""chromosome 11 open reading frame 29"", ""tripartite motif-containing 66"""	C11orf29		9205841	Standard	NM_014818		Approved	KIAA0298, TIF1D	uc010rbo.2	O15016	OTTHUMG00000150481	ENST00000299550.6:c.1884C>T	11.37:g.8646767G>A		43.0	0.0	0		34.0	8.0	0.235294	NM_014818	Q9BQQ4	Silent	SNP	ENST00000299550.6	37																																																																																				.	.	none		0.572	TRIM66-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_084529	
CEP128	145508	hgsc.bcm.edu	37	14	81329188	81329188	+	Missense_Mutation	SNP	C	C	A			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr14:81329188C>A	ENST00000555265.1	-	9	1050	c.675G>T	c.(673-675)caG>caT	p.Q225H	CEP128_ENST00000281129.3_Missense_Mutation_p.Q225H|CEP128_ENST00000216517.6_Missense_Mutation_p.Q225H			Q6ZU80	CE128_HUMAN	centrosomal protein 128kDa	225						centriole (GO:0005814)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)				NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	51						TCTCCAGTTCCTGAAGCCGCC	0.478																																					p.Q225H		Atlas-SNP	.											.	CEP128	146	.	0			c.G675T						PASS	.						74.0	67.0	69.0					14																	81329188		2203	4300	6503	SO:0001583	missense	145508	exon8			CAGTTCCTGAAGC	AK056756	CCDS32130.1	14q31.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000100629	ENSG00000100629			20359	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 61"", ""chromosome 14 open reading frame 145"""	C14orf61, C14orf145		21399614	Standard	NM_152446		Approved		uc001xux.2	Q6ZU80		ENST00000555265.1:c.675G>T	14.37:g.81329188C>A	ENSP00000451162:p.Gln225His	52.0	0.0	0		39.0	19.0	0.487179	NM_152446	B9EK52|Q86X97|Q96ML4	Missense_Mutation	SNP	ENST00000555265.1	37	CCDS32130.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.21|19.21	3.784243|3.784243	0.70222|0.70222	.|.	.|.	ENSG00000100629|ENSG00000100629	ENST00000281129;ENST00000555265;ENST00000393619;ENST00000216517|ENST00000554827	T;T;T|.	0.55052|.	1.18;1.18;0.54|.	6.08|6.08	2.89|2.89	0.33648|0.33648	.|.	0.069385|.	0.64402|.	D|.	0.000016|.	T|T	0.64843|0.64843	0.2635|0.2635	M|M	0.70275|0.70275	2.135|2.135	0.80722|0.80722	D|D	1|1	D;D;D|.	0.57257|.	0.979;0.963;0.963|.	P;P;P|.	0.60473|.	0.875;0.875;0.81|.	T|T	0.63207|0.63207	-0.6689|-0.6689	10|5	0.72032|.	D|.	0.01|.	.|.	10.0884|10.0884	0.42432|0.42432	0.0:0.6984:0.0:0.3016|0.0:0.6984:0.0:0.3016	.|.	225;106;225|.	Q6ZU80-3;Q8N3Z7;Q6ZU80|.	.;.;CE128_HUMAN|.	H|M	225|104	ENSP00000281129:Q225H;ENSP00000451162:Q225H;ENSP00000216517:Q225H|.	ENSP00000216517:Q225H|.	Q|R	-|-	3|2	2|0	CEP128|CEP128	80398941|80398941	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.815000|0.815000	0.46073|0.46073	1.282000|1.282000	0.33226|0.33226	0.919000|0.919000	0.36945|0.36945	0.655000|0.655000	0.94253|0.94253	CAG|AGG	.	.	none		0.478	CEP128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413415.1	NM_152446	
ZP4	57829	hgsc.bcm.edu	37	1	238049158	238049158	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr1:238049158T>G	ENST00000366570.4	-	7	1026	c.868A>C	c.(868-870)Agt>Cgt	p.S290R	RP11-193H5.1_ENST00000450451.1_RNA	NM_021186.3	NP_067009.1	Q12836	ZP4_HUMAN	zona pellucida glycoprotein 4	290	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				acrosomal vesicle exocytosis (GO:0060478)|binding of sperm to zona pellucida (GO:0007339)|intracellular signal transduction (GO:0035556)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of humoral immune response (GO:0002922)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of T cell proliferation (GO:0042102)|protein kinase A signaling (GO:0010737)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	acrosin binding (GO:0032190)|signal transducer activity (GO:0004871)			breast(6)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(8)|lung(42)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	73	Ovarian(103;0.103)	all_cancers(173;0.00175)|all_epithelial(177;0.162)|all_neural(198;0.164)|Melanoma(53;0.211)|Prostate(94;0.214)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			GAGTTGCTACTTACTGAGTAG	0.483																																					p.S290R	NSCLC(166;160 2029 11600 18754 19936)	Atlas-SNP	.											.	ZP4	161	.	0			c.A868C						PASS	.						149.0	144.0	146.0					1																	238049158		2203	4300	6503	SO:0001583	missense	57829	exon7			TGCTACTTACTGA	U05781	CCDS1615.1	1q43	2013-01-17			ENSG00000116996	ENSG00000116996		"""Zona pellucida glycoproteins"""	15770	protein-coding gene	gene with protein product		613514				7841460	Standard	NM_021186		Approved	ZPB	uc001hym.3	Q12836	OTTHUMG00000039586	ENST00000366570.4:c.868A>C	1.37:g.238049158T>G	ENSP00000355529:p.Ser290Arg	80.0	0.0	0		70.0	19.0	0.271429	NM_021186	B2RAE1	Missense_Mutation	SNP	ENST00000366570.4	37	CCDS1615.1	.	.	.	.	.	.	.	.	.	.	T	13.47	2.248183	0.39697	.	.	ENSG00000116996	ENST00000366570	D	0.82619	-1.63	4.32	1.89	0.25635	Zona pellucida sperm-binding protein (3);	0.550821	0.19053	N	0.123987	T	0.71134	0.3304	L	0.31804	0.96	0.09310	N	1	B	0.11235	0.004	B	0.17979	0.02	T	0.57341	-0.7828	10	0.34782	T	0.22	-1.9444	8.4328	0.32769	0.0:0.0:0.412:0.588	.	290	Q12836	ZP4_HUMAN	R	290	ENSP00000355529:S290R	ENSP00000355529:S290R	S	-	1	0	ZP4	236115781	0.002000	0.14202	0.000000	0.03702	0.817000	0.46193	1.245000	0.32790	0.194000	0.20326	0.528000	0.53228	AGT	.	.	none		0.483	ZP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095476.1		
DGKZ	8525	hgsc.bcm.edu	37	11	46397091	46397091	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr11:46397091T>G	ENST00000454345.1	+	21	2509	c.2384T>G	c.(2383-2385)cTt>cGt	p.L795R	DGKZ_ENST00000421244.2_Missense_Mutation_p.L607R|DGKZ_ENST00000343674.6_Missense_Mutation_p.L623R|DGKZ_ENST00000395574.3_Missense_Mutation_p.L573R|MIR4688_ENST00000577966.1_RNA|DGKZ_ENST00000528615.1_Missense_Mutation_p.L385R|DGKZ_ENST00000318201.8_Missense_Mutation_p.L584R|DGKZ_ENST00000543978.1_Intron|DGKZ_ENST00000532868.2_Missense_Mutation_p.L611R|DGKZ_ENST00000456247.2_Missense_Mutation_p.L606R|DGKZ_ENST00000527911.1_Missense_Mutation_p.L607R	NM_001105540.1	NP_001099010.1	Q13574	DGKZ_HUMAN	diacylglycerol kinase, zeta	795					blood coagulation (GO:0007596)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|lipid phosphorylation (GO:0046834)|mitotic G1 DNA damage checkpoint (GO:0031571)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of Ras protein signal transduction (GO:0046580)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|enzyme inhibitor activity (GO:0004857)|lipid kinase activity (GO:0001727)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|protein C-terminus binding (GO:0008022)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(12)|pancreas(1)|prostate(1)|skin(1)	25				GBM - Glioblastoma multiforme(35;0.0259)|Lung(87;0.141)		CCCTGCAAGCTTGCAGCCTCA	0.692																																					p.L795R		Atlas-SNP	.											.	DGKZ	199	.	0			c.T2384G						PASS	.						30.0	31.0	31.0					11																	46397091		2192	4294	6486	SO:0001583	missense	8525	exon21			GCAAGCTTGCAGC	U51477	CCDS7918.1, CCDS41640.1, CCDS44579.1, CCDS44580.1, CCDS55757.1, CCDS55758.1, CCDS55759.1, CCDS44579.2	11p11.2	2010-11-24	2010-11-24		ENSG00000149091	ENSG00000149091	2.7.1.107		2857	protein-coding gene	gene with protein product		601441	"""diacylglycerol kinase, zeta 104kDa"""			8626588	Standard	NM_003646		Approved	DAGK5, hDGKzeta, DGK-ZETA, DAGK6	uc001ncn.1	Q13574	OTTHUMG00000166437	ENST00000454345.1:c.2384T>G	11.37:g.46397091T>G	ENSP00000412178:p.Leu795Arg	59.0	0.0	0		76.0	21.0	0.276316	NM_001105540	B7Z2M9|B7Z6M3|E9PPW4|F6UCU9|G3V0F6|J3KNJ6|O00542|Q6ZVG7|Q8IVW9	Missense_Mutation	SNP	ENST00000454345.1	37	CCDS41640.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.2|25.2	4.618080|4.618080	0.87359|0.87359	.|.	.|.	ENSG00000149091|ENSG00000149091	ENST00000343674;ENST00000528615;ENST00000395574;ENST00000532868;ENST00000527911;ENST00000456247;ENST00000421244;ENST00000318201;ENST00000454345|ENST00000524869	T;T;T;T;T;T;T;T;T|T	0.27557|0.45276	2.24;2.45;2.44;2.5;3.42;2.25;2.32;2.44;1.66|0.9	4.19|4.19	4.19|4.19	0.49359|0.49359	.|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.55481|0.55481	0.1923|0.1923	M|M	0.72479|0.72479	2.2|2.2	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D;D;D|.	0.89917|.	1.0;0.999;1.0;1.0;1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D;D;D;D;D|.	0.85130|.	0.996;0.987;0.993;0.996;0.996;0.997;0.997;0.992;0.996|.	T|T	0.55774|0.55774	-0.8088|-0.8088	10|8	0.87932|0.36615	D|T	0|0.2	.|.	13.7246|13.7246	0.62750|0.62750	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	584;572;550;607;795;606;607;573;623|.	B7Z2M9;B7Z6M3;B7Z8F6;E9PPW4;Q13574;Q13574-2;G3V0F6;A8MVN1;Q6ZVG7|.	.;.;.;.;DGKZ_HUMAN;.;.;.;.|.	R|V	623;385;573;572;607;606;607;584;795|162	ENSP00000343065:L623R;ENSP00000434719:L385R;ENSP00000378941:L573R;ENSP00000436273:L572R;ENSP00000436291:L607R;ENSP00000395684:L606R;ENSP00000391021:L607R;ENSP00000320340:L584R;ENSP00000412178:L795R|ENSP00000434016:L162V	ENSP00000320340:L584R|ENSP00000434016:L162V	L|L	+|+	2|1	0|2	DGKZ|DGKZ	46353667|46353667	1.000000|1.000000	0.71417|0.71417	0.834000|0.834000	0.33040|0.33040	0.929000|0.929000	0.56500|0.56500	7.581000|7.581000	0.82535|0.82535	1.904000|1.904000	0.55121|0.55121	0.379000|0.379000	0.24179|0.24179	CTT|TTG	.	.	none		0.692	DGKZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389772.1	NM_001105540	
GSPT1	2935	hgsc.bcm.edu	37	16	12009383	12009383	+	Intron	SNP	G	G	C			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr16:12009383G>C	ENST00000420576.2	-	1	41				GSPT1_ENST00000439887.2_Missense_Mutation_p.F65L|GSPT1_ENST00000434724.2_Missense_Mutation_p.F65L|AC007216.1_ENST00000583357.1_RNA	NM_001130007.1	NP_001123479.1	P15170	ERF3A_HUMAN	G1 to S phase transition 1						G1/S transition of mitotic cell cycle (GO:0000082)|GTP catabolic process (GO:0006184)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein methylation (GO:0006479)|translational termination (GO:0006415)	intracellular (GO:0005622)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|translation release factor activity (GO:0003747)			breast(1)|central_nervous_system(1)|kidney(4)|lung(4)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	14						GTTGCCGGCTGAAGGCCGCGC	0.761																																					p.F65L		Atlas-SNP	.											.	GSPT1	71	.	0			c.C195G						PASS	.						10.0	13.0	12.0					16																	12009383		1526	3533	5059	SO:0001627	intron_variant	2935	exon1			CCGGCTGAAGGCC	BC008391	CCDS45412.1, CCDS45413.1, CCDS45414.1	16p13.1	2008-08-01							4621	protein-coding gene	gene with protein product		139259				2511002, 17700517	Standard	NM_002094		Approved	GST1, ETF3A, eRF3a	uc002dbt.3	P15170		ENST00000420576.2:c.61+515C>G	16.37:g.12009383G>C		47.0	0.0	0		101.0	22.0	0.217822	NM_001130006	J3KQG6|Q96GF2	Missense_Mutation	SNP	ENST00000420576.2	37	CCDS45414.1	.	.	.	.	.	.	.	.	.	.	g	13.05	2.121366	0.37436	.	.	ENSG00000103342	ENST00000434724;ENST00000439887	T;T	0.34472	1.42;1.36	5.09	4.13	0.48395	.	0.638850	0.14978	U	0.287426	T	0.24586	0.0596	.	.	.	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.003	T	0.03922	-1.0992	9	0.19590	T	0.45	-5.7554	10.5732	0.45212	0.0913:0.0:0.9087:0.0	.	65;62	E7EQZ3;Q96GF2	.;.	L	65	ENSP00000398131:F65L;ENSP00000408399:F65L	ENSP00000398131:F65L	F	-	3	2	GSPT1	11916884	1.000000	0.71417	1.000000	0.80357	0.072000	0.16883	2.931000	0.48932	1.129000	0.42072	0.457000	0.33378	TTC	.	.	none		0.761	GSPT1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000421514.1	NM_002094	
CARS2	79587	hgsc.bcm.edu	37	13	111340366	111340366	+	Splice_Site	SNP	C	C	A			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr13:111340366C>A	ENST00000257347.4	-	4	457		c.e4-1		CARS2_ENST00000535398.1_Splice_Site	NM_024537.2	NP_078813.1	Q9HA77	SYCM_HUMAN	cysteinyl-tRNA synthetase 2, mitochondrial (putative)						cysteinyl-tRNA aminoacylation (GO:0006423)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|cysteine-tRNA ligase activity (GO:0004817)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|prostate(4)|skin(1)	13	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.163)		L-Cysteine(DB00151)	AAATATTCATCTGCAGAAGGA	0.517																																					.		Atlas-SNP	.											.	CARS2	37	.	0			c.394-1G>T						PASS	.						54.0	50.0	52.0					13																	111340366		2203	4300	6503	SO:0001630	splice_region_variant	79587	exon5			ATTCATCTGCAGA	BC007220	CCDS9514.1	13q34	2011-07-01	2007-02-22		ENSG00000134905	ENSG00000134905	6.1.1.16	"""Aminoacyl tRNA synthetases / Class I"""	25695	protein-coding gene	gene with protein product	"""cysteine tRNA ligase 2, mitochondrial (putative)"""	612800				15779907	Standard	NM_024537		Approved	FLJ12118	uc001vrd.2	Q9HA77	OTTHUMG00000017347	ENST00000257347.4:c.394-1G>T	13.37:g.111340366C>A		57.0	0.0	0		42.0	13.0	0.309524	NM_024537	Q8NI84|Q96IV4	Splice_Site	SNP	ENST00000257347.4	37	CCDS9514.1	.	.	.	.	.	.	.	.	.	.	C	11.58	1.679757	0.29783	.	.	ENSG00000134905	ENST00000257347;ENST00000542709	.	.	.	4.93	4.93	0.64822	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.2901	0.87153	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CARS2	110138367	1.000000	0.71417	0.997000	0.53966	0.112000	0.19704	5.947000	0.70242	2.433000	0.82419	0.557000	0.71058	.	.	.	none		0.517	CARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045772.3	NM_024537	Intron
ANKRD44	91526	hgsc.bcm.edu	37	2	197878306	197878306	+	Missense_Mutation	SNP	G	G	A	rs145800695	byFrequency	TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr2:197878306G>A	ENST00000328737.2	-	18	1854	c.1778C>T	c.(1777-1779)gCg>gTg	p.A593V	ANKRD44_ENST00000450567.1_Missense_Mutation_p.A593V|ANKRD44_ENST00000337207.5_Missense_Mutation_p.A593V|ANKRD44_ENST00000282272.8_Missense_Mutation_p.A610V			Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	618										NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(20)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.246)			ATTGATAAGCGCTTCCACACA	0.507													G|||	8	0.00159744	0.0061	0.0	5008	,	,		20126	0.0		0.0	False		,,,				2504	0.0				p.A618V		Atlas-SNP	.											ANKRD44_ENST00000424317,NS,carcinoma,+1,2	ANKRD44	281	2	0			c.C1853T						scavenged	.	G	VAL/ALA	35,4371	40.8+/-73.8	0,35,2168	220.0	208.0	212.0		1853	4.4	1.0	2	dbSNP_134	212	0,8600		0,0,4300	yes	missense	ANKRD44	NM_001195144.1	64	0,35,6468	AA,AG,GG		0.0,0.7944,0.2691	benign	618/994	197878306	35,12971	2203	4300	6503	SO:0001583	missense	91526	exon18			ATAAGCGCTTCCA	AK097086	CCDS33355.1, CCDS33355.2, CCDS74619.1	2q33.1	2013-01-10			ENSG00000065413	ENSG00000065413		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"", ""Ankyrin repeat domain containing"""	25259	protein-coding gene	gene with protein product	"""protein phosphatase 6 ankyrin repeat subunit B"""						Standard	NM_153697		Approved	PP6-ARS-B	uc021vuj.1	Q8N8A2	OTTHUMG00000154411	ENST00000328737.2:c.1778C>T	2.37:g.197878306G>A	ENSP00000331516:p.Ala593Val	134.0	1.0	0.00746269		130.0	32.0	0.246154	NM_001195144	Q53SL9|Q6P480|Q86VL5|Q8IZ72|Q9UFA4	Missense_Mutation	SNP	ENST00000328737.2	37		5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	G	3.291	-0.144875	0.06627	0.007944	0.0	ENSG00000065413	ENST00000424317;ENST00000282272;ENST00000328737;ENST00000450567;ENST00000337207;ENST00000422886	T;T;T;T;T;T	0.63744	-0.06;-0.06;-0.06;-0.06;-0.06;-0.06	4.43	4.43	0.53597	.	0.060668	0.64402	D	0.000003	T	0.53786	0.1818	N	0.21240	0.645	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.52631	-0.8550	10	0.12103	T	0.63	.	10.8392	0.46704	0.0862:0.0:0.9138:0.0	.	636	Q8N8A2-2	.	V	433;610;593;593;593;293	ENSP00000403415:A433V;ENSP00000282272:A610V;ENSP00000331516:A593V;ENSP00000402420:A593V;ENSP00000338794:A593V;ENSP00000416319:A293V	ENSP00000282272:A610V	A	-	2	0	ANKRD44	197586551	0.996000	0.38824	0.993000	0.49108	0.714000	0.41099	2.528000	0.45624	2.294000	0.77228	0.655000	0.94253	GCG	G|0.997;A|0.003	0.003	strong		0.507	ANKRD44-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335113.1	NM_153697	
CREBBP	1387	hgsc.bcm.edu	37	16	3786764	3786764	+	Missense_Mutation	SNP	T	T	A			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr16:3786764T>A	ENST00000262367.5	-	27	5256	c.4447A>T	c.(4447-4449)Atc>Ttc	p.I1483F	CREBBP_ENST00000382070.3_Missense_Mutation_p.I1445F	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1483	CBP/p300-type HAT. {ECO:0000255|PROSITE- ProRule:PRU01065}.|Cys/His-rich.|Interaction with TRERF1.				cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		CAATGGAAGATGTAATCATCT	0.512			"""T, N, F, Mis, O"""	"""MLL, MORF, RUNXBP2"""	"""ALL, AML, DLBCL, B-NHL """		Rubinstein-Taybi syndrome																														p.I1483F		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	CREBBP,colon,carcinoma,+1,4	CREBBP	546	4	0			c.A4447T						PASS	.						225.0	192.0	203.0					16																	3786764		2197	4300	6497	SO:0001583	missense	1387	exon27			GGAAGATGTAATC	U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"""Chromatin-modifying enzymes / K-acetyltransferases"""	2348	protein-coding gene	gene with protein product		600140	"""Rubinstein-Taybi syndrome"""	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.4447A>T	16.37:g.3786764T>A	ENSP00000262367:p.Ile1483Phe	160.0	0.0	0		194.0	43.0	0.221649	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	t	21.2	4.116784	0.77323	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070;ENST00000323508	D;D	0.94793	-3.52;-3.52	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	D	0.97598	0.9213	M	0.90814	3.15	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.98516	1.0621	10	0.87932	D	0	-22.4571	14.6308	0.68655	0.0:0.0:0.0:1.0	.	1513;1483	Q4LE28;Q92793	.;CBP_HUMAN	F	1483;1513;1445;72	ENSP00000262367:I1483F;ENSP00000371502:I1445F	ENSP00000262367:I1483F	I	-	1	0	CREBBP	3726765	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.997000	0.88414	2.107000	0.64212	0.459000	0.35465	ATC	.	.	none		0.512	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380	
