#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_dbSNPPopFreq	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
ZBTB8OS	339487	hgsc.bcm.edu	37	1	33099257	33099257	+	Missense_Mutation	SNP	A	A	C			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr1:33099257A>C	ENST00000468695.1	-	4	370	c.352T>G	c.(352-354)Ttc>Gtc	p.F118V	ZBTB8OS_ENST00000373501.2_Missense_Mutation_p.F106V|ZBTB8OS_ENST00000492007.1_Intron|ZBTB8OS_ENST00000341885.5_Intron	NM_178547.2	NP_848642.1	Q8IWT0	ARCH_HUMAN	zinc finger and BTB domain containing 8 opposite strand	106					tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	extracellular vesicular exosome (GO:0070062)|tRNA-splicing ligase complex (GO:0072669)	metal ion binding (GO:0046872)			endometrium(1)|lung(4)|upper_aerodigestive_tract(1)	6		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				CGGGGTATGAAGAATTCATCA	0.313																																					p.F118V		Atlas-SNP	.											.	ZBTB8OS	9	.	0			c.T352G						PASS	.						52.0	56.0	55.0					1																	33099257		2203	4296	6499	SO:0001583	missense	339487	exon4			GTATGAAGAATTC	AY151084	CCDS365.1	1p35.1	2010-09-30			ENSG00000176261	ENSG00000176261			24094	protein-coding gene	gene with protein product	"""archease"""	615891				12477932	Standard	NM_178547		Approved	ARCH	uc001bvp.3	Q8IWT0	OTTHUMG00000007856	ENST00000468695.1:c.352T>G	chr1.hg19:g.33099257A>C	ENSP00000417677:p.Phe118Val	104.0	0.0	.		70.0	40.0	.	NM_178547	Q5TGK5|Q6PDA1|Q8IWS9|Q8NEV6|Q8NEV7	Missense_Mutation	SNP	ENST00000468695.1	hg19	CCDS365.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.0|22.0	4.225490|4.225490	0.79576|0.79576	.|.	.|.	ENSG00000176261|ENSG00000176261	ENST00000468695;ENST00000373501|ENST00000436661	.|.	.|.	.|.	5.4|5.4	5.4|5.4	0.78164|0.78164	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72431|0.72431	0.3459|0.3459	M|M	0.77820|0.77820	2.39|2.39	0.80722|0.80722	D|D	1|1	P;D|.	0.89917|.	0.712;1.0|.	P;D|.	0.87578|.	0.525;0.998|.	T|T	0.73855|0.73855	-0.3851|-0.3851	9|5	0.07990|.	T|.	0.79|.	-14.6218|-14.6218	10.1989|10.1989	0.43071|0.43071	0.8518:0.0:0.0:0.1482|0.8518:0.0:0.0:0.1482	.|.	106;118|.	Q8IWT0-2;A8K0B5|.	.;.|.	V|R	118;106|116	.|.	ENSP00000362600:F106V|.	F|L	-|-	1|2	0|0	ZBTB8OS|ZBTB8OS	32871844|32871844	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.227000|7.227000	0.78070|0.78070	2.180000|2.180000	0.69256|0.69256	0.533000|0.533000	0.62120|0.62120	TTC|CTT	.	.	.	none		0.313	ZBTB8OS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021669.3	NM_178547	
RLF	6018	hgsc.bcm.edu	37	1	40701983	40701983	+	Missense_Mutation	SNP	G	G	A			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr1:40701983G>A	ENST00000372771.4	+	8	1636	c.1609G>A	c.(1609-1611)Gac>Aac	p.D537N		NM_012421.3	NP_036553.2	Q13129	RLF_HUMAN	rearranged L-myc fusion	537					chromosome organization (GO:0051276)|DNA integration (GO:0015074)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(18)|lung(18)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(4)|urinary_tract(2)	68	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;5.87e-19)|Epithelial(16;7.02e-16)|all cancers(16;1.69e-14)|Lung(16;0.0427)|LUSC - Lung squamous cell carcinoma(16;0.0461)			GGAGAAAAGAGACAAAAAACC	0.358																																					p.D537N		Atlas-SNP	.											.	RLF	152	.	0			c.G1609A						PASS	.						65.0	70.0	68.0					1																	40701983		2199	4298	6497	SO:0001583	missense	6018	exon8			AAAAGAGACAAAA		CCDS448.1	1p32	2010-05-07	2005-08-16		ENSG00000117000	ENSG00000117000		"""Zinc fingers, C2H2-type"""	10025	protein-coding gene	gene with protein product		180610	"""rearranged L-myc fusion sequence"""			1649386	Standard	NM_012421		Approved	ZNF292L, Zn-15L	uc001cfc.4	Q13129	OTTHUMG00000005763	ENST00000372771.4:c.1609G>A	chr1.hg19:g.40701983G>A	ENSP00000361857:p.Asp537Asn	147.0	0.0	.		101.0	34.0	.	