PTPRA	5786	hgsc.bcm.edu	37	20	3007337	3007337	+	Nonsense_Mutation	SNP	T	T	G			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr20:3007337T>G	ENST00000216877.6	+	17	1992	c.1592T>G	c.(1591-1593)tTa>tGa	p.L531*	PTPRA_ENST00000425918.2_Nonsense_Mutation_p.L551*|PTPRA_ENST00000358719.4_Nonsense_Mutation_p.L396*|PTPRA_ENST00000356147.3_Nonsense_Mutation_p.L531*|PTPRA_ENST00000318266.5_Nonsense_Mutation_p.L531*|PTPRA_ENST00000380393.3_Nonsense_Mutation_p.L540*|PTPRA_ENST00000399903.2_Nonsense_Mutation_p.L540*	NM_080840.2	NP_543030.1	P18433	PTPRA_HUMAN	protein tyrosine phosphatase, receptor type, A	540					axon guidance (GO:0007411)|insulin receptor signaling pathway (GO:0008286)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein phosphorylation (GO:0006468)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						ATTCAGAAGTTAACATCAATC	0.463																																					p.L540X		Atlas-SNP	.											.	PTPRA	75	.	0			c.T1619G						PASS	.						80.0	64.0	69.0					20																	3007337		2203	4300	6503	SO:0001587	stop_gained	5786	exon22			AGAAGTTAACATC		CCDS13038.1, CCDS13039.1	20p13	2011-06-09			ENSG00000132670	ENSG00000132670		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9664	protein-coding gene	gene with protein product		176884		PTPRL2, PTPA		2172030, 2169617	Standard	NM_080840		Approved	LRP, HLPR, HPTPA, RPTPA	uc002whn.3	P18433	OTTHUMG00000031718	ENST00000216877.6:c.1592T>G	20.37:g.3007337T>G	ENSP00000216877:p.Leu531*	89.0	0.0	0		80.0	24.0	0.3	NM_002836	A8K2G8|D3DVX5|Q14513|Q7Z2I2|Q96TD9	Nonsense_Mutation	SNP	ENST00000216877.6	37	CCDS13039.1	.	.	.	.	.	.	.	.	.	.	T	38	7.281920	0.98186	.	.	ENSG00000132670	ENST00000380393;ENST00000216877;ENST00000399903;ENST00000358719;ENST00000542217;ENST00000425918;ENST00000318266;ENST00000356147	.	.	.	5.49	5.49	0.81192	.	0.000000	0.64402	U	0.000007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.8803	0.79197	0.0:0.0:0.0:1.0	.	.	.	.	X	540;531;540;396;150;551;531;531	.	ENSP00000216877:L531X	L	+	2	0	PTPRA	2955337	1.000000	0.71417	0.993000	0.49108	0.192000	0.23643	7.997000	0.88414	2.203000	0.70933	0.459000	0.35465	TTA	.	.	none		0.463	PTPRA-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077682.3		
MED13L	23389	hgsc.bcm.edu	37	12	116408551	116408551	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr12:116408551A>C	ENST00000281928.3	-	27	6121	c.5915T>G	c.(5914-5916)tTt>tGt	p.F1972C		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	1972						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)		ACTTCGGCCAAAAACAGAGCC	0.423																																					p.F1972C		Atlas-SNP	.											.	MED13L	193	.	0			c.T5915G						PASS	.						108.0	91.0	97.0					12																	116408551		2203	4300	6503	SO:0001583	missense	23389	exon27			CGGCCAAAAACAG	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.5915T>G	12.37:g.116408551A>C	ENSP00000281928:p.Phe1972Cys	94.0	0.0	0		94.0	14.0	0.148936	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Missense_Mutation	SNP	ENST00000281928.3	37	CCDS9177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	25.1|25.1	4.606136|4.606136	0.87157|0.87157	.|.	.|.	ENSG00000123066|ENSG00000123066	ENST00000281928|ENST00000552447	D|.	0.84370|.	-1.84|.	5.55|5.55	5.55|5.55	0.83447|0.83447	.|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.79112|0.79112	0.4391|0.4391	M|M	0.84846|0.84846	2.72|2.72	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	T|T	0.81389|0.81389	-0.0955|-0.0955	10|6	0.72032|.	D|.	0.01|.	.|.	15.8583|15.8583	0.79000|0.79000	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	1972|.	Q71F56|.	MD13L_HUMAN|.	C|L	1972|176	ENSP00000281928:F1972C|.	ENSP00000281928:F1972C|.	F|F	-|-	2|3	0|2	MED13L|MED13L	114892934|114892934	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	8.761000|8.761000	0.91691|0.91691	2.326000|2.326000	0.78906|0.78906	0.533000|0.533000	0.62120|0.62120	TTT|TTT	.	.	none		0.423	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3		
CCAR2	57805	hgsc.bcm.edu	37	8	22472491	22472491	+	Silent	SNP	T	T	A			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr8:22472491T>A	ENST00000308511.4	+	11	1431	c.1182T>A	c.(1180-1182)atT>atA	p.I394I	RP11-582J16.5_ENST00000521025.1_RNA|CCAR2_ENST00000389279.3_Silent_p.I394I|CCAR2_ENST00000520861.1_Silent_p.I69I			Q8N163	CCAR2_HUMAN	cell cycle and apoptosis regulator 2	394					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mRNA processing (GO:0006397)|negative regulation of catalytic activity (GO:0043086)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage checkpoint (GO:2000003)|regulation of circadian rhythm (GO:0042752)|regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of protein stability (GO:0031647)|response to UV (GO:0009411)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|DBIRD complex (GO:0044609)|mitochondrial matrix (GO:0005759)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)										AGACTGGCATTGATTTGAGCG	0.642																																					p.I394I		Atlas-SNP	.											.	KIAA1967	72	.	0			c.T1182A						PASS	.						43.0	32.0	36.0					8																	22472491		2202	4297	6499	SO:0001819	synonymous_variant	57805	exon11			TGGCATTGATTTG	AL834351	CCDS34863.1	8p22	2013-08-22	2013-08-22	2013-08-22		ENSG00000158941			23360	protein-coding gene	gene with protein product	"""deleted in breast cancer"""	607359	"""KIAA1967"""	KIAA1967		12370419	Standard	NM_021174		Approved	DBC-1, DBC1, NET35	uc003xci.3	Q8N163		ENST00000308511.4:c.1182T>A	8.37:g.22472491T>A		38.0	0.0	0		46.0	14.0	0.304348	NM_021174	A6NL03|B2RB79|D3DSR6|Q6P0Q9|Q8N3G7|Q8N8M1|Q8TF34|Q9H9Q9|Q9HD12|Q9NT55	Silent	SNP	ENST00000308511.4	37	CCDS34863.1	.	.	.	.	.	.	.	.	.	.	T	8.519	0.868204	0.17250	.	.	ENSG00000158941	ENST00000520738	.	.	.	5.53	-8.45	0.00946	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-15.7173	8.7499	0.34609	0.0777:0.1142:0.0771:0.7309	.	.	.	.	X	86	.	.	L	+	2	0	KIAA1967	22528436	0.238000	0.23825	0.522000	0.27862	0.623000	0.37688	-0.487000	0.06505	-1.792000	0.01259	-0.290000	0.09829	TTG	.	.	none		0.642	CCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375865.1	NM_021174	
RNF214	257160	hgsc.bcm.edu	37	11	117109653	117109653	+	Silent	SNP	T	T	C			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr11:117109653T>C	ENST00000531452.1	+	3	490	c.444T>C	c.(442-444)aaT>aaC	p.N148N	RNF214_ENST00000300650.4_Silent_p.N148N|RNF214_ENST00000530849.1_Intron|RNF214_ENST00000531287.1_Intron	NM_001077239.1|NM_001278249.1	NP_001070707.1|NP_001265178.1	Q8ND24	RN214_HUMAN	ring finger protein 214	148							zinc ion binding (GO:0008270)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	23	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.88e-05)|Epithelial(105;0.000397)|all cancers(92;0.00258)		CCTCCAGGAATTGCTCTGAAG	0.537																																					p.N148N		Atlas-SNP	.											.	RNF214	54	.	0			c.T444C						PASS	.						55.0	58.0	57.0					11																	117109653		1953	4151	6104	SO:0001819	synonymous_variant	257160	exon3			CAGGAATTGCTCT	AL834448	CCDS41720.1, CCDS60976.1	11q23.3	2014-02-12	2007-02-16		ENSG00000167257	ENSG00000167257		"""RING-type (C3HC4) zinc fingers"""	25335	protein-coding gene	gene with protein product							Standard	NM_001077239		Approved	DKFZp547C195	uc001pqt.4	Q8ND24	OTTHUMG00000167069	ENST00000531452.1:c.444T>C	11.37:g.117109653T>C		78.0	0.0	0		67.0	14.0	0.208955	NM_207343	B2RUW0|B4DTD1	Silent	SNP	ENST00000531452.1	37	CCDS41720.1																																																																																			.	.	none		0.537	RNF214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392884.1	NM_001077239	
HDAC2	3066	hgsc.bcm.edu	37	6	114262899	114262899	+	Missense_Mutation	SNP	T	T	A			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr6:114262899T>A	ENST00000519065.1	-	13	1785	c.1409A>T	c.(1408-1410)aAc>aTc	p.N470I	HDAC2_ENST00000368632.2_Missense_Mutation_p.N440I|HDAC2_ENST00000398283.2_Missense_Mutation_p.N564I|HDAC2_ENST00000519108.1_Missense_Mutation_p.N440I			Q92769	HDAC2_HUMAN	histone deacetylase 2	470					ATP-dependent chromatin remodeling (GO:0043044)|blood coagulation (GO:0007596)|cardiac muscle cell development (GO:0055013)|chromatin remodeling (GO:0006338)|circadian regulation of gene expression (GO:0032922)|dendrite development (GO:0016358)|embryonic digit morphogenesis (GO:0042733)|epidermal cell differentiation (GO:0009913)|eyelid development in camera-type eye (GO:0061029)|fungiform papilla formation (GO:0061198)|hair follicle placode formation (GO:0060789)|hippocampus development (GO:0021766)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|maintenance of chromatin silencing (GO:0006344)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of cell cycle (GO:0045786)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of neuron projection development (GO:0010977)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell proliferation (GO:0008284)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of proteolysis (GO:0045862)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of protein deacetylation (GO:0090311)|regulation of protein kinase B signaling (GO:0051896)|regulation of sarcomere organization (GO:0060297)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|heterochromatin (GO:0000792)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)|replication fork (GO:0005657)|Sin3 complex (GO:0016580)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|deacetylase activity (GO:0019213)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|poly(A) RNA binding (GO:0044822)|protein deacetylase activity (GO:0033558)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			biliary_tract(1)|central_nervous_system(5)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)|skin(2)	27		all_cancers(87;0.000629)|all_epithelial(87;0.00274)|Colorectal(196;0.0317)|all_lung(197;0.24)		all cancers(137;0.00318)|OV - Ovarian serous cystadenocarcinoma(136;0.00569)|Epithelial(106;0.0112)|GBM - Glioblastoma multiforme(226;0.0832)	Aminophylline(DB01223)|Lovastatin(DB00227)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Valproic Acid(DB00313)|Vorinostat(DB02546)	TTCACCACTGTTGTCCTTGGA	0.259																																					p.N470I		Atlas-SNP	.											.	HDAC2	102	.	0			c.A1409T						PASS	.						69.0	67.0	68.0					6																	114262899		1809	4070	5879	SO:0001583	missense	3066	exon13			CCACTGTTGTCCT	U31814	CCDS43493.1, CCDS43493.2	6q21	2008-08-29			ENSG00000196591	ENSG00000196591			4853	protein-coding gene	gene with protein product		605164				9782097	Standard	NM_001527		Approved	RPD3, YAF1	uc003pwd.2	Q92769	OTTHUMG00000015411	ENST00000519065.1:c.1409A>T	6.37:g.114262899T>A	ENSP00000430432:p.Asn470Ile	98.0	0.0	0		74.0	20.0	0.27027	NM_001527	B3KRS5|B4DL58|E1P561|Q5SRI8|Q5SZ86|Q8NEH4	Missense_Mutation	SNP	ENST00000519065.1	37	CCDS43493.2	.	.	.	.	.	.	.	.	.	.	T	14.56	2.570458	0.45798	.	.	ENSG00000196591	ENST00000519065;ENST00000398283;ENST00000519108;ENST00000368632	T;T;T;T	0.74421	-0.8;-0.84;-0.8;-0.8	5.76	-1.27	0.09347	.	0.077961	0.52532	D	0.000075	T	0.27900	0.0687	N	0.02802	-0.49	0.38410	D	0.945915	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.03157	-1.1066	10	0.37606	T	0.19	-17.9783	10.9454	0.47297	0.0:0.4618:0.0:0.5382	.	440;470	B3KRS5;Q92769	.;HDAC2_HUMAN	I	470;564;440;440	ENSP00000430432:N470I;ENSP00000381331:N564I;ENSP00000430008:N440I;ENSP00000357621:N440I	ENSP00000357621:N440I	N	-	2	0	HDAC2	114369592	0.695000	0.27747	0.882000	0.34594	0.996000	0.88848	-0.363000	0.07593	-0.108000	0.12066	0.528000	0.53228	AAC	.	.	none		0.259	HDAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041909.2		
FAM73B	84895	hgsc.bcm.edu	37	9	131821550	131821550	+	Splice_Site	SNP	G	G	A			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr9:131821550G>A	ENST00000358369.4	+	7	1019	c.793G>A	c.(793-795)Gag>Aag	p.E265K	FAM73B_ENST00000277475.5_Splice_Site_p.R305Q|FAM73B_ENST00000406926.2_Splice_Site_p.E265K	NM_032809.2	NP_116198.2	Q7L4E1	FA73B_HUMAN	family with sequence similarity 73, member B	265					bone development (GO:0060348)	integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(1)	13						GCTAGACCTCGGTGAGCTGGG	0.642																																					p.E265K		Atlas-SNP	.											.	FAM73B	37	.	0			c.G793A						PASS	.						26.0	22.0	23.0					9																	131821550		2198	4297	6495	SO:0001630	splice_region_variant	84895	exon7			GACCTCGGTGAGC	AK074127	CCDS6917.1	9q34.13	2008-02-05	2005-08-11	2005-08-11	ENSG00000148343	ENSG00000148343			23621	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 54"""	C9orf54			Standard	NM_032809		Approved	FLJ14596, FLJ00199	uc004bxa.3	Q7L4E1	OTTHUMG00000020770	ENST00000358369.4:c.793+1G>A	9.37:g.131821550G>A		65.0	0.0	0		72.0	20.0	0.277778	NM_032809	Q8NBM3|Q8TEJ6|Q969E6	Missense_Mutation	SNP	ENST00000358369.4	37	CCDS6917.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.6|20.6	4.009961|4.009961	0.75046|0.75046	.|.	.|.	ENSG00000148343|ENSG00000148343	ENST00000358369;ENST00000406926|ENST00000277475	T;T|T	0.23147|0.16597	1.92;1.92|2.33	5.13|5.13	5.13|5.13	0.70059|0.70059	.|.	0.052634|.	0.85682|.	D|.	0.000000|.	T|T	0.34193|0.34193	0.0889|0.0889	M|M	0.71581|0.71581	2.175|2.175	0.35587|0.35587	D|D	0.806755|0.806755	D;D|.	0.89917|.	1.0;0.982|.	D;P|.	0.83275|.	0.996;0.85|.	T|T	0.32402|0.32402	-0.9908|-0.9908	10|7	0.62326|0.23302	D|T	0.03|0.38	-27.6397|-27.6397	17.5609|17.5609	0.87906|0.87906	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	329;265|.	B4DZP8;Q7L4E1|.	.;FA73B_HUMAN|.	K|Q	265|305	ENSP00000351138:E265K;ENSP00000384662:E265K|ENSP00000277475:R305Q	ENSP00000351138:E265K|ENSP00000277475:R305Q	E|R	+|+	1|2	0|0	FAM73B|FAM73B	130861371|130861371	1.000000|1.000000	0.71417|0.71417	0.962000|0.962000	0.40283|0.40283	0.122000|0.122000	0.20287|0.20287	9.238000|9.238000	0.95380|0.95380	2.376000|2.376000	0.81061|0.81061	0.491000|0.491000	0.48974|0.48974	GAG|CGA	.	.	none		0.642	FAM73B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054542.7	NM_032809	Missense_Mutation
ANKRD10	55608	hgsc.bcm.edu	37	13	111532094	111532094	+	Missense_Mutation	SNP	C	C	G			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr13:111532094C>G	ENST00000267339.2	-	6	1287	c.1153G>C	c.(1153-1155)Gaa>Caa	p.E385Q	ANKRD10_ENST00000375758.5_3'UTR	NM_017664.2	NP_060134.2	Q9NXR5	ANR10_HUMAN	ankyrin repeat domain 10	385								p.E385K(1)		central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(3)	9	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		all cancers(43;0.0882)|BRCA - Breast invasive adenocarcinoma(86;0.188)|Lung(89;0.208)			GGGATGCTTTCAGCAGTGTCC	0.567																																					p.E385Q		Atlas-SNP	.											ANKRD10,NS,carcinoma,0,1	ANKRD10	24	1	1	Substitution - Missense(1)	lung(1)	c.G1153C						PASS	.						152.0	107.0	122.0					13																	111532094		2203	4300	6503	SO:0001583	missense	55608	exon6			TGCTTTCAGCAGT	AK000100	CCDS9520.1, CCDS66580.1	13q33.3	2013-01-10			ENSG00000088448	ENSG00000088448		"""Ankyrin repeat domain containing"""	20265	protein-coding gene	gene with protein product							Standard	NM_017664		Approved	FLJ20093	uc001vrn.3	Q9NXR5	OTTHUMG00000017349	ENST00000267339.2:c.1153G>C	13.37:g.111532094C>G	ENSP00000267339:p.Glu385Gln	58.0	0.0	0		35.0	19.0	0.542857	NM_017664	Q5VW12|Q9BV12	Missense_Mutation	SNP	ENST00000267339.2	37	CCDS9520.1	.	.	.	.	.	.	.	.	.	.	C	17.55	3.417175	0.62511	.	.	ENSG00000088448	ENST00000267339	T	0.77750	-1.12	5.52	5.52	0.82312	.	0.053640	0.64402	D	0.000001	D	0.88388	0.6423	M	0.75264	2.295	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.89186	0.3547	10	0.87932	D	0	-17.5215	19.4338	0.94783	0.0:1.0:0.0:0.0	.	385	Q9NXR5	ANR10_HUMAN	Q	385	ENSP00000267339:E385Q	ENSP00000267339:E385Q	E	-	1	0	ANKRD10	110330095	1.000000	0.71417	0.259000	0.24435	0.152000	0.21847	5.793000	0.69060	2.598000	0.87819	0.650000	0.86243	GAA	.	.	none		0.567	ANKRD10-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045783.1		
ASPM	259266	hgsc.bcm.edu	37	1	197069752	197069752	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr1:197069752T>G	ENST00000367409.4	-	18	8885	c.8629A>C	c.(8629-8631)Aaa>Caa	p.K2877Q	ASPM_ENST00000294732.7_Intron|ASPM_ENST00000367408.1_Intron	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	2877	IQ 32. {ECO:0000255|PROSITE- ProRule:PRU00116}.				developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						AAAAACTGTTTTCTGGTTTGC	0.373																																					p.K2877Q		Atlas-SNP	.											.	ASPM	444	.	0			c.A8629C						PASS	.						52.0	55.0	54.0					1																	197069752		2203	4298	6501	SO:0001583	missense	259266	exon18			ACTGTTTTCTGGT	AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"""microcephaly, primary autosomal recessive 5"", ""asp (abnormal spindle)-like, microcephaly associated (Drosophila)"""	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.8629A>C	1.37:g.197069752T>G	ENSP00000356379:p.Lys2877Gln	151.0	0.0	0		110.0	30.0	0.272727	NM_018136	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	37	CCDS1389.1	.	.	.	.	.	.	.	.	.	.	T	11.88	1.769791	0.31320	.	.	ENSG00000066279	ENST00000367409;ENST00000367406	T	0.35789	1.29	4.76	4.76	0.60689	.	0.827867	0.10966	N	0.614361	T	0.48714	0.1515	L	0.49571	1.57	0.28913	N	0.89257	D;D	0.60160	0.969;0.987	D;P	0.70227	0.968;0.9	T	0.38001	-0.9681	10	0.31617	T	0.26	.	5.7651	0.18221	0.1604:0.0847:0.0:0.7549	.	863;2877	E7EQ84;Q8IZT6	.;ASPM_HUMAN	Q	2877;863	ENSP00000356379:K2877Q	ENSP00000356376:K863Q	K	-	1	0	ASPM	195336375	0.003000	0.15002	0.093000	0.20910	0.442000	0.32017	0.921000	0.28718	1.908000	0.55244	0.460000	0.39030	AAA	.	.	none		0.373	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136	
SPOP	8405	hgsc.bcm.edu	37	17	47696644	47696644	+	Missense_Mutation	SNP	A	A	T			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr17:47696644A>T	ENST00000393328.2	-	5	669	c.304T>A	c.(304-306)Ttc>Atc	p.F102I	SPOP_ENST00000503676.1_Missense_Mutation_p.F102I|SPOP_ENST00000393331.3_Missense_Mutation_p.F102I|SPOP_ENST00000504102.1_Missense_Mutation_p.F102I|SPOP_ENST00000347630.2_Missense_Mutation_p.F102I|SPOP_ENST00000513080.1_5'Flank	NM_003563.3	NP_003554.1	O43791	SPOP_HUMAN	speckle-type POZ protein	102	MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.|Required for nuclear localization.				glucose homeostasis (GO:0042593)|positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902237)|positive regulation of type B pancreatic cell apoptotic process (GO:2000676)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	Cul3-RING ubiquitin ligase complex (GO:0031463)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	ubiquitin protein ligase binding (GO:0031625)			endometrium(18)|kidney(1)|large_intestine(3)|liver(1)|lung(4)|ovary(3)|prostate(33)	63						GAGAATTTGAATTTTGCCCGA	0.408										Prostate(2;0.17)																											p.F102I		Atlas-SNP	.											SPOP,NS,adenoma,+1,3	SPOP	91	3	0			c.T304A						PASS	.						147.0	136.0	140.0					17																	47696644		2203	4300	6503	SO:0001583	missense	8405	exon4			ATTTGAATTTTGC	AJ000644	CCDS11551.1	17q21.33	2013-01-09			ENSG00000121067	ENSG00000121067		"""BTB/POZ domain containing"""	11254	protein-coding gene	gene with protein product		602650				9414087	Standard	NM_001007227		Approved	TEF2, BTBD32	uc002ipg.3	O43791	OTTHUMG00000161496	ENST00000393328.2:c.304T>A	17.37:g.47696644A>T	ENSP00000377001:p.Phe102Ile	98.0	0.0	0		114.0	33.0	0.289474	NM_001007228	B2R6S3|D3DTW7|Q53HJ1	Missense_Mutation	SNP	ENST00000393328.2	37	CCDS11551.1	.	.	.	.	.	.	.	.	.	.	A	31	5.059254	0.93846	.	.	ENSG00000121067	ENST00000393328;ENST00000393331;ENST00000347630;ENST00000504102;ENST00000503676;ENST00000513872;ENST00000509079;ENST00000505581;ENST00000507970;ENST00000514121;ENST00000515508	T;T;T;T;T;T;T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29;-0.29;-0.29;-0.29;-0.29;-0.29;-0.29	5.52	5.52	0.82312	TRAF-type (1);TRAF-like (1);MATH (3);	0.000000	0.85682	D	0.000000	D	0.83459	0.5259	M	0.87180	2.865	0.80722	D	1	D	0.76494	0.999	D	0.69824	0.966	D	0.86433	0.1762	10	0.72032	D	0.01	-11.8278	15.4649	0.75390	1.0:0.0:0.0:0.0	.	102	O43791	SPOP_HUMAN	I	102;102;102;102;102;55;102;102;102;102;102	ENSP00000377001:F102I;ENSP00000377004:F102I;ENSP00000240327:F102I;ENSP00000425905:F102I;ENSP00000420908:F102I;ENSP00000426986:F102I;ENSP00000420960:F102I;ENSP00000426262:F102I;ENSP00000424119:F102I;ENSP00000426537:F102I	ENSP00000240327:F102I	F	-	1	0	SPOP	45051643	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.135000	0.94478	2.317000	0.78254	0.460000	0.39030	TTC	.	.	none		0.408	SPOP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365154.2	NM_003563	
CS	1431	hgsc.bcm.edu	37	12	56676766	56676766	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr12:56676766A>C	ENST00000351328.3	-	5	467	c.277T>G	c.(277-279)Ttc>Gtc	p.F93V	CS_ENST00000542324.2_Missense_Mutation_p.F80V|CS_ENST00000548567.1_Missense_Mutation_p.F27V	NM_004077.2	NP_004068.2	O75390	CISY_HUMAN	citrate synthase	93					carbohydrate metabolic process (GO:0005975)|cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	citrate (Si)-synthase activity (GO:0004108)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	17		Myeloproliferative disorder(1001;0.000374)		BRCA - Breast invasive adenocarcinoma(357;6.17e-07)		AAGCCTCGGAAACGGATGCCC	0.483																																					p.F93V		Atlas-SNP	.											.	CS	44	.	0			c.T277G						PASS	.						75.0	79.0	78.0					12																	56676766		2203	4300	6503	SO:0001583	missense	1431	exon5			CTCGGAAACGGAT		CCDS8913.1	12q13.2	2012-10-02				ENSG00000062485	2.3.3.1		2422	protein-coding gene	gene with protein product		118950					Standard	NM_004077		Approved		uc001sks.1	O75390	OTTHUMG00000170344	ENST00000351328.3:c.277T>G	12.37:g.56676766A>C	ENSP00000342056:p.Phe93Val	45.0	0.0	0		55.0	16.0	0.290909	NM_004077	Q71UT9|Q7KZH0|Q96FZ8|Q9BWN8	Missense_Mutation	SNP	ENST00000351328.3	37	CCDS8913.1	.	.	.	.	.	.	.	.	.	.	A	26.2	4.719196	0.89205	.	.	ENSG00000062485	ENST00000548567;ENST00000351328;ENST00000542324;ENST00000549221;ENST00000548041;ENST00000551936;ENST00000550734;ENST00000551253;ENST00000552688;ENST00000551473;ENST00000547298;ENST00000551137;ENST00000550655;ENST00000550159;ENST00000551430	.	.	.	4.55	4.55	0.56014	Citrate synthase-like, large alpha subdomain (1);Citrate synthase-like, core (1);	0.000000	0.85682	D	0.000000	D	0.87418	0.6172	H	0.97758	4.07	0.80722	D	1	D;D;D;D	0.76494	0.998;0.999;0.997;0.999	D;D;D;D	0.79108	0.987;0.992;0.986;0.992	D	0.91554	0.5259	9	0.87932	D	0	-14.8489	13.594	0.61978	1.0:0.0:0.0:0.0	.	27;80;48;93	B7Z1E1;B4DJV2;B3KTN4;O75390	.;.;.;CISY_HUMAN	V	27;93;80;18;93;27;27;27;57;27;27;27;93;27;27	.	ENSP00000342056:F93V	F	-	1	0	CS	54963033	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.639000	0.91023	1.995000	0.58328	0.528000	0.53228	TTC	.	.	none		0.483	CS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408588.2	NM_004077	
KCTD20	222658	hgsc.bcm.edu	37	6	36454876	36454876	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr6:36454876A>C	ENST00000373731.2	+	8	1575	c.1184A>C	c.(1183-1185)cAc>cCc	p.H395P	KCTD20_ENST00000449081.2_Missense_Mutation_p.H229P|KCTD20_ENST00000544295.1_Missense_Mutation_p.H149P|KCTD20_ENST00000474988.1_3'UTR|KCTD20_ENST00000536244.1_Missense_Mutation_p.H250P	NM_173562.3	NP_775833.2	Q7Z5Y7	KCD20_HUMAN	potassium channel tetramerization domain containing 20	395					protein homooligomerization (GO:0051260)					central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|skin(1)	15						TTAATGCATCACCCACCCCAA	0.502																																					p.H395P		Atlas-SNP	.											KCTD20,NS,lymphoid_neoplasm,+1,1	KCTD20	37	1	0			c.A1184C						scavenged	.						214.0	214.0	214.0					6																	36454876		2203	4300	6503	SO:0001583	missense	222658	exon8			TGCATCACCCACC	BC023525	CCDS4821.1, CCDS69096.1, CCDS69097.1	6p21.31	2013-06-20	2013-06-20	2006-06-26	ENSG00000112078	ENSG00000112078			21052	protein-coding gene	gene with protein product		615932	"""chromosome 6 open reading frame 69"", ""potassium channel tetramerisation domain containing 20"""	C6orf69			Standard	NM_001286580		Approved	dJ108K11.3, MGC14254	uc003ome.3	Q7Z5Y7	OTTHUMG00000014597	ENST00000373731.2:c.1184A>C	6.37:g.36454876A>C	ENSP00000362836:p.His395Pro	186.0	1.0	0.00537634		184.0	40.0	0.217391	NM_173562	B4DZD3|B4E2Q3|F5H3T3|Q5W105|Q69YQ7|Q8IZ55	Missense_Mutation	SNP	ENST00000373731.2	37	CCDS4821.1	.	.	.	.	.	.	.	.	.	.	A	17.15	3.315570	0.60524	.	.	ENSG00000112078	ENST00000373731;ENST00000544295;ENST00000449081;ENST00000536244	T;T	0.44881	0.91;0.97	5.91	5.91	0.95273	.	0.121605	0.56097	D	0.000028	T	0.10551	0.0258	N	0.04508	-0.205	0.51012	D	0.9999	B;B	0.12013	0.004;0.005	B;B	0.12156	0.007;0.006	T	0.12528	-1.0544	10	0.27785	T	0.31	-22.5018	12.2309	0.54486	0.8582:0.1418:0.0:0.0	.	229;395	Q7Z5Y7-2;Q7Z5Y7	.;KCD20_HUMAN	P	395;149;229;250	ENSP00000362836:H395P;ENSP00000439118:H250P	ENSP00000362836:H395P	H	+	2	0	KCTD20	36562854	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	4.355000	0.59424	2.252000	0.74401	0.533000	0.62120	CAC	.	.	none		0.502	KCTD20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040345.2	NM_173562	
ZSWIM6	57688	hgsc.bcm.edu	37	5	60831355	60831355	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr5:60831355G>A	ENST00000252744.5	+	10	2290	c.2290G>A	c.(2290-2292)Gtt>Att	p.V764I		NM_020928.1	NP_065979.1	Q9HCJ5	ZSWM6_HUMAN	zinc finger, SWIM-type containing 6	764					neuron projection morphogenesis (GO:0048812)|regulation of neuron migration (GO:2001222)		zinc ion binding (GO:0008270)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)	8						TCGGGAGAGCGTTCCAATGCA	0.423																																					p.V764I		Atlas-SNP	.											ZSWIM6,colon,carcinoma,0,1	ZSWIM6	51	1	0			c.G2290A						PASS	.						241.0	193.0	207.0					5																	60831355		692	1591	2283	SO:0001583	missense	57688	exon10			GAGAGCGTTCCAA	BC039438	CCDS47215.1	5q12.1	2011-03-17			ENSG00000130449	ENSG00000130449		"""Zinc fingers, SWIM-type"""	29316	protein-coding gene	gene with protein product		615951				10997877, 16427614	Standard	NM_020928		Approved	KIAA1577	uc003jsr.3	Q9HCJ5	OTTHUMG00000162388	ENST00000252744.5:c.2290G>A	5.37:g.60831355G>A	ENSP00000252744:p.Val764Ile	136.0	0.0	0		148.0	46.0	0.310811	NM_020928		Missense_Mutation	SNP	ENST00000252744.5	37	CCDS47215.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.680816	0.88542	.	.	ENSG00000130449	ENST00000252744	T	0.50548	0.74	5.16	5.16	0.70880	.	0.198464	0.43919	D	0.000501	T	0.41650	0.1168	L	0.53249	1.67	0.44966	D	0.997988	P	0.38473	0.633	B	0.35859	0.212	T	0.24012	-1.0172	10	0.31617	T	0.26	-9.3556	12.5292	0.56104	0.0759:0.0:0.9241:0.0	.	764	Q9HCJ5	ZSWM6_HUMAN	I	764	ENSP00000252744:V764I	ENSP00000252744:V764I	V	+	1	0	ZSWIM6	60867112	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	7.805000	0.86005	2.840000	0.97914	0.655000	0.94253	GTT	.	.	none		0.423	ZSWIM6-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368710.1	NM_020928	
RYR1	6261	hgsc.bcm.edu	37	19	38931449	38931449	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr19:38931449C>T	ENST00000359596.3	+	2	110	c.110C>T	c.(109-111)gCc>gTc	p.A37V	RYR1_ENST00000355481.4_Missense_Mutation_p.A37V|RYR1_ENST00000360985.3_Missense_Mutation_p.A37V			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	37					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CTCTGCCTGGCCGCCGAGGGC	0.682																																					p.A37V		Atlas-SNP	.											.	RYR1	708	.	0			c.C110T						PASS	.						17.0	17.0	17.0					19																	38931449		2196	4289	6485	SO:0001583	missense	6261	exon2			GCCTGGCCGCCGA	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.110C>T	19.37:g.38931449C>T	ENSP00000352608:p.Ala37Val	116.0	0.0	0		92.0	29.0	0.315217	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	c	15.49	2.848708	0.51164	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.98419	-4.92;-4.92;-4.92	4.68	4.68	0.58851	Inositol 1,4,5-trisphosphate/ryanodine receptor (1);	0.302095	0.25291	U	0.031737	D	0.98548	0.9515	M	0.77820	2.39	0.34501	D	0.706091	D;D	0.89917	0.994;1.0	P;D	0.68039	0.642;0.955	D	0.99967	1.1892	10	0.87932	D	0	.	11.0484	0.47872	0.0:0.8112:0.1888:0.0	.	37;37	P21817-2;P21817	.;RYR1_HUMAN	V	37	ENSP00000352608:A37V;ENSP00000347667:A37V;ENSP00000354254:A37V	ENSP00000347667:A37V	A	+	2	0	RYR1	43623289	1.000000	0.71417	0.988000	0.46212	0.475000	0.33008	5.618000	0.67722	2.150000	0.67090	0.556000	0.70494	GCC	.	.	none		0.682	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
TBC1D10B	26000	hgsc.bcm.edu	37	16	30381303	30381303	+	Missense_Mutation	SNP	C	C	G	rs12930787	byFrequency	TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr16:30381303C>G	ENST00000409939.3	-	1	282	c.202G>C	c.(202-204)Gag>Cag	p.E68Q		NM_015527.3	NP_056342.3	Q4KMP7	TB10B_HUMAN	TBC1 domain family, member 10B	68	Pro-rich.				positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab GTPase activity (GO:0032313)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)			endometrium(2)|kidney(1)|lung(2)|urinary_tract(1)	6			Colorectal(24;0.193)			gcAGAGGTCTCGGCCGACCCC	0.786													G|||	1131	0.225839	0.2224	0.2219	5008	,	,		5407	0.0794		0.327	False		,,,				2504	0.2802				p.E68Q		Atlas-SNP	.											.	TBC1D10B	32	.	0			c.G202C						PASS	.						1.0	1.0	1.0					16																	30381303		132	419	551	SO:0001583	missense	26000	exon1			AGGTCTCGGCCGA	BC063112	CCDS10676.2	16p11.2	2013-07-09			ENSG00000169221	ENSG00000169221			24510	protein-coding gene	gene with protein product		613620				20404108	Standard	NM_015527		Approved	DKFZP434P1750, Rab27A-GAPbeta, FLJ13130, EPI64B	uc002dxt.3	Q4KMP7	OTTHUMG00000132396	ENST00000409939.3:c.202G>C	16.37:g.30381303C>G	ENSP00000386538:p.Glu68Gln	0.0	0.0	.		5.0	5.0	1	NM_015527	B9A6L0|Q6IN54|Q6P530|Q71RG7|Q86VC5|Q9H8Z2|Q9NUN6|Q9UFP2	Missense_Mutation	SNP	ENST00000409939.3	37	CCDS10676.2	476	0.21794871794871795	101	0.20528455284552846	86	0.23756906077348067	47	0.08216783216783216	242	0.31926121372031663	G	0.004	-2.356799	0.00214	.	.	ENSG00000169221	ENST00000409939	T	0.04156	3.69	3.57	-0.0103	0.13997	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45366	-0.9266	8	0.02654	T	1	.	5.7944	0.18379	0.2033:0.4717:0.325:0.0	rs12930787	68	Q4KMP7	TB10B_HUMAN	Q	68	ENSP00000386538:E68Q	ENSP00000386538:E68Q	E	-	1	0	TBC1D10B	30288804	0.000000	0.05858	0.000000	0.03702	0.178000	0.23041	0.290000	0.18975	-0.070000	0.12908	-0.647000	0.03941	GAG	C|0.776;G|0.224	0.224	strong		0.786	TBC1D10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255527.3	NM_015527	
UBR4	23352	hgsc.bcm.edu	37	1	19503103	19503103	+	Missense_Mutation	SNP	G	G	C			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr1:19503103G>C	ENST00000375254.3	-	20	2783	c.2756C>G	c.(2755-2757)tCt>tGt	p.S919C	UBR4_ENST00000375217.2_Missense_Mutation_p.S919C|UBR4_ENST00000375226.2_Missense_Mutation_p.S919C|UBR4_ENST00000375267.2_Missense_Mutation_p.S919C	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	919					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		GAAATGCTTAGACCAGTTTTC	0.468																																					p.S919C		Atlas-SNP	.											.	UBR4	415	.	0			c.C2756G						PASS	.						104.0	99.0	101.0					1																	19503103		2203	4300	6503	SO:0001583	missense	23352	exon20			TGCTTAGACCAGT	AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"""Ubiquitin protein ligase E3 component n-recognins"""	30313	protein-coding gene	gene with protein product		609890	"""zinc finger, UBR1 type 1"""	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.2756C>G	1.37:g.19503103G>C	ENSP00000364403:p.Ser919Cys	100.0	0.0	0		99.0	30.0	0.30303	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	37	CCDS189.1	.	.	.	.	.	.	.	.	.	.	G	13.91	2.379097	0.42207	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000419533	T;T;T;T	0.40225	1.04;1.04;1.04;1.04	5.97	4.02	0.46733	.	0.441462	0.24085	N	0.041697	T	0.23249	0.0562	N	0.08118	0	0.80722	D	1	B	0.28512	0.214	B	0.24541	0.054	T	0.11867	-1.0570	10	0.62326	D	0.03	.	12.3615	0.55205	0.0678:0.1211:0.8112:0.0	.	919	Q5T4S7	UBR4_HUMAN	C	919;919;919;919;135	ENSP00000364403:S919C;ENSP00000364416:S919C;ENSP00000364365:S919C;ENSP00000364374:S919C	ENSP00000364365:S919C	S	-	2	0	UBR4	19375690	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.809000	0.55606	2.836000	0.97738	0.655000	0.94253	TCT	.	.	none		0.468	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765	
CS	1431	hgsc.bcm.edu	37	12	56676685	56676685	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr12:56676685A>C	ENST00000351328.3	-	5	548	c.358T>G	c.(358-360)Ttt>Gtt	p.F120V	CS_ENST00000542324.2_Missense_Mutation_p.F107V|CS_ENST00000548567.1_Missense_Mutation_p.F54V	NM_004077.2	NP_004068.2	O75390	CISY_HUMAN	citrate synthase	120					carbohydrate metabolic process (GO:0005975)|cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	citrate (Si)-synthase activity (GO:0004108)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	17		Myeloproliferative disorder(1001;0.000374)		BRCA - Breast invasive adenocarcinoma(357;6.17e-07)		AGCAGCCAAAATAAGCCCTCA	0.483																																					p.F120V		Atlas-SNP	.											.	CS	44	.	0			c.T358G						PASS	.						109.0	111.0	110.0					12																	56676685		2203	4300	6503	SO:0001583	missense	1431	exon5			GCCAAAATAAGCC		CCDS8913.1	12q13.2	2012-10-02				ENSG00000062485	2.3.3.1		2422	protein-coding gene	gene with protein product		118950					Standard	NM_004077		Approved		uc001sks.1	O75390	OTTHUMG00000170344	ENST00000351328.3:c.358T>G	12.37:g.56676685A>C	ENSP00000342056:p.Phe120Val	71.0	0.0	0		83.0	23.0	0.277108	NM_004077	Q71UT9|Q7KZH0|Q96FZ8|Q9BWN8	Missense_Mutation	SNP	ENST00000351328.3	37	CCDS8913.1	.	.	.	.	.	.	.	.	.	.	A	28.4	4.920811	0.92249	.	.	ENSG00000062485	ENST00000548567;ENST00000351328;ENST00000542324;ENST00000549221;ENST00000548041;ENST00000551936;ENST00000550734;ENST00000551253;ENST00000552688;ENST00000546554;ENST00000551473;ENST00000547298;ENST00000551137;ENST00000550655;ENST00000551968;ENST00000550159;ENST00000551430	.	.	.	4.61	4.61	0.57282	Citrate synthase-like, large alpha subdomain (1);Citrate synthase-like, core (1);	0.000000	0.85682	D	0.000000	D	0.85053	0.5609	H	0.95187	3.635	0.80722	D	1	P;P;P;P	0.51057	0.892;0.941;0.941;0.941	P;P;P;P	0.60682	0.783;0.809;0.752;0.878	D	0.89441	0.3723	9	0.87932	D	0	-12.2063	13.7141	0.62687	1.0:0.0:0.0:0.0	.	54;107;75;120	B7Z1E1;B4DJV2;B3KTN4;O75390	.;.;.;CISY_HUMAN	V	54;120;107;45;120;54;54;54;84;70;54;54;54;120;92;54;54	.	ENSP00000342056:F120V	F	-	1	0	CS	54962952	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.542000	0.90647	2.023000	0.59567	0.528000	0.53228	TTT	.	.	none		0.483	CS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408588.2	NM_004077	
TP53	7157	hgsc.bcm.edu	37	17	7574035	7574035	+	Splice_Site	SNP	T	T	C			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr17:7574035T>C	ENST00000269305.4	-	10	1183		c.e10-2		TP53_ENST00000359597.4_Intron|TP53_ENST00000445888.2_Splice_Site|TP53_ENST00000413465.2_Intron|TP53_ENST00000420246.2_Splice_Site|TP53_ENST00000455263.2_Splice_Site	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53						apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|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 transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.?(10)|p.0?(8)|p.I332fs*49(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CCCACGGATCTGCAGCAACAG	0.507		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											.	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	TP53_ENST00000269305,NS,carcinoma,0,13	TP53	33396	13	19	Unknown(10)|Whole gene deletion(8)|Insertion - Frameshift(1)	lung(5)|haematopoietic_and_lymphoid_tissue(4)|bone(4)|central_nervous_system(2)|liver(2)|stomach(1)|breast(1)	c.994-2A>G						PASS	.						44.0	36.0	38.0					17																	7574035		2203	4300	6503	SO:0001630	splice_region_variant	7157	exon11	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	CGGATCTGCAGCA	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.994-2A>G	17.37:g.7574035T>C		93.0	0.0	0		63.0	26.0	0.412698	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Splice_Site	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	12.31	1.898270	0.33535	.	.	ENSG00000141510	ENST00000269305;ENST00000445888;ENST00000396473	.	.	.	5.13	5.13	0.70059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.1784	0.59641	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	TP53	7514760	1.000000	0.71417	0.937000	0.37676	0.131000	0.20780	6.590000	0.74085	2.061000	0.61500	0.459000	0.35465	.	.	.	none		0.507	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	Intron
PTCH1	5727	hgsc.bcm.edu	37	9	98241333	98241333	+	Missense_Mutation	SNP	G	G	C	rs201602238		TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr9:98241333G>C	ENST00000331920.6	-	8	1463	c.1164C>G	c.(1162-1164)aaC>aaG	p.N388K	PTCH1_ENST00000429896.2_Missense_Mutation_p.N237K|PTCH1_ENST00000418258.1_Missense_Mutation_p.N237K|PTCH1_ENST00000375274.2_Missense_Mutation_p.N387K|PTCH1_ENST00000548379.1_5'Flank|PTCH1_ENST00000421141.1_Missense_Mutation_p.N237K|PTCH1_ENST00000430669.2_Missense_Mutation_p.N322K|PTCH1_ENST00000437951.1_Missense_Mutation_p.N322K	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	388					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)			NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				CTTTGTCCTCGTTCCAGTTGA	0.537																																					p.N388K		Atlas-SNP	.											.	PTCH1	1850	.	0			c.C1164G						PASS	.						173.0	128.0	143.0					9																	98241333		2203	4300	6503	SO:0001583	missense	5727	exon8			GTCCTCGTTCCAG	AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"""patched (Drosophila) homolog"", ""patched homolog (Drosophila)"", ""patched homolog 1 (Drosophila)"""	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.1164C>G	9.37:g.98241333G>C	ENSP00000332353:p.Asn388Lys	108.0	0.0	0		105.0	30.0	0.285714	NM_000264	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Missense_Mutation	SNP	ENST00000331920.6	37	CCDS6714.1	.	.	.	.	.	.	.	.	.	.	G	18.57	3.652082	0.67472	.	.	ENSG00000185920	ENST00000331920;ENST00000437951;ENST00000421141;ENST00000418258;ENST00000430669;ENST00000429896;ENST00000375274;ENST00000375271	D;D;D;D;D;D;D;D	0.90955	-2.7;-2.69;-2.68;-2.68;-2.69;-2.68;-2.7;-2.76	6.17	-9.99	0.00435	.	0.000000	0.85682	D	0.000000	D	0.92251	0.7542	M	0.68593	2.085	0.37604	D	0.920694	D;D;D;D	0.56746	0.976;0.971;0.976;0.977	P;P;P;P	0.61533	0.89;0.875;0.875;0.889	D	0.92850	0.6296	10	0.45353	T	0.12	-28.9913	22.0603	0.99966	0.7933:0.0:0.2067:0.0	.	237;322;387;388	Q13635-4;Q13635-3;Q13635-2;Q13635	.;.;.;PTC1_HUMAN	K	388;322;237;237;322;237;387;105	ENSP00000332353:N388K;ENSP00000389744:N322K;ENSP00000399981:N237K;ENSP00000396135:N237K;ENSP00000410287:N322K;ENSP00000414823:N237K;ENSP00000364423:N387K;ENSP00000364420:N105K	ENSP00000332353:N388K	N	-	3	2	PTCH1	97281154	0.001000	0.12720	0.416000	0.26546	0.846000	0.48090	-1.360000	0.02600	-2.160000	0.00786	-0.940000	0.02684	AAC	G|1.000;A|0.000	.	alt		0.537	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264	
RBBP6	5930	hgsc.bcm.edu	37	16	24557518	24557518	+	Missense_Mutation	SNP	T	T	A			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr16:24557518T>A	ENST00000319715.4	+	2	633	c.201T>A	c.(199-201)aaT>aaA	p.N67K	RBBP6_ENST00000452655.2_Missense_Mutation_p.N67K|RBBP6_ENST00000381039.3_Missense_Mutation_p.N67K|RBBP6_ENST00000348022.2_Missense_Mutation_p.N67K	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	67	DWNN. {ECO:0000255|PROSITE- ProRule:PRU00612}.				embryonic organ development (GO:0048568)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|somite development (GO:0061053)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(1)	46				GBM - Glioblastoma multiforme(48;0.0518)		TTCCTAAGAATTCTTCTGTAA	0.299																																					p.N67K		Atlas-SNP	.											.	RBBP6	158	.	0			c.T201A						PASS	.						39.0	42.0	41.0					16																	24557518		2192	4278	6470	SO:0001583	missense	5930	exon2			TAAGAATTCTTCT		CCDS10621.1, CCDS10622.1, CCDS45444.1	16p12.2	2008-08-04	2001-11-28		ENSG00000122257	ENSG00000122257			9889	protein-coding gene	gene with protein product	"""proliferation potential-related protein"""	600938	"""retinoblastoma-binding protein 6"""			8595913, 16396680	Standard	NM_006910		Approved	P2P-R, PACT, SNAMA	uc002dmh.3	Q7Z6E9	OTTHUMG00000096991	ENST00000319715.4:c.201T>A	16.37:g.24557518T>A	ENSP00000317872:p.Asn67Lys	82.0	0.0	0		107.0	31.0	0.28972	NM_018703	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Missense_Mutation	SNP	ENST00000319715.4	37	CCDS10621.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.103777	0.76983	.	.	ENSG00000122257	ENST00000381039;ENST00000452655;ENST00000319715;ENST00000348022	T;T;T;T	0.45668	0.89;0.89;0.89;0.89	6.08	1.31	0.21738	DWNN domain (2);	0.091915	0.64402	D	0.000001	T	0.64148	0.2572	M	0.86573	2.825	0.51767	D	0.999934	D;D;D;D	0.76494	0.999;0.996;0.997;0.996	D;D;D;P	0.74023	0.982;0.937;0.962;0.894	T	0.66380	-0.5938	10	0.87932	D	0	-31.0125	10.2634	0.43441	0.0:0.4392:0.0:0.5608	.	67;67;67;67	Q7Z6E9-4;Q7Z6E9-2;Q7Z6E9;Q7Z6E9-3	.;.;RBBP6_HUMAN;.	K	67	ENSP00000370427:N67K;ENSP00000390537:N67K;ENSP00000317872:N67K;ENSP00000316291:N67K	ENSP00000317872:N67K	N	+	3	2	RBBP6	24465019	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	1.119000	0.31258	0.161000	0.19458	0.482000	0.46254	AAT	.	.	none		0.299	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910	
SETD1B	23067	hgsc.bcm.edu	37	12	122257461	122257461	+	Silent	SNP	G	G	A			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr12:122257461G>A	ENST00000604567.1	+	11	3638	c.3570G>A	c.(3568-3570)gaG>gaA	p.E1190E	SETD1B_ENST00000542440.1_Silent_p.E1147E|SETD1B_ENST00000267197.5_Silent_p.E1147E			Q9UPS6	SET1B_HUMAN	SET domain containing 1B	1190	Glu-rich.|Pro-rich.				histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone-lysine N-methyltransferase activity (GO:0018024)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|endometrium(6)|kidney(2)|prostate(2)	11						aggaagaagaggaggaggagg	0.617																																					p.E1147E		Atlas-SNP	.											.	SETD1B	105	.	0			c.G3441A						PASS	.						64.0	75.0	72.0					12																	122257461		692	1591	2283	SO:0001819	synonymous_variant	23067	exon11			AGAAGAGGAGGAG	AB028999	CCDS53838.1	12q24.31	2013-02-12			ENSG00000139718	ENSG00000139718		"""Chromatin-modifying enzymes / K-methyltransferases"", ""RNA binding motif (RRM) containing"""	29187	protein-coding gene	gene with protein product		611055				10470851, 17355966	Standard	NM_015048		Approved	KIAA1076, Set1B, KMT2G	uc001ubi.3	Q9UPS6	OTTHUMG00000169080	ENST00000604567.1:c.3570G>A	12.37:g.122257461G>A		50.0	0.0	0		58.0	4.0	0.0689655	NM_015048	F6MFW1	Silent	SNP	ENST00000604567.1	37																																																																																				.	.	none		0.617	SETD1B-002	PUTATIVE	non_canonical_U12|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000468264.1	XM_037523	
FBXO34	55030	hgsc.bcm.edu	37	14	55817618	55817618	+	Silent	SNP	T	T	G			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr14:55817618T>G	ENST00000313833.4	+	2	755	c.510T>G	c.(508-510)gtT>gtG	p.V170V	FBXO34_ENST00000440021.1_Silent_p.V170V	NM_017943.3	NP_060413.2	Q9NWN3	FBX34_HUMAN	F-box protein 34	170										breast(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(3)	22						TGAGGGAGGTTAACAGCAGGT	0.473																																					p.V170V		Atlas-SNP	.											.	FBXO34	61	.	0			c.T510G						PASS	.						88.0	75.0	79.0					14																	55817618		2203	4300	6503	SO:0001819	synonymous_variant	55030	exon2			GGAGGTTAACAGC	AK000732	CCDS32086.1	14q22.1	2004-08-24	2004-06-15			ENSG00000178974		"""F-boxes /  ""other"""""	20201	protein-coding gene	gene with protein product		609104	"""F-box only protein 34"""				Standard	NM_017943		Approved	FLJ20725, Fbx34	uc010aoo.3	Q9NWN3		ENST00000313833.4:c.510T>G	14.37:g.55817618T>G		134.0	0.0	0		109.0	26.0	0.238532	NM_017943	Q2VPB5|Q4VBP5|Q86TY4	Silent	SNP	ENST00000313833.4	37	CCDS32086.1																																																																																			.	.	none		0.473	FBXO34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411322.1		
SIGLEC1	6614	hgsc.bcm.edu	37	20	3679921	3679921	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr20:3679921A>G	ENST00000344754.4	-	7	1713	c.1714T>C	c.(1714-1716)Tca>Cca	p.S572P	SIGLEC1_ENST00000202578.4_Missense_Mutation_p.S572P	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	572	Ig-like C2-type 5.				cell-matrix adhesion (GO:0007160)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of T cell apoptotic process (GO:0070234)|single organismal cell-cell adhesion (GO:0016337)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|liver(2)|lung(24)|ovary(3)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)	70						CAGTGGTATGAGCCGGCGTCA	0.672																																					p.S572P		Atlas-SNP	.											.	SIGLEC1	210	.	0			c.T1714C						PASS	.						18.0	17.0	17.0					20																	3679921		2202	4296	6498	SO:0001583	missense	6614	exon7			GGTATGAGCCGGC	AF230073	CCDS13060.1	20p13	2013-01-29	2006-01-19	2006-01-19	ENSG00000088827	ENSG00000088827		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	11127	protein-coding gene	gene with protein product		600751	"""sialoadhesin"""	SN		8530048	Standard	XM_006723610		Approved	SIGLEC-1, CD169, FLJ00051, FLJ00055, FLJ00073, FLJ32150, dJ1009E24.1, sialoadhesin	uc002wja.3	Q9BZZ2	OTTHUMG00000031757	ENST00000344754.4:c.1714T>C	20.37:g.3679921A>G	ENSP00000341141:p.Ser572Pro	99.0	0.0	0		117.0	5.0	0.042735	NM_023068	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	Missense_Mutation	SNP	ENST00000344754.4	37	CCDS13060.1	.	.	.	.	.	.	.	.	.	.	A	15.50	2.852055	0.51270	.	.	ENSG00000088827	ENST00000344754;ENST00000202578	T;T	0.12672	2.66;2.66	5.46	4.3	0.51218	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	0.000000	0.34986	N	0.003523	T	0.24122	0.0584	L	0.39898	1.24	0.37064	D	0.898214	D;D	0.76494	0.999;0.999	D;D	0.91635	0.999;0.994	T	0.05321	-1.0892	10	0.35671	T	0.21	.	8.8204	0.35023	0.8101:0.1899:0.0:0.0	.	572;572	Q9BZZ2;Q9BZZ2-3	SN_HUMAN;.	P	572	ENSP00000341141:S572P;ENSP00000202578:S572P	ENSP00000202578:S572P	S	-	1	0	SIGLEC1	3627921	0.258000	0.24033	0.989000	0.46669	0.183000	0.23260	0.313000	0.19415	2.081000	0.62600	0.533000	0.62120	TCA	.	.	none		0.672	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	NM_023068	
ATG4C	84938	hgsc.bcm.edu	37	1	63300503	63300503	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr1:63300503A>C	ENST00000317868.4	+	9	1276	c.1069A>C	c.(1069-1071)Ata>Cta	p.I357L	ATG4C_ENST00000371120.3_Missense_Mutation_p.I357L	NM_032852.3	NP_116241.2	Q96DT6	ATG4C_HUMAN	autophagy related 4C, cysteine peptidase	357					autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|protein targeting to membrane (GO:0006612)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)	cysteine-type endopeptidase activity (GO:0004197)|peptidase activity (GO:0008233)		ATG4C/FBXO38(2)	NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(3)|ovary(1)|prostate(2)	19						AGATGTCAGCATAAAGGATTT	0.343																																					p.I357L		Atlas-SNP	.											.	ATG4C	96	.	0			c.A1069C						PASS	.						162.0	140.0	147.0					1																	63300503		2203	4300	6503	SO:0001583	missense	84938	exon9			GTCAGCATAAAGG	AK027773	CCDS623.1	1p31.3	2014-02-12	2012-06-06	2005-09-11	ENSG00000125703	ENSG00000125703			16040	protein-coding gene	gene with protein product		611339	"""AUT (S. cerevisiae)-like 1, cysteine endopeptidase; AUT-like 1, cysteine endopeptidase (S. cerevisiae)"", ""APG4 autophagy 4 homolog C (S. cerevisiae)"", ""ATG4 autophagy related 4 homolog C (S. cerevisiae)"""	AUTL1, APG4C		12446702	Standard	NM_032852		Approved	FLJ14867, AUTL3	uc001dau.3	Q96DT6	OTTHUMG00000009142	ENST00000317868.4:c.1069A>C	1.37:g.63300503A>C	ENSP00000322159:p.Ile357Leu	167.0	0.0	0		135.0	28.0	0.207407	NM_178221	A6NLR8|D3DQ58|Q96K04	Missense_Mutation	SNP	ENST00000317868.4	37	CCDS623.1	.	.	.	.	.	.	.	.	.	.	A	11.55	1.672343	0.29693	.	.	ENSG00000125703	ENST00000317868;ENST00000371120;ENST00000540025;ENST00000414558	T;T	0.40476	1.03;1.03	5.24	2.91	0.33838	.	0.176121	0.64402	D	0.000009	T	0.21550	0.0519	L	0.61387	1.9	0.35343	D	0.786638	B	0.25667	0.131	B	0.32393	0.145	T	0.03750	-1.1007	10	0.27785	T	0.31	-13.9202	8.0732	0.30701	0.7766:0.0:0.2234:0.0	.	357	Q96DT6	ATG4C_HUMAN	L	357;357;357;101	ENSP00000322159:I357L;ENSP00000360161:I357L	ENSP00000322159:I357L	I	+	1	0	ATG4C	63073091	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	5.058000	0.64300	0.411000	0.25702	-0.334000	0.08254	ATA	.	.	none		0.343	ATG4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025332.2	NM_032852	
ANKRD46	157567	hgsc.bcm.edu	37	8	101541987	101541987	+	Missense_Mutation	SNP	A	A	T			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr8:101541987A>T	ENST00000520552.1	-	3	236	c.75T>A	c.(73-75)ttT>ttA	p.F25L	ANKRD46_ENST00000335659.3_Missense_Mutation_p.F25L|ANKRD46_ENST00000519316.1_Missense_Mutation_p.F25L|ANKRD46_ENST00000519597.1_Missense_Mutation_p.F25L|ANKRD46_ENST00000520311.1_Missense_Mutation_p.F25L	NM_001270379.1	NP_001257308.1	Q86W74	ANR46_HUMAN	ankyrin repeat domain 46	25						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(4)	7	all_cancers(14;5.07e-05)|all_epithelial(15;2.84e-07)|Lung NSC(17;0.000353)|all_lung(17;0.000998)		Epithelial(11;2.61e-11)|all cancers(13;5.03e-09)|OV - Ovarian serous cystadenocarcinoma(57;4.49e-06)|STAD - Stomach adenocarcinoma(118;0.0957)			TGGAATAATTAAAGTCCCCAT	0.468																																					p.F25L		Atlas-SNP	.											.	ANKRD46	13	.	0			c.T75A						PASS	.						74.0	70.0	71.0					8																	101541987		2203	4300	6503	SO:0001583	missense	157567	exon3			ATAATTAAAGTCC	AB077205	CCDS6287.1, CCDS59109.1	8q22.3	2013-01-10						"""Ankyrin repeat domain containing"""	27229	protein-coding gene	gene with protein product							Standard	NM_001270377		Approved		uc003yjm.4	Q86W74		ENST00000520552.1:c.75T>A	8.37:g.101541987A>T	ENSP00000429015:p.Phe25Leu	150.0	0.0	0		138.0	38.0	0.275362	NM_001270378	Q6P9B7	Missense_Mutation	SNP	ENST00000520552.1	37	CCDS59109.1	.	.	.	.	.	.	.	.	.	.	A	9.293	1.051020	0.19827	.	.	ENSG00000186106	ENST00000520552;ENST00000335659;ENST00000519597;ENST00000520311;ENST00000519316;ENST00000358990;ENST00000524072;ENST00000523000;ENST00000521345	T;T;T;T;T;T;T;T;T	0.61040	0.18;0.18;0.18;0.18;0.18;0.18;0.18;0.18;0.14	5.78	0.537	0.17144	Ankyrin repeat-containing domain (4);	0.178647	0.51477	D	0.000097	T	0.17831	0.0428	N	0.00960	-1.095	0.43740	D	0.99623	B;B	0.02656	0.0;0.0	B;B	0.06405	0.0;0.002	T	0.31861	-0.9928	10	0.02654	T	1	.	5.2114	0.15318	0.5244:0.1482:0.3274:0.0	.	25;25	Q86W74-2;Q86W74	.;ANR46_HUMAN	L	25	ENSP00000429015:F25L;ENSP00000335287:F25L;ENSP00000430056:F25L;ENSP00000428388:F25L;ENSP00000430827:F25L;ENSP00000351881:F25L;ENSP00000430357:F25L;ENSP00000430800:F25L;ENSP00000429647:F25L	ENSP00000335287:F25L	F	-	3	2	ANKRD46	101611163	0.999000	0.42202	1.000000	0.80357	0.986000	0.74619	0.814000	0.27239	0.139000	0.18822	0.533000	0.62120	TTT	.	.	none		0.468	ANKRD46-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000379899.1	NM_198401	
RBM23	55147	hgsc.bcm.edu	37	14	23371265	23371265	+	Silent	SNP	G	G	A	rs376457710|rs568447355	byFrequency	TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr14:23371265G>A	ENST00000359890.3	-	12	1365	c.1170C>T	c.(1168-1170)gcC>gcT	p.A390A	RBM23_ENST00000555209.1_Silent_p.A140A|RBM23_ENST00000346528.5_Silent_p.A356A|RBM23_ENST00000399922.2_Silent_p.A374A|RBM23_ENST00000542016.2_Silent_p.A220A	NM_001077351.1	NP_001070819.1	Q86U06	RBM23_HUMAN	RNA binding motif protein 23	390	Ala-rich.				mRNA processing (GO:0006397)	membrane (GO:0016020)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(3)|kidney(2)|lung(3)|prostate(1)|skin(1)	10	all_cancers(95;4.69e-05)			GBM - Glioblastoma multiforme(265;0.0128)		GGgcggcggcggcagcagcag	0.552													G|||	3	0.000599042	0.0008	0.0014	5008	,	,		16976	0.0		0.001	False		,,,				2504	0.0				p.A390A		Atlas-SNP	.											.	RBM23	44	.	0			c.C1170T						PASS	.						36.0	39.0	38.0					14																	23371265		1973	4161	6134	SO:0001819	synonymous_variant	55147	exon12			GGCGGCGGCAGCA	AF275678	CCDS41919.1, CCDS41920.1, CCDS41921.1	14q11.1	2014-07-03	2004-04-23	2004-04-23		ENSG00000100461		"""RNA binding motif (RRM) containing"""	20155	protein-coding gene	gene with protein product	"""coactivator of activating protein-1 and estrogen recep- tors beta"""		"""RNA-binding region (RNP1, RRM) containing 4"""	RNPC4		15694343	Standard	NM_018107		Approved	FLJ10482, CAPERbeta	uc001whg.3	Q86U06		ENST00000359890.3:c.1170C>T	14.37:g.23371265G>A		63.0	0.0	0		65.0	6.0	0.0923077	NM_001077351	D3DS32|Q8ND16|Q8TB88|Q8WY40|Q9BUJ1|Q9NVV7	Silent	SNP	ENST00000359890.3	37	CCDS41921.1	.	.	.	.	.	.	.	.	.	.	G	0.006	-2.085813	0.00371	.	.	ENSG00000100461	ENST00000553884	.	.	.	1.37	-1.47	0.08772	.	.	.	.	.	T	0.27594	0.0678	.	.	.	0.29570	N	0.850013	.	.	.	.	.	.	T	0.32613	-0.9900	4	.	.	.	-1.1482	4.4328	0.11536	0.5883:0.0:0.4117:0.0	.	.	.	.	C	165	.	.	R	-	1	0	RBM23	22441105	0.019000	0.18553	0.046000	0.18839	0.018000	0.09664	-1.748000	0.01826	-0.441000	0.07201	-2.474000	0.00201	CGC	.	.	none		0.552	RBM23-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000413545.3		
MTHFD1	4522	hgsc.bcm.edu	37	14	64921449	64921449	+	Silent	SNP	G	G	A			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr14:64921449G>A	ENST00000545908.1	+	26	2971	c.2742G>A	c.(2740-2742)ggG>ggA	p.G914G	ZBTB25_ENST00000555220.1_Intron|MTHFD1_ENST00000216605.8_Silent_p.G858G|MTHFD1_ENST00000556284.1_3'UTR|ZBTB25_ENST00000555424.1_Intron			P11586	C1TC_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase	858	Formyltetrahydrofolate synthetase.				folic acid metabolic process (GO:0046655)|folic acid-containing compound biosynthetic process (GO:0009396)|histidine biosynthetic process (GO:0000105)|methionine biosynthetic process (GO:0009086)|one-carbon metabolic process (GO:0006730)|purine nucleotide biosynthetic process (GO:0006164)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|formate-tetrahydrofolate ligase activity (GO:0004329)|methenyltetrahydrofolate cyclohydrolase activity (GO:0004477)|methylenetetrahydrofolate dehydrogenase (NADP+) activity (GO:0004488)|methylenetetrahydrofolate dehydrogenase [NAD(P)+] activity (GO:0004486)			endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	30				OV - Ovarian serous cystadenocarcinoma(108;8.7e-12)|all cancers(60;3.29e-11)|BRCA - Breast invasive adenocarcinoma(234;0.0488)	Tetrahydrofolic acid(DB00116)	AGGGCTTTGGGAATCTCCCCA	0.488																																					p.G858G	Colon(18;220 581 13419 18191 31512)|GBM(126;343 1658 28700 44425 52519)	Atlas-SNP	.											.	MTHFD1	61	.	0			c.G2574A						PASS	.						103.0	91.0	95.0					14																	64921449		2203	4300	6503	SO:0001819	synonymous_variant	4522	exon26			CTTTGGGAATCTC	J04031	CCDS9763.1	14q24	2004-12-13			ENSG00000100714	ENSG00000100714	1.5.1.15, 3.5.4.-		7432	protein-coding gene	gene with protein product		172460		MTHFC, MTHFD		3053686, 2786332	Standard	NM_005956		Approved		uc001xhb.3	P11586	OTTHUMG00000141309	ENST00000545908.1:c.2742G>A	14.37:g.64921449G>A		79.0	0.0	0		75.0	27.0	0.36	NM_005956	B2R5Y2|G3V2B8|Q86VC9|Q9BVP5	Silent	SNP	ENST00000545908.1	37																																																																																				.	.	none		0.488	MTHFD1-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000412167.1		
CIART	148523	hgsc.bcm.edu	37	1	150256253	150256253	+	Silent	SNP	C	C	T			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr1:150256253C>T	ENST00000290363.5	+	2	854	c.405C>T	c.(403-405)gaC>gaT	p.D135D	C1orf51_ENST00000369094.1_Silent_p.D47D|C1orf51_ENST00000369095.1_Silent_p.D135D|C1orf51_ENST00000469255.1_Intron	NM_144697.2	NP_653298.1	Q8N365	CIART_HUMAN		135					circadian regulation of gene expression (GO:0032922)|locomotor rhythm (GO:0045475)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|E-box binding (GO:0070888)			endometrium(3)|large_intestine(2)|lung(3)|urinary_tract(2)	10	Lung NSC(24;7.29e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			CTCTCACAGACCTACTCAATG	0.428																																					p.D135D		Atlas-SNP	.											.	C1orf51	35	.	0			c.C405T						PASS	.						121.0	106.0	111.0					1																	150256253		2203	4300	6503	SO:0001819	synonymous_variant	148523	exon2			CACAGACCTACTC																												ENST00000290363.5:c.405C>T	1.37:g.150256253C>T		155.0	0.0	0		121.0	36.0	0.297521	NM_144697	B2RD43|D3DV01|Q8N795|Q96MG6	Silent	SNP	ENST00000290363.5	37	CCDS949.1																																																																																			.	.	none		0.428	C1orf51-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035058.1		
MUC2	4583	hgsc.bcm.edu	37	11	1093342	1093342	+	Missense_Mutation	SNP	C	C	A	rs55695633		TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr11:1093342C>A	ENST00000441003.2	+	30	5188	c.5161C>A	c.(5161-5163)Ccg>Acg	p.P1721T	MUC2_ENST00000359061.5_Missense_Mutation_p.P1688T|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_Missense_Mutation_p.P9T	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)	gaccccaaccccgacacccat	0.642																																					p.P1721T		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,-2,2	MUC2	614	2	0			c.C5161A						scavenged	.						234.0	273.0	260.0					11																	1093342		1973	3751	5724	SO:0001583	missense	4583	exon30			CCAACCCCGACAC	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.5161C>A	11.37:g.1093342C>A	ENSP00000415183:p.Pro1721Thr	68.0	2.0	0.0294118		74.0	9.0	0.121622	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	5.758	0.324335	0.10900	.	.	ENSG00000198788	ENST00000441003;ENST00000359061;ENST00000333592	T;T;T	0.04917	3.53;3.69;3.76	1.4	0.392	0.16288	.	2.679550	0.04278	N	0.343350	T	0.06325	0.0163	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42832	-0.9428	9	0.87932	D	0	.	6.4437	0.21865	0.291:0.709:0.0:0.0	.	1721	E7EUV1	.	T	1721;1688;9	ENSP00000415183:P1721T;ENSP00000351956:P1688T;ENSP00000331373:P9T	ENSP00000331373:P9T	P	+	1	0	MUC2	1083342	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-2.316000	0.01123	-0.071000	0.12886	-1.119000	0.02030	CCG	.	.	alt		0.642	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
AGA	175	hgsc.bcm.edu	37	4	178355534	178355534	+	Splice_Site	SNP	A	A	G			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr4:178355534A>G	ENST00000264595.2	-	7	934		c.e7+1		AGA_ENST00000506853.1_5'Flank	NM_000027.3|NM_001171988.1	NP_000018.2|NP_001165459.1	P20933	ASPG_HUMAN	aspartylglucosaminidase						protein deglycosylation (GO:0006517)|protein maturation (GO:0051604)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity (GO:0003948)|peptidase activity (GO:0008233)			endometrium(1)|kidney(2)|large_intestine(6)|lung(5)|skin(2)	16		all_lung(41;1.27e-09)|Lung NSC(41;1.1e-08)|Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Hepatocellular(41;0.148)|all_neural(102;0.164)|Colorectal(36;0.245)		all cancers(43;1.37e-22)|Epithelial(43;3.86e-20)|OV - Ovarian serous cystadenocarcinoma(60;3.8e-11)|Colorectal(24;6.98e-05)|GBM - Glioblastoma multiforme(59;0.000362)|COAD - Colon adenocarcinoma(29;0.000462)|STAD - Stomach adenocarcinoma(60;0.0029)|LUSC - Lung squamous cell carcinoma(193;0.0328)|READ - Rectum adenocarcinoma(43;0.163)		AAGAAGTCATACCTTGGCAGG	0.448																																					.		Atlas-SNP	.											.	AGA	39	.	0			c.806+2T>C						PASS	.						127.0	124.0	125.0					4																	178355534		2203	4300	6503	SO:0001630	splice_region_variant	175	exon8			AGTCATACCTTGG	X55330	CCDS3829.1	4q34.3	2014-06-23			ENSG00000038002	ENSG00000038002	3.5.1.26		318	protein-coding gene	gene with protein product	"""glycosylasparaginase"", ""N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase"""	613228					Standard	NM_000027		Approved	ASRG	uc003iuu.2	P20933	OTTHUMG00000160723	ENST00000264595.2:c.806+1T>C	4.37:g.178355534A>G		235.0	0.0	0		199.0	55.0	0.276382	NM_000027	B2R7H2|D3DP47|Q4W5Q2|Q6FHN6|Q9UCK6|Q9UCK7|Q9UCK8	Splice_Site	SNP	ENST00000264595.2	37	CCDS3829.1	.	.	.	.	.	.	.	.	.	.	A	12.58	1.980000	0.34942	.	.	ENSG00000038002	ENST00000264595;ENST00000502310	.	.	.	5.41	5.41	0.78517	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1232	0.72460	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	AGA	178592528	1.000000	0.71417	0.913000	0.36048	0.145000	0.21501	8.511000	0.90535	2.059000	0.61396	0.528000	0.53228	.	.	.	none		0.448	AGA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361916.1	NM_000027	Intron
CARS2	79587	hgsc.bcm.edu	37	13	111340329	111340329	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr13:111340329C>T	ENST00000257347.4	-	4	493	c.430G>A	c.(430-432)Gag>Aag	p.E144K	CARS2_ENST00000535398.1_5'UTR	NM_024537.2	NP_078813.1	Q9HA77	SYCM_HUMAN	cysteinyl-tRNA synthetase 2, mitochondrial (putative)	144					cysteinyl-tRNA aminoacylation (GO:0006423)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|cysteine-tRNA ligase activity (GO:0004817)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|prostate(4)|skin(1)	13	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.163)		L-Cysteine(DB00151)	AAGTCTTCCTCATAAAGACTG	0.532																																					p.E144K		Atlas-SNP	.											.	CARS2	37	.	0			c.G430A						PASS	.						75.0	66.0	69.0					13																	111340329		2203	4300	6503	SO:0001583	missense	79587	exon4			CTTCCTCATAAAG	BC007220	CCDS9514.1	13q34	2011-07-01	2007-02-22		ENSG00000134905	ENSG00000134905	6.1.1.16	"""Aminoacyl tRNA synthetases / Class I"""	25695	protein-coding gene	gene with protein product	"""cysteine tRNA ligase 2, mitochondrial (putative)"""	612800				15779907	Standard	NM_024537		Approved	FLJ12118	uc001vrd.2	Q9HA77	OTTHUMG00000017347	ENST00000257347.4:c.430G>A	13.37:g.111340329C>T	ENSP00000257347:p.Glu144Lys	81.0	0.0	0		52.0	16.0	0.307692	NM_024537	Q8NI84|Q96IV4	Missense_Mutation	SNP	ENST00000257347.4	37	CCDS9514.1	.	.	.	.	.	.	.	.	.	.	C	15.43	2.831407	0.50845	.	.	ENSG00000134905	ENST00000257347;ENST00000542709	T	0.35973	1.28	4.71	3.85	0.44370	Rossmann-like alpha/beta/alpha sandwich fold (1);	0.000000	0.85682	D	0.000000	T	0.64962	0.2646	M	0.89478	3.035	0.58432	D	0.999996	D	0.89917	1.0	D	0.91635	0.999	T	0.72301	-0.4334	10	0.62326	D	0.03	-30.7203	14.0156	0.64523	0.0:0.8467:0.1533:0.0	.	144	Q9HA77	SYCM_HUMAN	K	144;135	ENSP00000257347:E144K	ENSP00000257347:E144K	E	-	1	0	CARS2	110138330	1.000000	0.71417	0.472000	0.27241	0.023000	0.10783	5.937000	0.70162	1.073000	0.40885	-0.310000	0.09108	GAG	.	.	none		0.532	CARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045772.3	NM_024537	
FKRP	79147	hgsc.bcm.edu	37	19	47258887	47258887	+	Missense_Mutation	SNP	C	C	G			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr19:47258887C>G	ENST00000318584.5	+	4	477	c.180C>G	c.(178-180)gaC>gaG	p.D60E	FKRP_ENST00000600646.1_Intron|FKRP_ENST00000391909.3_Missense_Mutation_p.D60E	NM_001039885.2|NM_024301.4	NP_001034974.1|NP_077277.1	Q9H9S5	FKRP_HUMAN	fukutin related protein	60					glycoprotein biosynthetic process (GO:0009101)|protein processing (GO:0016485)	dystrophin-associated glycoprotein complex (GO:0016010)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|rough endoplasmic reticulum (GO:0005791)|sarcolemma (GO:0042383)	transferase activity (GO:0016740)			NS(1)|large_intestine(1)|lung(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	7		all_epithelial(76;5.08e-05)|Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000541)|all cancers(93;0.00128)|Epithelial(262;0.0207)|GBM - Glioblastoma multiforme(486;0.0336)		AGGCATTTGACAACGCGGTGC	0.706																																					p.D60E		Atlas-SNP	.											.	FKRP	16	.	0			c.C180G						PASS	.						37.0	30.0	32.0					19																	47258887		2201	4300	6501	SO:0001583	missense	79147	exon4			ATTTGACAACGCG	AJ314847	CCDS12691.1	19q13.32	2014-09-17			ENSG00000181027	ENSG00000181027			17997	protein-coding gene	gene with protein product		606596				11592034, 11741828	Standard	NM_024301		Approved	LGMD2I, MDC1C	uc002pfp.2	Q9H9S5		ENST00000318584.5:c.180C>G	19.37:g.47258887C>G	ENSP00000326570:p.Asp60Glu	61.0	0.0	0		46.0	26.0	0.565217	NM_024301	A8K5G7	Missense_Mutation	SNP	ENST00000318584.5	37	CCDS12691.1	.	.	.	.	.	.	.	.	.	.	C	1.655	-0.512864	0.04200	.	.	ENSG00000181027	ENST00000391909;ENST00000318584	D;D	0.99277	-5.67;-5.67	4.79	4.79	0.61399	.	0.056531	0.64402	D	0.000002	D	0.92996	0.7771	N	0.01209	-0.955	0.38410	D	0.945893	B	0.20261	0.043	B	0.14023	0.01	D	0.91027	0.4861	10	0.02654	T	1	-33.5211	8.247	0.31695	0.1748:0.6561:0.1691:0.0	.	60	Q9H9S5	FKRP_HUMAN	E	60	ENSP00000375776:D60E;ENSP00000326570:D60E	ENSP00000326570:D60E	D	+	3	2	FKRP	51950727	0.999000	0.42202	1.000000	0.80357	0.801000	0.45260	0.458000	0.21892	2.491000	0.84063	0.555000	0.69702	GAC	.	.	none		0.706	FKRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465473.1	NM_024301	
FAM161A	84140	hgsc.bcm.edu	37	2	62065671	62065671	+	Intron	SNP	A	A	G			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr2:62065671A>G	ENST00000405894.3	-	3	1685				FAM161A_ENST00000404929.1_Splice_Site	NM_032180.2	NP_115556.2	Q3B820	F161A_HUMAN	family with sequence similarity 161, member A						cilium assembly (GO:0042384)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|photoreceptor connecting cilium (GO:0032391)				breast(1)|endometrium(5)|large_intestine(8)|lung(4)|ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TTTTCATGATACCTGAGACAT	0.333																																					.		Atlas-SNP	.											.	FAM161A	200	.	0			c.1751+2T>C						PASS	.						138.0	142.0	141.0					2																	62065671		876	1991	2867	SO:0001627	intron_variant	84140	exon5			CATGATACCTGAG		CCDS42687.2, CCDS56120.1	2p15	2011-03-15			ENSG00000170264	ENSG00000170264			25808	protein-coding gene	gene with protein product		613596	"""retinitis pigmentosa 28 (autosomal recessive)"""	RP28		10507729, 20705278, 20705279	Standard	NM_032180		Approved	FLJ13305	uc002sbm.4	Q3B820	OTTHUMG00000152165	ENST00000405894.3:c.1583+884T>C	2.37:g.62065671A>G		119.0	0.0	0		105.0	27.0	0.257143	NM_001201543	B4DJV7|Q9H8R2	Splice_Site	SNP	ENST00000405894.3	37	CCDS42687.2	.	.	.	.	.	.	.	.	.	.	A	16.60	3.168024	0.57476	.	.	ENSG00000170264	ENST00000404929	.	.	.	5.05	5.05	0.67936	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.1966	0.59743	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	FAM161A	61919175	1.000000	0.71417	1.000000	0.80357	0.815000	0.46073	7.556000	0.82233	2.139000	0.66308	0.383000	0.25322	.	.	.	none		0.333	FAM161A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325537.2	NM_032180	
PPP1R18	170954	hgsc.bcm.edu	37	6	30652888	30652888	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr6:30652888G>T	ENST00000274853.3	-	1	2784	c.908C>A	c.(907-909)gCc>gAc	p.A303D	PPP1R18_ENST00000488324.1_Intron|NRM_ENST00000470733.1_5'Flank|PPP1R18_ENST00000399199.3_Missense_Mutation_p.A303D	NM_133471.3	NP_597728.1	Q6NYC8	PPR18_HUMAN	protein phosphatase 1, regulatory subunit 18	303						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.A303V(1)									GTTGCCTTGGGCCTCCCTTGT	0.572																																					p.A303D		Atlas-SNP	.											KIAA1949,rectum,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	large_intestine(1)	c.C908A						PASS	.						88.0	107.0	101.0					6																	30652888		1431	2652	4083	SO:0001583	missense	170954	exon2			CCTTGGGCCTCCC	AK097089	CCDS43444.1	6p21.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000146112	ENSG00000146112		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29413	protein-coding gene	gene with protein product	"""protein phosphatase 1 F-actin cytoskeleton targeting subunit"""	610990	"""KIAA1949"""	KIAA1949		11853319	Standard	NM_001134870		Approved	phostensin	uc003nra.3	Q6NYC8	OTTHUMG00000031237	ENST00000274853.3:c.908C>A	6.37:g.30652888G>T	ENSP00000274853:p.Ala303Asp	56.0	0.0	0		65.0	5.0	0.0769231	NM_001134870	A2AB01|A2AIB8|A4UBI6|A6NCB7|A8MSS7|B7ZCV7|Q68CK8|Q6ZTV1|Q6ZUJ6|Q8NDQ4|Q8TF52|Q9BRL9	Missense_Mutation	SNP	ENST00000274853.3	37	CCDS43444.1	.	.	.	.	.	.	.	.	.	.	G	7.611	0.674709	0.14841	.	.	ENSG00000146112	ENST00000274853;ENST00000399199;ENST00000376424	T;T	0.23950	1.88;1.88	5.27	-3.84	0.04256	.	1.204620	0.06234	N	0.689171	T	0.05731	0.0150	L	0.27053	0.805	0.09310	N	1	B	0.29432	0.244	B	0.29176	0.099	T	0.42882	-0.9425	10	0.48119	T	0.1	0.5484	6.0357	0.19706	0.3447:0.3544:0.3008:0.0	.	303	Q6NYC8	PPR18_HUMAN	D	303	ENSP00000274853:A303D;ENSP00000382150:A303D	ENSP00000274853:A303D	A	-	2	0	KIAA1949	30760867	0.000000	0.05858	0.000000	0.03702	0.165000	0.22458	-0.144000	0.10280	-0.347000	0.08299	0.561000	0.74099	GCC	.	.	none		0.572	PPP1R18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076498.2	NM_133471	
APOBR	55911	hgsc.bcm.edu	37	16	28507424	28507424	+	Intron	SNP	C	C	T	rs148114931|rs441214	byFrequency	TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr16:28507424C>T	ENST00000431282.1	+	3	1058				APOBR_ENST00000328423.5_Intron|CLN3_ENST00000569430.1_5'Flank|APOBR_ENST00000564831.1_Silent_p.A354A|CLN3_ENST00000567160.1_5'Flank			Q0VD83	APOBR_HUMAN	apolipoprotein B receptor						cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|triglyceride metabolic process (GO:0006641)	chylomicron (GO:0042627)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	very-low-density lipoprotein particle receptor activity (GO:0030229)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|skin(2)|stomach(1)	29						GGGAGGAGGCCGGGACAGCCT	0.711																																					p.A354A		Atlas-SNP	.											.	APOBR	89	.	0			c.C1062T						PASS	.						8.0	11.0	10.0					16																	28507424		1858	4004	5862	SO:0001627	intron_variant	55911	exon2			GGAGGCCGGGACA	AK025123	CCDS58442.1	16p11.2	2011-02-14			ENSG00000184730	ENSG00000184730			24087	protein-coding gene	gene with protein product	"""apolipoprotein B48 receptor"", ""apolipoprotein B100 receptor"""	605220				10852956	Standard	NM_018690		Approved	APOB48R, APOB100R	uc002dqb.2	Q0VD83		ENST00000431282.1:c.1049-14C>T	16.37:g.28507424C>T		17.0	0.0	0		18.0	6.0	0.333333	NM_018690	H3BU97|Q0VD81|Q8NC15|Q9NPJ9	Silent	SNP	ENST00000431282.1	37																																																																																				C|0.500;T|0.500	0.500	strong		0.711	APOBR-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_182804	
COL4A3	1285	hgsc.bcm.edu	37	2	228172583	228172583	+	Silent	SNP	G	G	A			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr2:228172583G>A	ENST00000396578.3	+	48	4572	c.4410G>A	c.(4408-4410)ggG>ggA	p.G1470G	AC097662.2_ENST00000433324.1_RNA|AC097662.2_ENST00000439598.2_RNA|AC097662.2_ENST00000396588.2_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	1470	Collagen IV NC1. {ECO:0000255|PROSITE- ProRule:PRU00736}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|blood circulation (GO:0008015)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|collagen catabolic process (GO:0030574)|endothelial cell apoptotic process (GO:0072577)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|sensory perception of sound (GO:0007605)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metalloendopeptidase inhibitor activity (GO:0008191)|structural molecule activity (GO:0005198)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247)		Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187)		TCTACAGTGGGTTTTCTTTTC	0.498																																					p.G1470G		Atlas-SNP	.											.	COL4A3	293	.	0			c.G4410A						PASS	.						91.0	87.0	88.0					2																	228172583		1900	4112	6012	SO:0001819	synonymous_variant	1285	exon48			CAGTGGGTTTTCT		CCDS42829.1	2q36-q37	2014-09-17			ENSG00000169031	ENSG00000169031		"""Collagens"""	2204	protein-coding gene	gene with protein product	"""tumstatin"""	120070				1737849	Standard	NM_000091		Approved		uc002vom.2	Q01955	OTTHUMG00000149891	ENST00000396578.3:c.4410G>A	2.37:g.228172583G>A		180.0	0.0	0		147.0	38.0	0.258503	NM_000091	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Silent	SNP	ENST00000396578.3	37	CCDS42829.1																																																																																			.	.	none		0.498	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091	
FPGT	8790	hgsc.bcm.edu	37	1	74670196	74670196	+	Silent	SNP	C	C	T			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr1:74670196C>T	ENST00000609362.1	+	4	502	c.465C>T	c.(463-465)ccC>ccT	p.P155P	FPGT_ENST00000524915.1_Intron|TNNI3K_ENST00000370891.2_Intron|FPGT-TNNI3K_ENST00000533006.1_Intron|FPGT_ENST00000467578.2_3'UTR|FPGT-TNNI3K_ENST00000370895.1_Intron|FPGT-TNNI3K_ENST00000557284.2_Intron|FPGT-TNNI3K_ENST00000370899.3_Intron|FPGT_ENST00000534056.1_Intron|FPGT-TNNI3K_ENST00000370893.1_Intron|FPGT_ENST00000370894.5_Intron|FPGT_ENST00000370898.3_Silent_p.P168P	NM_003838.4	NP_003829.3	O14772	FPGT_HUMAN	fucose-1-phosphate guanylyltransferase	155					fucose metabolic process (GO:0006004)	cytoplasm (GO:0005737)	catalytic activity (GO:0003824)|fucose-1-phosphate guanylyltransferase activity (GO:0047341)|GTP binding (GO:0005525)			breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	39						TTGATTTCCCCTTAAATATGA	0.353																																					p.P155P		Atlas-SNP	.											.	FPGT	77	.	0			c.C465T						PASS	.						110.0	114.0	112.0					1																	74670196		2203	4300	6503	SO:0001819	synonymous_variant	8790	exon4			TTTCCCCTTAAAT	AF017445	CCDS663.1, CCDS663.2	1p31.1	2013-09-24			ENSG00000254685	ENSG00000254685	2.7.7.30		3825	protein-coding gene	gene with protein product		603609				9804772	Standard	NM_003838		Approved	GFPP		O14772	OTTHUMG00000009571	ENST00000609362.1:c.465C>T	1.37:g.74670196C>T		152.0	0.0	0		154.0	54.0	0.350649	NM_003838	A6NMH3|B4DRX2|B4E2Y7|E9PNQ2|Q8N5J7	Silent	SNP	ENST00000609362.1	37	CCDS663.1																																																																																			.	.	none		0.353	FPGT-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
TPR	7175	hgsc.bcm.edu	37	1	186306183	186306183	+	Missense_Mutation	SNP	A	A	T			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr1:186306183A>T	ENST00000367478.4	-	32	4764	c.4468T>A	c.(4468-4470)Tca>Aca	p.S1490T		NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	1490					carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)			autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		AGTGATTTTGATTTTGTTTCA	0.423			T	NTRK1	papillary thyroid																																p.S1490T		Atlas-SNP	.		Dom	yes		1	1q25	7175	translocated promoter region		E	.	TPR	441	.	0			c.T4468A						PASS	.						231.0	209.0	216.0					1																	186306183		1900	4128	6028	SO:0001583	missense	7175	exon32			ATTTTGATTTTGT	U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"""translocated promoter region (to activated MET oncogene)"""			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.4468T>A	1.37:g.186306183A>T	ENSP00000356448:p.Ser1490Thr	103.0	0.0	0		89.0	18.0	0.202247	NM_003292	Q15655|Q5SWY0|Q99968	Missense_Mutation	SNP	ENST00000367478.4	37	CCDS41446.1	.	.	.	.	.	.	.	.	.	.	A	7.171	0.587708	0.13812	.	.	ENSG00000047410	ENST00000367478	T	0.22336	1.96	5.91	-5.49	0.02584	Seryl-tRNA synthetase, class IIa, N-terminal (1);	0.471414	0.24638	N	0.036825	T	0.02571	0.0078	N	0.00162	-1.95	0.19945	N	0.999941	B	0.02656	0.0	B	0.01281	0.0	T	0.43294	-0.9400	10	0.07030	T	0.85	.	7.7025	0.28632	0.2781:0.1562:0.0:0.5657	.	1490	P12270	TPR_HUMAN	T	1490	ENSP00000356448:S1490T	ENSP00000356448:S1490T	S	-	1	0	TPR	184572806	1.000000	0.71417	0.927000	0.36925	0.836000	0.47400	0.896000	0.28377	-0.614000	0.05687	0.533000	0.62120	TCA	.	.	none		0.423	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292	
SGPP1	81537	hgsc.bcm.edu	37	14	64165346	64165346	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr14:64165346G>T	ENST00000247225.6	-	2	809	c.715C>A	c.(715-717)Ccc>Acc	p.P239T		NM_030791.2	NP_110418.1	Q9BX95	SGPP1_HUMAN	sphingosine-1-phosphate phosphatase 1	239					extrinsic apoptotic signaling pathway (GO:0097191)|intrinsic apoptotic signaling pathway (GO:0097193)|small molecule metabolic process (GO:0044281)|sphinganine-1-phosphate metabolic process (GO:0006668)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	sphingosine-1-phosphate phosphatase activity (GO:0042392)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(4)|skin(2)	10				OV - Ovarian serous cystadenocarcinoma(108;0.0056)|all cancers(60;0.0141)|BRCA - Breast invasive adenocarcinoma(234;0.103)		CACCAGCAGGGAATAAGAATC	0.289																																					p.P239T		Atlas-SNP	.											.	SGPP1	29	.	0			c.C715A						PASS	.						64.0	64.0	64.0					14																	64165346		2203	4295	6498	SO:0001583	missense	81537	exon2			AGCAGGGAATAAG	AJ293294	CCDS9760.1	14q23.1	2003-09-17			ENSG00000126821	ENSG00000126821			17720	protein-coding gene	gene with protein product		612826				10859351	Standard	NM_030791		Approved		uc001xgj.3	Q9BX95	OTTHUMG00000029080	ENST00000247225.6:c.715C>A	14.37:g.64165346G>T	ENSP00000247225:p.Pro239Thr	449.0	0.0	0		457.0	97.0	0.212254	NM_030791	B2RAH0|Q9H189	Missense_Mutation	SNP	ENST00000247225.6	37	CCDS9760.1	.	.	.	.	.	.	.	.	.	.	G	9.884	1.202340	0.22121	.	.	ENSG00000126821	ENST00000247225	T	0.51574	0.7	5.6	2.62	0.31277	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.568287	0.19623	N	0.109879	T	0.13243	0.0321	N	0.00873	-1.125	0.27550	N	0.950526	B	0.17038	0.02	B	0.14578	0.011	T	0.11012	-1.0605	10	0.22109	T	0.4	-25.1553	1.6276	0.02726	0.1449:0.2663:0.343:0.2458	.	239	Q9BX95	SGPP1_HUMAN	T	239	ENSP00000247225:P239T	ENSP00000247225:P239T	P	-	1	0	SGPP1	63235099	0.916000	0.31088	1.000000	0.80357	0.996000	0.88848	0.599000	0.24089	1.500000	0.48636	-0.165000	0.13383	CCC	.	.	none		0.289	SGPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072626.3	NM_030791	
ACCS	84680	hgsc.bcm.edu	37	11	44092850	44092850	+	Silent	SNP	C	C	T			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr11:44092850C>T	ENST00000263776.8	+	3	767	c.333C>T	c.(331-333)gaC>gaT	p.D111D	CTD-2609K8.3_ENST00000531268.1_RNA|ACCS_ENST00000533208.1_3'UTR|ACCS_ENST00000432284.2_Silent_p.D111D	NM_001127219.1|NM_032592.3	NP_001120691.1|NP_115981.1	Q96QU6	1A1L1_HUMAN	1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)	111					biosynthetic process (GO:0009058)		catalytic activity (GO:0003824)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)			breast(4)|endometrium(3)|large_intestine(11)|lung(15)|ovary(1)|skin(1)	35						TCTGCTTTGACCTGCTGTCCT	0.577																																					p.D111D	Esophageal Squamous(158;148 1889 8077 23160 41213)	Atlas-SNP	.											.	ACCS	64	.	0			c.C333T						PASS	.						126.0	116.0	119.0					11																	44092850		2203	4300	6503	SO:0001819	synonymous_variant	84680	exon3			CTTTGACCTGCTG	AY026508	CCDS7907.1	11p11	2008-03-12	2008-01-28		ENSG00000110455	ENSG00000110455			23989	protein-coding gene	gene with protein product		608405				11470512	Standard	NM_032592		Approved	PHACS, ACS	uc009yks.1	Q96QU6	OTTHUMG00000166427	ENST00000263776.8:c.333C>T	11.37:g.44092850C>T		112.0	0.0	0		87.0	18.0	0.206897	NM_032592	B4E219|Q8WUL4|Q96LX5	Silent	SNP	ENST00000263776.8	37	CCDS7907.1																																																																																			.	.	none		0.577	ACCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389721.1	NM_032592	
OCIAD1	54940	hgsc.bcm.edu	37	4	48835428	48835428	+	Silent	SNP	T	T	A			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr4:48835428T>A	ENST00000381473.3	+	3	487	c.69T>A	c.(67-69)ccT>ccA	p.P23P	OCIAD1_ENST00000513391.2_Silent_p.P23P|OCIAD1_ENST00000444354.2_Silent_p.P23P|OCIAD1_ENST00000508293.1_Silent_p.P23P|OCIAD1_ENST00000264312.7_Silent_p.P23P|OCIAD1_ENST00000509122.1_Intron|OCIAD1_ENST00000512981.1_3'UTR|OCIAD1_ENST00000506801.1_Intron|OCIAD1_ENST00000396448.2_Silent_p.P23P|OCIAD1_ENST00000425583.2_Silent_p.P23P	NM_001079839.2	NP_001073308.1	Q9NX40	OCAD1_HUMAN	OCIA domain containing 1	23	OCIA.					endosome (GO:0005768)|membrane (GO:0016020)|mitochondrion (GO:0005739)				breast(2)|large_intestine(2)|lung(2)|prostate(1)|skin(2)	9						ACATAGGGCCTGATTACATTC	0.328																																					p.P28P		Atlas-SNP	.											.	OCIAD1	27	.	0			c.T84A						PASS	.						62.0	65.0	64.0					4																	48835428		2203	4300	6503	SO:0001819	synonymous_variant	54940	exon3			AGGGCCTGATTAC	AF324350	CCDS3484.1, CCDS43228.1, CCDS47052.1	4p11	2010-03-19			ENSG00000109180	ENSG00000109180			16074	protein-coding gene	gene with protein product						11162530, 18328549	Standard	NM_017830		Approved	FLJ20455, TPA018, OCIA, Asrij	uc010igk.3	Q9NX40	OTTHUMG00000102095	ENST00000381473.3:c.69T>A	4.37:g.48835428T>A		290.0	0.0	0		324.0	82.0	0.253086	NM_001168254	C9K030|G8JLN7|Q9BZE8	Silent	SNP	ENST00000381473.3	37	CCDS3484.1																																																																																			.	.	none		0.328	OCIAD1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361812.3	NM_017830	
STAB2	55576	hgsc.bcm.edu	37	12	104071379	104071379	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr12:104071379G>A	ENST00000388887.2	+	25	2999	c.2795G>A	c.(2794-2796)gGt>gAt	p.G932D		NM_017564.9	NP_060034.9			stabilin 2											NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						TTGTATGTGGGTCCCGGGCAG	0.547																																					p.G932D		Atlas-SNP	.											.	STAB2	370	.	0			c.G2795A						PASS	.						83.0	81.0	82.0					12																	104071379		2203	4300	6503	SO:0001583	missense	55576	exon25			ATGTGGGTCCCGG	AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"""hyaluronic acid receptor for endocytosis"""	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.2795G>A	12.37:g.104071379G>A	ENSP00000373539:p.Gly932Asp	56.0	0.0	0		60.0	9.0	0.15	NM_017564		Missense_Mutation	SNP	ENST00000388887.2	37	CCDS31888.1	.	.	.	.	.	.	.	.	.	.	G	18.51	3.638706	0.67130	.	.	ENSG00000136011	ENST00000388887	T	0.64438	-0.1	5.55	5.55	0.83447	Growth factor, receptor (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	T	0.79890	0.4524	M	0.78916	2.43	0.58432	D	0.999998	D	0.89917	1.0	D	0.91635	0.999	T	0.78365	-0.2232	10	0.37606	T	0.19	.	18.2638	0.90044	0.0:0.0:1.0:0.0	.	932	Q8WWQ8	STAB2_HUMAN	D	932	ENSP00000373539:G932D	ENSP00000373539:G932D	G	+	2	0	STAB2	102595509	1.000000	0.71417	0.996000	0.52242	0.194000	0.23727	8.757000	0.91657	2.623000	0.88846	0.563000	0.77884	GGT	.	.	none		0.547	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1		
STRBP	55342	hgsc.bcm.edu	37	9	125923280	125923280	+	Silent	SNP	A	A	G			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr9:125923280A>G	ENST00000348403.5	-	7	1032	c.603T>C	c.(601-603)tcT>tcC	p.S201S	STRBP_ENST00000447404.2_Silent_p.S201S|STRBP_ENST00000360998.3_Silent_p.S187S	NM_018387.4	NP_060857.2	Q96SI9	STRBP_HUMAN	spermatid perinuclear RNA binding protein	201	DZF. {ECO:0000255|PROSITE- ProRule:PRU01040}.				cellular component movement (GO:0006928)|mechanosensory behavior (GO:0007638)|multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(6)|prostate(1)|skin(2)	26						CATGTCGAAGAGACGCCAAGG	0.388																																					p.S201S		Atlas-SNP	.											.	STRBP	73	.	0			c.T603C						PASS	.						46.0	44.0	45.0					9																	125923280		2203	4300	6503	SO:0001819	synonymous_variant	55342	exon7			TCGAAGAGACGCC	AK002169	CCDS6851.1, CCDS55337.1	9q33.1-q33.3	2008-08-29	2001-11-28		ENSG00000165209	ENSG00000165209			16462	protein-coding gene	gene with protein product		611138	"""spermatid perinuclear RNA-binding protein"", ""interleukin enhancer binding factor 3-like"""	ILF3L			Standard	NM_018387		Approved	FLJ11307, SPNR	uc004bns.3	Q96SI9	OTTHUMG00000020636	ENST00000348403.5:c.603T>C	9.37:g.125923280A>G		298.0	0.0	0		318.0	95.0	0.298742	NM_018387	Q32NB9|Q9BUE1|Q9BXG4|Q9H0B4|Q9H7V1|Q9NUK4	Silent	SNP	ENST00000348403.5	37	CCDS6851.1																																																																																			.	.	none		0.388	STRBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053982.1		
ATM	472	hgsc.bcm.edu	37	11	108202718	108202718	+	Missense_Mutation	SNP	G	G	C			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr11:108202718G>C	ENST00000452508.2	+	53	7931	c.7742G>C	c.(7741-7743)aGc>aCc	p.S2581T	C11orf65_ENST00000525729.1_Intron|ATM_ENST00000278616.4_Missense_Mutation_p.S2581T			Q13315	ATM_HUMAN	ATM serine/threonine kinase	2581					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	GCCAGAAGAAGCAGAATAACT	0.368			"""D, Mis, N, F, S"""		T-PLL	"""leukemia, lymphoma, medulloblastoma, glioma"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																											p.S2581T		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"""L, O"""	.	ATM	1657	.	0			c.G7742C						PASS	.						88.0	87.0	87.0					11																	108202718		2201	4298	6499	SO:0001583	missense	472	exon52	Familial Cancer Database	AT, Louis-Bar syndrome	GAAGAAGCAGAAT	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"""TEL1, telomere maintenance 1, homolog (S. cerevisiae)"""	607585	"""ataxia telangiectasia mutated (includes complementation groups A, C and D)"", ""ataxia telangiectasia mutated"""	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.7742G>C	11.37:g.108202718G>C	ENSP00000388058:p.Ser2581Thr	125.0	0.0	0		116.0	30.0	0.258621	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	G	4.758	0.141006	0.09083	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	T;T	0.79141	-1.24;-1.24	5.18	3.26	0.37387	Armadillo-type fold (1);	0.434069	0.29040	N	0.013336	T	0.70979	0.3286	M	0.72894	2.215	0.80722	D	1	B	0.17667	0.023	B	0.15484	0.013	T	0.59941	-0.7359	10	0.15952	T	0.53	.	7.6319	0.28245	0.1605:0.1368:0.7027:0.0	.	2581	Q13315	ATM_HUMAN	T	2581	ENSP00000278616:S2581T;ENSP00000388058:S2581T	ENSP00000278616:S2581T	S	+	2	0	ATM	107707928	0.281000	0.24258	0.637000	0.29366	0.172000	0.22775	0.471000	0.22100	0.537000	0.28751	-0.282000	0.10007	AGC	.	.	none		0.368	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	
ATXN7L1	222255	hgsc.bcm.edu	37	7	105254603	105254603	+	Silent	SNP	G	G	A	rs147930086	byFrequency	TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr7:105254603G>A	ENST00000419735.3	-	10	2223	c.2178C>T	c.(2176-2178)ccC>ccT	p.P726P	ATXN7L1_ENST00000477775.1_Silent_p.P602P|ATXN7L1_ENST00000388807.4_Silent_p.P386P	NM_020725.1	NP_065776.1	Q9ULK2	AT7L1_HUMAN	ataxin 7-like 1	726	Ser-rich.									endometrium(1)|large_intestine(4)|lung(5)	10						CTATGTCCGCGGGGCCGCCGG	0.647													G|||	4	0.000798722	0.0015	0.0014	5008	,	,		15422	0.0		0.001	False		,,,				2504	0.0				p.P726P		Atlas-SNP	.											.	ATXN7L1	56	.	0			c.C2178T						PASS	.						29.0	29.0	29.0					7																	105254603		692	1591	2283	SO:0001819	synonymous_variant	222255	exon10			GTCCGCGGGGCCG	AB033044	CCDS34727.1, CCDS47682.1, CCDS47683.1	7q22.1	2007-11-13			ENSG00000146776	ENSG00000146776			22210	protein-coding gene	gene with protein product			"""ataxin 7-like 4"""	ATXN7L4		15115762	Standard	NM_152749		Approved	KIAA1218, MGC33190	uc003vde.2	Q9ULK2	OTTHUMG00000157521	ENST00000419735.3:c.2178C>T	7.37:g.105254603G>A		57.0	0.0	0		81.0	24.0	0.296296	NM_020725	A4D0Q2|B4DTS1|Q8N2T0	Silent	SNP	ENST00000419735.3	37	CCDS47682.1																																																																																			G|0.998;A|0.002	0.002	strong		0.647	ATXN7L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349037.2		
ART5	116969	hgsc.bcm.edu	37	11	3661044	3661044	+	Silent	SNP	G	G	A			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr11:3661044G>A	ENST00000397068.3	-	2	1007	c.615C>T	c.(613-615)tgC>tgT	p.C205C	TRPC2_ENST00000526541.1_RNA|ART5_ENST00000359918.4_Silent_p.C205C|ART5_ENST00000397067.3_Intron	NM_053017.3	NP_443750.2	Q96L15	NAR5_HUMAN	ADP-ribosyltransferase 5	205					protein ADP-ribosylation (GO:0006471)	extracellular region (GO:0005576)|membrane (GO:0016020)	NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|NAD+ nucleosidase activity (GO:0003953)			breast(1)|central_nervous_system(1)|large_intestine(2)|lung(6)|ovary(1)	11		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0336)|LUSC - Lung squamous cell carcinoma(625;0.19)		GGGCCCCAAAGCAAGTTGTTA	0.542																																					p.C205C		Atlas-SNP	.											.	ART5	38	.	0			c.C615T						PASS	.						74.0	87.0	82.0					11																	3661044		2201	4298	6499	SO:0001819	synonymous_variant	116969	exon2			CCCAAAGCAAGTT	Y16835	CCDS7743.1, CCDS73242.1	11p15.4	2008-02-05			ENSG00000167311	ENSG00000167311			24049	protein-coding gene	gene with protein product		610625				11587854, 10448534	Standard	NM_001079536		Approved		uc001lyb.1	Q96L15	OTTHUMG00000011842	ENST00000397068.3:c.615C>T	11.37:g.3661044G>A		144.0	0.0	0		94.0	28.0	0.297872	NM_053017	C9IYG7|Q6UX84|Q86W02	Silent	SNP	ENST00000397068.3	37	CCDS7743.1	.	.	.	.	.	.	.	.	.	.	G	8.700	0.909544	0.17833	.	.	ENSG00000167311	ENST00000453353	.	.	.	6.17	1.32	0.21799	.	.	.	.	.	T	0.58764	0.2145	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53380	-0.8447	4	.	.	.	-28.2147	10.4319	0.44413	0.3324:0.0:0.6676:0.0	.	.	.	.	F	162	.	.	L	-	1	0	ART5	3617620	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.992000	0.40737	0.351000	0.24027	0.655000	0.94253	CTT	.	.	none		0.542	ART5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032760.2	NM_053017	
HIST1H1C	3006	hgsc.bcm.edu	37	6	26056500	26056500	+	Missense_Mutation	SNP	C	C	T	rs372319415		TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr6:26056500C>T	ENST00000343677.2	-	1	199	c.157G>A	c.(157-159)Gag>Aag	p.E53K		NM_005319.3	NP_005310.1	P16403	H12_HUMAN	histone cluster 1, H1c	53	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						CCGCTACGCTCTTTAGAGGCG	0.552																																					p.E53K		Atlas-SNP	.											.	HIST1H1C	80	.	0			c.G157A						PASS	.						65.0	74.0	71.0					6																	26056500		2203	4300	6503	SO:0001583	missense	3006	exon1			TACGCTCTTTAGA	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.157G>A	6.37:g.26056500C>T	ENSP00000339566:p.Glu53Lys	108.0	0.0	0		117.0	66.0	0.564103	NM_005319	A8K4I2	Missense_Mutation	SNP	ENST00000343677.2	37	CCDS4577.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.297068	0.81025	.	.	ENSG00000187837	ENST00000343677	T	0.35048	1.33	5.73	5.73	0.89815	Histone H1/H5 (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.180300	0.47852	D	0.000208	T	0.72350	0.3449	H	0.97635	4.045	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.81922	-0.0711	10	0.87932	D	0	-77.7995	19.248	0.93909	0.0:1.0:0.0:0.0	.	53	P16403	H12_HUMAN	K	53	ENSP00000339566:E53K	ENSP00000339566:E53K	E	-	1	0	HIST1H1C	26164479	1.000000	0.71417	1.000000	0.80357	0.065000	0.16274	5.774000	0.68906	2.861000	0.98227	0.655000	0.94253	GAG	.	.	alt		0.552	HIST1H1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043372.1	NM_005319	
OBSCN	84033	hgsc.bcm.edu	37	1	228564799	228564799	+	Missense_Mutation	SNP	C	C	T	rs541725106		TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr1:228564799C>T	ENST00000422127.1	+	101	23130	c.23086C>T	c.(23086-23088)Cgg>Tgg	p.R7696W	OBSCN_ENST00000570156.2_Missense_Mutation_p.R8653W|OBSCN_ENST00000366707.4_Missense_Mutation_p.R5330W	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	7696	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GGCCAGCGGGCGGGCGCTGGC	0.687													C|||	1	0.000199681	0.0	0.0	5008	,	,		15332	0.001		0.0	False		,,,				2504	0.0				p.R8653W		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C25957T						PASS	.						13.0	17.0	15.0					1																	228564799		2005	4163	6168	SO:0001583	missense	84033	exon112			AGCGGGCGGGCGC	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.23086C>T	1.37:g.228564799C>T	ENSP00000409493:p.Arg7696Trp	31.0	0.0	0		52.0	17.0	0.326923	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.50|16.50	3.139945|3.139945	0.56936|0.56936	.|.	.|.	ENSG00000154358|ENSG00000154358	ENST00000441106|ENST00000422127;ENST00000366707	.|T;T	.|0.66995	.|-0.24;-0.24	4.82|4.82	4.82|4.82	0.62117|0.62117	.|Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.|0.259072	.|0.31660	.|N	.|0.007272	T|T	0.78610|0.78610	0.4310|0.4310	M|M	0.89214|0.89214	3.015|3.015	0.58432|0.58432	D|D	0.999991|0.999991	.|D	.|0.71674	.|0.998	.|P	.|0.54210	.|0.745	T|T	0.82948|0.82948	-0.0204|-0.0204	5|10	.|0.72032	.|D	.|0.01	.|.	11.3533|11.3533	0.49600|0.49600	0.3162:0.6838:0.0:0.0|0.3162:0.6838:0.0:0.0	.|.	.|7696	.|Q5VST9	.|OBSCN_HUMAN	V|W	2312|7696;5330	.|ENSP00000409493:R7696W;ENSP00000355668:R5330W	.|ENSP00000355668:R5330W	A|R	+|+	2|1	0|2	OBSCN|OBSCN	226631422|226631422	0.056000|0.056000	0.20664|0.20664	0.048000|0.048000	0.18961|0.18961	0.006000|0.006000	0.05464|0.05464	1.933000|1.933000	0.40153|0.40153	2.239000|2.239000	0.73571|0.73571	0.313000|0.313000	0.20887|0.20887	GCG|CGG	.	.	none		0.687	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
ZNF768	79724	hgsc.bcm.edu	37	16	30537265	30537265	+	Missense_Mutation	SNP	C	C	G			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr16:30537265C>G	ENST00000380412.5	-	2	371	c.196G>C	c.(196-198)Gag>Cag	p.E66Q	ZNF747_ENST00000535210.1_3'UTR|ZNF768_ENST00000562803.1_Missense_Mutation_p.E35Q|ZNF747_ENST00000569360.1_3'UTR	NM_024671.3	NP_078947.3	Q9H5H4	ZN768_HUMAN	zinc finger protein 768	66	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	DNA-directed RNA polymerase II, core complex (GO:0005665)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|prostate(1)	15						CTTTGTGGCTCAAACCCAGGG	0.547																																					p.E66Q		Atlas-SNP	.											.	ZNF768	28	.	0			c.G196C						PASS	.						73.0	78.0	76.0					16																	30537265		2197	4300	6497	SO:0001583	missense	79724	exon2			GTGGCTCAAACCC	BC013760	CCDS10681.2	16p11.2	2013-01-08			ENSG00000169957	ENSG00000169957		"""Zinc fingers, C2H2-type"""	26273	protein-coding gene	gene with protein product						12477932	Standard	NM_024671		Approved	FLJ23436	uc002dyk.4	Q9H5H4	OTTHUMG00000132392	ENST00000380412.5:c.196G>C	16.37:g.30537265C>G	ENSP00000369777:p.Glu66Gln	56.0	0.0	0		87.0	18.0	0.206897	NM_024671	Q569L7|Q96CX4	Missense_Mutation	SNP	ENST00000380412.5	37	CCDS10681.2	.	.	.	.	.	.	.	.	.	.	C	15.07	2.723574	0.48728	.	.	ENSG00000169957	ENST00000380412;ENST00000538507	T	0.06687	3.27	4.28	4.28	0.50868	.	0.204949	0.24429	N	0.038613	T	0.07773	0.0195	N	0.24115	0.695	0.80722	D	1	B	0.23937	0.094	B	0.32149	0.141	T	0.37430	-0.9706	10	0.24483	T	0.36	-4.1654	14.2663	0.66121	0.0:1.0:0.0:0.0	.	66	Q9H5H4	ZN768_HUMAN	Q	66;35	ENSP00000369777:E66Q	ENSP00000369777:E66Q	E	-	1	0	ZNF768	30444766	0.990000	0.36364	0.998000	0.56505	0.992000	0.81027	2.717000	0.47227	2.236000	0.73375	0.561000	0.74099	GAG	.	.	none		0.547	ZNF768-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255522.2	NM_024671	
PITPNC1	26207	hgsc.bcm.edu	37	17	65574302	65574302	+	Splice_Site	SNP	T	T	A			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr17:65574302T>A	ENST00000581322.1	+	5	295	c.295T>A	c.(295-297)Tgt>Agt	p.C99S	PITPNC1_ENST00000580974.1_Splice_Site_p.C99S|PITPNC1_ENST00000299954.9_Missense_Mutation_p.C99S|PITPNC1_ENST00000335257.6_Missense_Mutation_p.C99S			Q9UKF7	PITC1_HUMAN	phosphatidylinositol transfer protein, cytoplasmic 1	99					phospholipid transport (GO:0015914)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	lipid binding (GO:0008289)|phosphatidylinositol transporter activity (GO:0008526)			breast(1)|kidney(2)|large_intestine(3)|liver(2)|lung(4)|prostate(2)|skin(3)	17	all_cancers(12;3.03e-10)		BRCA - Breast invasive adenocarcinoma(8;2.08e-08)|Colorectal(3;0.198)			TCTCCCACAGTGTTCCTTTCT	0.423																																					p.C99S		Atlas-SNP	.											.	PITPNC1	47	.	0			c.T295A						PASS	.						73.0	72.0	72.0					17																	65574302		1943	4146	6089	SO:0001630	splice_region_variant	26207	exon5			CCACAGTGTTCCT	AF171102	CCDS58587.1, CCDS58588.1	17q24.3	2008-02-05							21045	protein-coding gene	gene with protein product		605134				10531358	Standard	NM_012417		Approved	RDGBB1, RDGBB, RDGB-BETA	uc002jgc.4	Q9UKF7		ENST00000581322.1:c.295-1T>A	17.37:g.65574302T>A		65.0	0.0	0		53.0	19.0	0.358491	NM_012417	A8K473|J3QR20|Q96I07	Missense_Mutation	SNP	ENST00000581322.1	37	CCDS58588.1	.	.	.	.	.	.	.	.	.	.	T	14.85	2.659119	0.47467	.	.	ENSG00000154217	ENST00000335257;ENST00000299954	T;T	0.44482	0.92;0.92	5.47	5.47	0.80525	START-like domain (1);	0.000000	0.85682	D	0.000000	T	0.61375	0.2342	M	0.66560	2.04	0.80722	D	1	D;D	0.69078	0.996;0.997	D;D	0.74348	0.983;0.978	T	0.58736	-0.7584	10	0.30854	T	0.27	-4.8363	15.4926	0.75619	0.0:0.0:0.0:1.0	.	99;99	Q9UKF7;Q9UKF7-2	PITC1_HUMAN;.	S	99	ENSP00000335618:C99S;ENSP00000299954:C99S	ENSP00000299954:C99S	C	+	1	0	PITPNC1	63004764	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.332000	0.79203	2.198000	0.70561	0.459000	0.35465	TGT	.	.	none		0.423	PITPNC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447194.1	NM_012417	Missense_Mutation
NME8	51314	hgsc.bcm.edu	37	7	37907335	37907335	+	Missense_Mutation	SNP	C	C	G			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr7:37907335C>G	ENST00000199447.4	+	11	1025	c.653C>G	c.(652-654)aCa>aGa	p.T218R	EPDR1_ENST00000476620.1_Intron|NME8_ENST00000440017.1_Missense_Mutation_p.T218R	NM_016616.4	NP_057700.3	Q8N427	TXND3_HUMAN	NME/NM23 family member 8	218	NDK 1.				cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)|UTP biosynthetic process (GO:0006228)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)										TCTTTTATGACAAGTGGCTTA	0.398																																					p.T218R		Atlas-SNP	.											.	.	.	.	0			c.C653G						PASS	.						128.0	121.0	123.0					7																	37907335		2203	4300	6503	SO:0001583	missense	51314	exon11			TTATGACAAGTGG	AF202051	CCDS5452.1	7p15.2	2012-05-18	2012-05-18	2012-05-18	ENSG00000086288	ENSG00000086288			16473	protein-coding gene	gene with protein product	"""sperm-specific thioredoxin 2"""	607421	"""thioredoxin domain containing 3 (spermatozoa)"""	TXNDC3		11737268, 11768308, 19852809	Standard	NM_016616		Approved	CILD6, SPTRX2, NM23-H8	uc003tfn.3	Q8N427	OTTHUMG00000023716	ENST00000199447.4:c.653C>G	7.37:g.37907335C>G	ENSP00000199447:p.Thr218Arg	145.0	0.0	0		138.0	29.0	0.210145	NM_016616	Q9NZH1	Missense_Mutation	SNP	ENST00000199447.4	37	CCDS5452.1	.	.	.	.	.	.	.	.	.	.	C	12.78	2.039377	0.35989	.	.	ENSG00000086288	ENST00000199447;ENST00000440017	T;T	0.50001	0.76;0.76	5.1	4.21	0.49690	.	0.000000	0.47093	D	0.000242	T	0.67335	0.2882	M	0.87758	2.905	0.31171	N	0.703179	D	0.58970	0.984	D	0.66847	0.947	T	0.71009	-0.4716	10	0.62326	D	0.03	-34.9938	8.5596	0.33503	0.0:0.8992:0.0:0.1007	.	218	Q8N427	TXND3_HUMAN	R	218	ENSP00000199447:T218R;ENSP00000397063:T218R	ENSP00000199447:T218R	T	+	2	0	TXNDC3	37873860	0.195000	0.23338	0.984000	0.44739	0.025000	0.11179	0.270000	0.18607	2.756000	0.94617	0.563000	0.77884	ACA	.	.	none		0.398	NME8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219946.1	NM_016616	
FAS	355	hgsc.bcm.edu	37	10	90770574	90770574	+	Splice_Site	SNP	T	T	A			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr10:90770574T>A	ENST00000355279.2	+	6	568		c.e6+2		FAS_ENST00000355740.2_Splice_Site|FAS_ENST00000313771.5_Splice_Site|FAS_ENST00000357339.2_Intron|FAS_ENST00000352159.4_Splice_Site			P49327	FAS_HUMAN	Fas cell surface death receptor						acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.0161)		Colorectal(12;0.000136)|COAD - Colon adenocarcinoma(12;0.000193)	Cerulenin(DB01034)|Orlistat(DB01083)	TTGTTTGGGGTAAGTTCTTGC	0.368																																					.		Atlas-SNP	.											.	FAS	47	.	0			c.568+2T>A						PASS	.						248.0	222.0	231.0					10																	90770574		2203	4300	6503	SO:0001630	splice_region_variant	355	exon6			TTGGGGTAAGTTC	M67454	CCDS7393.1, CCDS7394.1, CCDS7395.1	10q24.1	2014-09-17	2013-05-22	2005-01-07	ENSG00000026103	ENSG00000026103		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11920	protein-coding gene	gene with protein product	"""TNF receptor superfamily member 6"""	134637	"""tumor necrosis factor receptor superfamily, member 6"", ""Fas (TNF receptor superfamily, member 6)"""	FAS1, APT1, TNFRSF6		1385299, 1385309	Standard	NM_000043		Approved	CD95, APO-1	uc001kfr.3	P25445	OTTHUMG00000018701	ENST00000355279.2:c.568+2T>A	10.37:g.90770574T>A		153.0	0.0	0		92.0	35.0	0.380435	NM_152872	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Splice_Site	SNP	ENST00000355279.2	37	CCDS7395.1	.	.	.	.	.	.	.	.	.	.	T	11.07	1.530798	0.27387	.	.	ENSG00000026103	ENST00000540197;ENST00000355740;ENST00000352159;ENST00000355279;ENST00000371875	.	.	.	3.9	3.9	0.45041	.	.	.	.	.	.	.	.	.	.	.	0.54753	D	0.999987	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.4431	0.38681	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	FAS	90760554	0.996000	0.38824	0.241000	0.24154	0.039000	0.13416	1.607000	0.36836	2.012000	0.59069	0.528000	0.53228	.	.	.	none		0.368	FAS-011	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000049280.2		Intron
SULF2	55959	hgsc.bcm.edu	37	20	46331406	46331406	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr20:46331406C>T	ENST00000359930.4	-	4	1275	c.424G>A	c.(424-426)Ggg>Agg	p.G142R	SULF2_ENST00000361612.4_Missense_Mutation_p.G142R|SULF2_ENST00000484875.1_Missense_Mutation_p.G142R|SULF2_ENST00000467815.1_Missense_Mutation_p.G142R	NM_018837.3	NP_061325.1	Q8IWU5	SULF2_HUMAN	sulfatase 2	142					bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)			breast(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	54						AGATACTTCCCGAAGAAAGCT	0.512																																					p.G142R		Atlas-SNP	.											.	SULF2	131	.	0			c.G424A						PASS	.						40.0	35.0	37.0					20																	46331406		2203	4300	6503	SO:0001583	missense	55959	exon4			ACTTCCCGAAGAA	AY101176	CCDS13408.1, CCDS13409.1, CCDS13409.2	20q13.12-q13.13	2008-05-14			ENSG00000196562	ENSG00000196562			20392	protein-coding gene	gene with protein product		610013				12368295	Standard	NM_018837		Approved	KIAA1247, HSULF-2, SULF-2	uc002xto.3	Q8IWU5	OTTHUMG00000032675	ENST00000359930.4:c.424G>A	20.37:g.46331406C>T	ENSP00000353007:p.Gly142Arg	42.0	0.0	0		52.0	12.0	0.230769	NM_001161841	E1P5U6|Q5JYE1|Q6UX86|Q96SG2|Q9H1H0|Q9UJR3|Q9ULH3	Missense_Mutation	SNP	ENST00000359930.4	37	CCDS13408.1	.	.	.	.	.	.	.	.	.	.	C	33	5.285132	0.95517	.	.	ENSG00000196562	ENST00000359930;ENST00000484875;ENST00000361612;ENST00000467815;ENST00000437955	D;D;D;D;D	0.99859	-4.83;-4.83;-4.83;-4.83;-7.24	5.08	5.08	0.68730	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	D	0.99924	0.9965	H	0.98833	4.345	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.95859	0.8881	10	0.87932	D	0	-19.458	18.4712	0.90776	0.0:1.0:0.0:0.0	.	142;142;142	G3XAE6;Q8IWU5-2;Q8IWU5	.;.;SULF2_HUMAN	R	142	ENSP00000353007:G142R;ENSP00000418290:G142R;ENSP00000354662:G142R;ENSP00000418442:G142R;ENSP00000410026:G142R	ENSP00000353007:G142R	G	-	1	0	SULF2	45764813	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	7.814000	0.86154	2.355000	0.79922	0.561000	0.74099	GGG	.	.	none		0.512	SULF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079606.1	NM_018837	
AARD	441376	hgsc.bcm.edu	37	8	117950758	117950758	+	Missense_Mutation	SNP	G	G	T	rs111477672	byFrequency	TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr8:117950758G>T	ENST00000378279.3	+	1	321	c.276G>T	c.(274-276)caG>caT	p.Q92H		NM_001025357.2	NP_001020528.1	Q4LEZ3	AARD_HUMAN	alanine and arginine rich domain containing protein	92	Ala/Arg-rich.				lung development (GO:0030324)												GGGAGGAgcagagctggacgg	0.761													G|||	75	0.014976	0.0015	0.0159	5008	,	,		9938	0.0		0.0547	False		,,,				2504	0.0072				p.Q92H		Atlas-SNP	.											.	.	.	.	0			c.G276T						PASS	.						2.0	3.0	2.0					8																	117950758		1194	2634	3828	SO:0001583	missense	441376	exon1			GGAGCAGAGCTGG	AB181519, BC140924	CCDS34935.1	8q24.11	2012-04-19	2012-04-19	2012-04-19	ENSG00000205002	ENSG00000205002			33842	protein-coding gene	gene with protein product	"""Alanine and arginine-rich domain-containing protein"""		"""chromosome 8 open reading frame 85"""	C8orf85			Standard	NM_001025357		Approved	LOC441376	uc003yof.3	Q4LEZ3	OTTHUMG00000164961	ENST00000378279.3:c.276G>T	8.37:g.117950758G>T	ENSP00000367528:p.Gln92His	1.0	0.0	0		11.0	10.0	0.909091	NM_001025357	A5PKU8	Missense_Mutation	SNP	ENST00000378279.3	37	CCDS34935.1	53	0.024267399267399268	5	0.01016260162601626	7	0.019337016574585635	0	0.0	41	0.05408970976253298	G	7.346	0.621816	0.14193	.	.	ENSG00000205002	ENST00000378279	T	0.32515	1.45	3.52	0.485	0.16830	.	1.349340	0.05344	N	0.530724	T	0.05456	0.0144	N	0.24115	0.695	0.09310	N	1	D	0.60160	0.987	P	0.57548	0.823	T	0.06445	-1.0826	10	0.30854	T	0.27	-0.5551	2.1438	0.03782	0.1165:0.1949:0.4883:0.2002	.	92	Q4LEZ3	AARD_HUMAN	H	92	ENSP00000367528:Q92H	ENSP00000367528:Q92H	Q	+	3	2	C8orf85	118019939	0.000000	0.05858	0.004000	0.12327	0.408000	0.30992	0.044000	0.13992	-0.030000	0.13804	0.455000	0.32223	CAG	G|0.976;T|0.024	0.024	strong		0.761	AARD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381195.1	NM_001025357	
LPIN1	23175	hgsc.bcm.edu	37	2	11955228	11955228	+	Missense_Mutation	SNP	T	T	A			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr2:11955228T>A	ENST00000256720.2	+	17	2249	c.2156T>A	c.(2155-2157)tTt>tAt	p.F719Y	LPIN1_ENST00000404113.2_Missense_Mutation_p.F220Y|LPIN1_ENST00000449576.2_Missense_Mutation_p.F804Y|LPIN1_ENST00000425416.2_Missense_Mutation_p.F725Y|LPIN1_ENST00000396097.1_Missense_Mutation_p.F449Y|LPIN1_ENST00000396099.1_Missense_Mutation_p.F761Y	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	719	C-LIP.				cellular lipid metabolic process (GO:0044255)|fatty acid catabolic process (GO:0009062)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)|triglyceride mobilization (GO:0006642)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(15)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	45	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		GGATATAAATTTCTCTACTGT	0.502																																					p.F804Y		Atlas-SNP	.											.	LPIN1	99	.	0			c.T2411A						PASS	.						53.0	52.0	52.0					2																	11955228		2203	4300	6503	SO:0001583	missense	23175	exon19			ATAAATTTCTCTA	D80010	CCDS1682.1, CCDS58699.1, CCDS58700.1, CCDS58701.1	2p25.1	2008-05-23			ENSG00000134324	ENSG00000134324			13345	protein-coding gene	gene with protein product		605518				11138012, 8724849, 16950137	Standard	NM_145693		Approved	KIAA0188	uc010yjm.3	Q14693	OTTHUMG00000119082	ENST00000256720.2:c.2156T>A	2.37:g.11955228T>A	ENSP00000256720:p.Phe719Tyr	125.0	0.0	0		119.0	23.0	0.193277	NM_001261428	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Missense_Mutation	SNP	ENST00000256720.2	37	CCDS1682.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.551618	0.86127	.	.	ENSG00000134324	ENST00000449576;ENST00000396099;ENST00000425416;ENST00000256720;ENST00000396097;ENST00000404113	T;T;T;T;T;T	0.77229	-1.08;-1.08;-1.08;-1.08;-1.08;-1.08	4.69	4.69	0.59074	HAD-like domain (2);LNS2, Lipin/Ned1/Smp2 (2);	0.000000	0.85682	D	0.000000	D	0.88991	0.6588	M	0.87547	2.89	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.91635	0.998;0.999;0.986	D	0.91033	0.4865	10	0.87932	D	0	-18.1031	14.1851	0.65601	0.0:0.0:0.0:1.0	.	220;804;719	B4DET9;F5GY24;Q14693	.;.;LPIN1_HUMAN	Y	804;761;725;719;449;220	ENSP00000397908:F804Y;ENSP00000379406:F761Y;ENSP00000401522:F725Y;ENSP00000256720:F719Y;ENSP00000379404:F449Y;ENSP00000386120:F220Y	ENSP00000256720:F719Y	F	+	2	0	LPIN1	11872679	1.000000	0.71417	0.997000	0.53966	0.775000	0.43874	7.544000	0.82117	1.752000	0.51891	0.533000	0.62120	TTT	.	.	none		0.502	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239296.3	NM_145693	
FARSB	10056	hgsc.bcm.edu	37	2	223504317	223504317	+	Nonsense_Mutation	SNP	A	A	T			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr2:223504317A>T	ENST00000281828.6	-	5	700	c.437T>A	c.(436-438)tTa>tAa	p.L146*	FARSB_ENST00000536361.1_Nonsense_Mutation_p.L47*	NM_005687.3	NP_005678.3	Q9NSD9	SYFB_HUMAN	phenylalanyl-tRNA synthetase, beta subunit	146					gene expression (GO:0010467)|phenylalanyl-tRNA aminoacylation (GO:0006432)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|phenylalanine-tRNA ligase activity (GO:0004826)|RNA binding (GO:0003723)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	24		Renal(207;0.0183)		Epithelial(121;3.47e-10)|all cancers(144;1.86e-07)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.011)	L-Phenylalanine(DB00120)	ATTCTGATGTAATTTCTCCTG	0.423																																					p.L146X		Atlas-SNP	.											.	FARSB	49	.	0			c.T437A						PASS	.						126.0	123.0	124.0					2																	223504317		2203	4300	6503	SO:0001587	stop_gained	10056	exon5			TGATGTAATTTCT	AF042346	CCDS2454.1	2q36.2	2011-07-01	2007-02-23	2007-02-23	ENSG00000116120	ENSG00000116120	6.1.1.20	"""Aminoacyl tRNA synthetases / Class II"""	17800	protein-coding gene	gene with protein product	"""phenylalanine tRNA ligase 1, beta, cytoplasmic"""	609690	"""phenylalanyl-tRNA synthetase-like, beta subunit"""	FARSLB		10049785	Standard	NM_005687		Approved	PheHB, FRSB	uc002vne.1	Q9NSD9	OTTHUMG00000133155	ENST00000281828.6:c.437T>A	2.37:g.223504317A>T	ENSP00000281828:p.Leu146*	94.0	0.0	0		101.0	20.0	0.19802	NM_005687	B4DFM0|O95708|Q4ZFX1|Q57ZJ5|Q9NZZ6	Nonsense_Mutation	SNP	ENST00000281828.6	37	CCDS2454.1	.	.	.	.	.	.	.	.	.	.	A	40	8.314864	0.98757	.	.	ENSG00000116120	ENST00000281828;ENST00000536361	.	.	.	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.0598	16.2824	0.82697	1.0:0.0:0.0:0.0	.	.	.	.	X	146;47	.	ENSP00000281828:L146X	L	-	2	0	FARSB	223212561	1.000000	0.71417	0.160000	0.22671	0.957000	0.61999	8.826000	0.92034	2.250000	0.74265	0.533000	0.62120	TTA	.	.	none		0.423	FARSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256855.2	NM_005687	
ERICH1	157697	hgsc.bcm.edu	37	8	623759	623759	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr8:623759T>G	ENST00000262109.7	-	4	670	c.593A>C	c.(592-594)gAa>gCa	p.E198A	ERICH1_ENST00000522706.1_Missense_Mutation_p.E104A|ERICH1_ENST00000518277.1_5'Flank	NM_207332.1	NP_997215.1	Q86X53	ERIC1_HUMAN	glutamate-rich 1	198	Glu-rich.									endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|pancreas(1)	20		Colorectal(14;0.158)|Ovarian(12;0.17)|Myeloproliferative disorder(644;0.185)|Hepatocellular(245;0.236)		Epithelial(5;3.29e-14)|BRCA - Breast invasive adenocarcinoma(11;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(5;3.65e-06)|READ - Rectum adenocarcinoma(1;0.0325)		GCCTTCCCCTTCATTGCTGCT	0.547																																					p.E198A		Atlas-SNP	.											.	ERICH1	50	.	0			c.A593C						PASS	.						92.0	87.0	89.0					8																	623759		2203	4300	6503	SO:0001583	missense	157697	exon4			TCCCCTTCATTGC		CCDS5955.1	8p23.3	2005-09-01			ENSG00000104714	ENSG00000104714			27234	protein-coding gene	gene with protein product							Standard	NM_207332		Approved		uc003wph.3	Q86X53	OTTHUMG00000129163	ENST00000262109.7:c.593A>C	8.37:g.623759T>G	ENSP00000262109:p.Glu198Ala	73.0	0.0	0		69.0	10.0	0.144928	NM_207332	A8K2J9|Q9P063	Missense_Mutation	SNP	ENST00000262109.7	37	CCDS5955.1	.	.	.	.	.	.	.	.	.	.	T	13.57	2.275783	0.40294	.	.	ENSG00000104714	ENST00000543819;ENST00000522706;ENST00000262109	T;T	0.39787	1.06;1.08	5.84	5.84	0.93424	.	0.402558	0.26883	N	0.022004	T	0.46698	0.1406	L	0.34521	1.04	0.28111	N	0.930986	D;D;D	0.69078	0.997;0.997;0.997	D;D;D	0.66196	0.91;0.91;0.942	T	0.38672	-0.9650	10	0.19147	T	0.46	-8.068	9.445	0.38693	0.1582:0.0:0.0:0.8418	.	198;198;104	B4DMI5;Q86X53;E5RHA3	.;ERIC1_HUMAN;.	A	198;104;198	ENSP00000428635:E104A;ENSP00000262109:E198A	ENSP00000262109:E198A	E	-	2	0	ERICH1	613759	0.869000	0.29996	0.467000	0.27180	0.016000	0.09150	2.241000	0.43097	2.216000	0.71823	0.533000	0.62120	GAA	.	.	none		0.547	ERICH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251228.3	NM_207332	
CACNG5	27091	hgsc.bcm.edu	37	17	64881273	64881273	+	Silent	SNP	C	C	T			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr17:64881273C>T	ENST00000533854.1	+	6	981	c.744C>T	c.(742-744)agC>agT	p.S248S	CACNG5_ENST00000307139.3_Silent_p.S248S			Q9UF02	CCG5_HUMAN	calcium channel, voltage-dependent, gamma subunit 5	248				SAGVMSVYLFMKRYTAEDMYRPHPGFYRPRLSNCSDYSGQF LHPDAWVRGRSPSDISSEASLQMNSNYPALLKCPDYDQMSS SPC -> VKPVTLSMDRLGLGTAPLSRGEWGWGRRDIPQPF WTPDHPLYFPSSSQNVSLSYLSGSPPARMSPGPCSCPHVHF PPHSSCVLCRPQPREMRQAPAASPSSAVFSL (in Ref. 1; AAF03089). {ECO:0000305}.	regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ion transmembrane transporter activity (GO:0015075)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)|skin(2)	24			BRCA - Breast invasive adenocarcinoma(6;1.61e-08)			ACATCTCCAGCGAGGCCTCCC	0.637																																					p.S248S		Atlas-SNP	.											.	CACNG5	77	.	0			c.C744T						PASS	.						54.0	48.0	50.0					17																	64881273		2203	4300	6503	SO:0001819	synonymous_variant	27091	exon5			CTCCAGCGAGGCC	AF148220	CCDS11665.1	17q24	2004-02-16				ENSG00000075429		"""Calcium channel subunits"""	1409	protein-coding gene	gene with protein product		606405				10613843	Standard	NM_145811		Approved		uc010wqj.2	Q9UF02		ENST00000533854.1:c.744C>T	17.37:g.64881273C>T		37.0	0.0	0		45.0	16.0	0.355556	NM_145811	A8K2A6|Q547R3|Q8WXS7|Q9UHM3	Silent	SNP	ENST00000533854.1	37	CCDS11665.1																																																																																			.	.	none		0.637	CACNG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389882.1	NM_014404, NM_145811	
CARD11	84433	hgsc.bcm.edu	37	7	2977614	2977614	+	Missense_Mutation	SNP	T	T	A			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr7:2977614T>A	ENST00000396946.4	-	8	1473	c.1070A>T	c.(1069-1071)gAc>gTc	p.D357V		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	357					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)	p.D350V(1)		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)		CATTTCACAGTCCTTTCCCAG	0.567			Mis		DLBCL																																p.D357V		Atlas-SNP	.		Dom	yes		7	7p22	84433	"""caspase recruitment domain family, member 11"""		L	CARD11,NS,lymphoid_neoplasm,0,4	CARD11	339	4	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.A1070T						PASS	.						153.0	124.0	134.0					7																	2977614		2203	4300	6503	SO:0001583	missense	84433	exon8			TCACAGTCCTTTC	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.1070A>T	7.37:g.2977614T>A	ENSP00000380150:p.Asp357Val	48.0	0.0	0		44.0	23.0	0.522727	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	37	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	T	24.8	4.568717	0.86439	.	.	ENSG00000198286	ENST00000396946	T	0.35605	1.3	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.56906	0.2017	M	0.64997	1.995	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.60682	-0.7215	10	0.72032	D	0.01	-47.8827	13.8813	0.63684	0.0:0.0:0.0:1.0	.	357	Q9BXL7	CAR11_HUMAN	V	357	ENSP00000380150:D357V	ENSP00000380150:D357V	D	-	2	0	CARD11	2944140	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.794000	0.85869	1.878000	0.54408	0.482000	0.46254	GAC	.	.	none		0.567	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415	
DYNC2H1	79659	hgsc.bcm.edu	37	11	103070165	103070165	+	Missense_Mutation	SNP	G	G	C			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr11:103070165G>C	ENST00000375735.2	+	49	8192	c.8048G>C	c.(8047-8049)aGa>aCa	p.R2683T	DYNC2H1_ENST00000398093.3_Missense_Mutation_p.R2683T|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	2683	AAA 4. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		AAGATTTCCAGAGGATATGAA	0.403																																					p.R2683T		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.G8048C						PASS	.						85.0	78.0	80.0					11																	103070165		1882	4126	6008	SO:0001583	missense	79659	exon49			TTTCCAGAGGATA	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"""Cytoplasmic dyneins"""	2962	protein-coding gene	gene with protein product		603297	"""dynein, cytoplasmic, heavy polypeptide 2"""	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.8048G>C	11.37:g.103070165G>C	ENSP00000364887:p.Arg2683Thr	121.0	0.0	0		88.0	30.0	0.340909	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	37	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.848139	0.91277	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.44083	0.93;0.93	6.17	6.17	0.99709	Dynein heavy chain, P-loop containing D4 domain (1);	0.000000	0.64402	U	0.000005	T	0.69242	0.3089	M	0.92649	3.33	0.80722	D	1	D;P	0.56287	0.975;0.86	P;P	0.53722	0.733;0.535	T	0.75966	-0.3131	10	0.87932	D	0	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	2683;2683	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	T	2683	ENSP00000364887:R2683T;ENSP00000381167:R2683T	ENSP00000364887:R2683T	R	+	2	0	DYNC2H1	102575375	1.000000	0.71417	0.996000	0.52242	0.994000	0.84299	9.766000	0.98957	2.941000	0.99782	0.655000	0.94253	AGA	.	.	none		0.403	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
ARID1A	8289	hgsc.bcm.edu	37	1	27101097	27101097	+	Missense_Mutation	SNP	G	G	C			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr1:27101097G>C	ENST00000324856.7	+	18	4750	c.4379G>C	c.(4378-4380)gGc>gCc	p.G1460A	ARID1A_ENST00000457599.2_Intron|ARID1A_ENST00000540690.1_Intron|ARID1A_ENST00000374152.2_Missense_Mutation_p.G1077A	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1460					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		TTCCAGTTTGGCCGAGACCGT	0.582			"""Mis, N, F, S, D"""		"""clear cell ovarian carcinoma, RCC"""																																p.G1460A		Atlas-SNP	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.G4379C						PASS	.						69.0	73.0	72.0					1																	27101097		2203	4300	6503	SO:0001583	missense	8289	exon18			AGTTTGGCCGAGA	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"""-"""	11110	protein-coding gene	gene with protein product		603024	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1"", ""AT rich interactive domain 1A (SWI- like)"""	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.4379G>C	1.37:g.27101097G>C	ENSP00000320485:p.Gly1460Ala	114.0	0.0	0		124.0	38.0	0.306452	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Missense_Mutation	SNP	ENST00000324856.7	37	CCDS285.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.76|18.76	3.691728|3.691728	0.68271|0.68271	.|.	.|.	ENSG00000117713|ENSG00000117713	ENST00000324856;ENST00000374152|ENST00000430799	T;T|.	0.02606|.	4.39;4.23|.	5.54|5.54	4.63|4.63	0.57726|0.57726	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.59838|0.59838	0.2223|0.2223	L|L	0.43923|0.43923	1.385|1.385	0.80722|0.80722	D|D	1|1	D;P;D|.	0.89917|.	1.0;0.952;0.982|.	D;P;P|.	0.87578|.	0.998;0.607;0.73|.	T|T	0.57545|0.57545	-0.7793|-0.7793	10|5	0.37606|.	T|.	0.19|.	-10.3623|-10.3623	14.2699|14.2699	0.66145|0.66145	0.0706:0.0:0.9294:0.0|0.0706:0.0:0.9294:0.0	.|.	1077;1460;1113|.	O14497-3;O14497;Q4LE49|.	.;ARI1A_HUMAN;.|.	A|C	1460;1077|356	ENSP00000320485:G1460A;ENSP00000363267:G1077A|.	ENSP00000320485:G1460A|.	G|W	+|+	2|3	0|0	ARID1A|ARID1A	26973684|26973684	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	6.134000|6.134000	0.71689|0.71689	1.586000|1.586000	0.49944|0.49944	0.650000|0.650000	0.86243|0.86243	GGC|TGG	.	.	none		0.582	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135	
CHST2	9435	hgsc.bcm.edu	37	3	142839977	142839977	+	Missense_Mutation	SNP	G	G	A	rs185111962	byFrequency	TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr3:142839977G>A	ENST00000309575.3	+	2	1703	c.319G>A	c.(319-321)Ggg>Agg	p.G107R		NM_004267.4	NP_004258.2	Q9Y4C5	CHST2_HUMAN	carbohydrate (N-acetylglucosamine-6-O) sulfotransferase 2	107					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|inflammatory response (GO:0006954)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|multicellular organismal development (GO:0007275)|N-acetylglucosamine metabolic process (GO:0006044)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)|trans-Golgi network (GO:0005802)	N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)|sulfotransferase activity (GO:0008146)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(2)	22						ggggcgcccagggccgcctcc	0.761													G|||	32	0.00638978	0.0008	0.0115	5008	,	,		9166	0.0		0.0179	False		,,,				2504	0.0051				p.G107R		Atlas-SNP	.											.	CHST2	67	.	0			c.G319A						PASS	.	G	ARG/GLY	6,3188		0,6,1591	2.0	2.0	2.0		319	2.4	0.8	3		2	29,6187		0,29,3079	no	missense	CHST2	NM_004267.4	125	0,35,4670	AA,AG,GG		0.4665,0.1879,0.3719	benign	107/531	142839977	35,9375	1597	3108	4705	SO:0001583	missense	9435	exon2			CGCCCAGGGCCGC	BC042160	CCDS3129.1	3q24	2007-03-14			ENSG00000175040	ENSG00000175040		"""Sulfotransferases, membrane-bound"""	1970	protein-coding gene	gene with protein product		603798				10049591	Standard	NM_004267		Approved	C6ST	uc003evm.3	Q9Y4C5	OTTHUMG00000159351	ENST00000309575.3:c.319G>A	3.37:g.142839977G>A	ENSP00000307911:p.Gly107Arg	1.0	0.0	0		13.0	9.0	0.692308	NM_004267	D3DNG5|Q2M370|Q9GZN5|Q9UED5|Q9Y6F2	Missense_Mutation	SNP	ENST00000309575.3	37	CCDS3129.1	22	0.010073260073260074	6	0.012195121951219513	4	0.011049723756906077	0	0.0	12	0.0158311345646438	G	4.642	0.119345	0.08881	0.001879	0.004665	ENSG00000175040	ENST00000309575	D	0.97041	-4.22	3.3	2.42	0.29668	.	.	.	.	.	D	0.85225	0.5648	N	0.14661	0.345	0.27986	N	0.935857	B	0.06786	0.001	B	0.08055	0.003	T	0.82478	-0.0437	9	0.51188	T	0.08	-12.4417	4.825	0.13412	0.1239:0.2213:0.6548:0.0	.	107	Q9Y4C5	CHST2_HUMAN	R	107	ENSP00000307911:G107R	ENSP00000307911:G107R	G	+	1	0	CHST2	144322667	0.000000	0.05858	0.845000	0.33349	0.137000	0.21094	-0.018000	0.12568	0.947000	0.37659	0.407000	0.27541	GGG	G|0.990;A|0.010	0.010	strong		0.761	CHST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354850.1	NM_004267	