NM_012421	Q14CQ1|Q9NU60	Missense_Mutation	SNP	ENST00000372771.4	hg19	CCDS448.1	.	.	.	.	.	.	.	.	.	.	G	15.03	2.710822	0.48517	.	.	ENSG00000117000	ENST00000372771;ENST00000535839	T	0.36699	1.24	6.07	6.07	0.98685	.	0.378317	0.33144	N	0.005225	T	0.42877	0.1222	L	0.40543	1.245	0.37876	D	0.930215	B;D	0.67145	0.23;0.996	B;P	0.56216	0.064;0.794	T	0.15983	-1.0418	10	0.18710	T	0.47	-14.4249	14.7663	0.69642	0.0684:0.0:0.9316:0.0	.	230;537	F5H2M5;Q13129	.;RLF_HUMAN	N	537;230	ENSP00000361857:D537N	ENSP00000361857:D537N	D	+	1	0	RLF	40474570	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.802000	0.47916	2.885000	0.99019	0.655000	0.94253	GAC	.	.	.	none		0.358	RLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015767.1	NM_012421	
TMEM53	79639	hgsc.bcm.edu	37	1	45120714	45120714	+	Silent	SNP	G	G	T			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr1:45120714G>T	ENST00000372237.3	-	3	514	c.351C>A	c.(349-351)gtC>gtA	p.V117V	TMEM53_ENST00000476724.1_5'UTR|TMEM53_ENST00000372243.3_Intron|TMEM53_ENST00000372242.3_Silent_p.V117V|TMEM53_ENST00000372235.3_Silent_p.V87V|TMEM53_ENST00000372244.3_Intron	NM_024587.2	NP_078863.2	Q6P2H8	TMM53_HUMAN	transmembrane protein 53	117						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(3)|ovary(2)|urinary_tract(1)	10	Acute lymphoblastic leukemia(166;0.155)					GGTACAGCATGACGCCACCGT	0.577											OREG0013446	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V117V		Atlas-SNP	.											.	TMEM53	40	.	0			c.C351A						PASS	.						60.0	62.0	62.0					1																	45120714		2203	4300	6503	SO:0001819	synonymous_variant	79639	exon3			CAGCATGACGCCA		CCDS511.1, CCDS72773.1	1p34.1	2008-02-26			ENSG00000126106	ENSG00000126106			26186	protein-coding gene	gene with protein product						12958361	Standard	XR_425151		Approved	FLJ22353, NET4	uc001cmc.3	Q6P2H8	OTTHUMG00000007833	ENST00000372237.3:c.351C>A	chr1.hg19:g.45120714G>T		82.0	0.0	.	929	46.0	26.0	.	NM_024587	B4DKG0|Q5JPH2|Q6IA07|Q9H6E2	Silent	SNP	ENST00000372237.3	hg19	CCDS511.1																																																																																			.	.	.	none		0.577	TMEM53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021599.1	NM_024587	
DAP3	7818	hgsc.bcm.edu	37	1	155695186	155695186	+	Missense_Mutation	SNP	G	G	A			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr1:155695186G>A	ENST00000368336.5	+	5	408	c.284G>A	c.(283-285)aGt>aAt	p.S95N	DAP3_ENST00000535183.1_Missense_Mutation_p.S54N|DAP3_ENST00000496863.1_3'UTR|DAP3_ENST00000471642.2_Missense_Mutation_p.S54N|DAP3_ENST00000421487.2_Missense_Mutation_p.S61N|MSTO1_ENST00000538143.1_Intron|MSTO1_ENST00000452804.2_Intron|DAP3_ENST00000343043.3_Missense_Mutation_p.S95N	NM_001199849.1|NM_004632.3	NP_001186778.1|NP_004623.1	P51398	RT29_HUMAN	death associated protein 3	95					apoptotic mitochondrial changes (GO:0008637)|apoptotic signaling pathway (GO:0097190)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|small ribosomal subunit (GO:0015935)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	24	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)					AAGACATTCAGTGAAGCTTGC	0.453																																					p.S95N		Atlas-SNP	.											.	DAP3	46	.	0			c.G284A						PASS	.						187.0	174.0	178.0					1																	155695186		2203	4300	6503	SO:0001583	missense	7818	exon5			CATTCAGTGAAGC	X83544	CCDS1120.1, CCDS55646.1, CCDS55647.1	1q22	2012-11-14			ENSG00000132676	ENSG00000132676		"""Mitochondrial ribosomal proteins / small subunits"""	2673	protein-coding gene	gene with protein product	"""mitochondrial 28S ribosomal protein S29"""	602074				7499268, 9284927	Standard	NM_004632		Approved	MRPS29, DAP-3, MRP-S29, bMRP-10, MGC126058, MGC126059, DKFZp686G12159	uc001flr.3	P51398	OTTHUMG00000035439	ENST00000368336.5:c.284G>A	chr1.hg19:g.155695186G>A	ENSP00000357320:p.Ser95Asn	165.0	0.0	.		182.0	66.0	.	NM_033657	B4DP59|B4DY62|E7EM60|Q13044|Q68CT7|Q96Q20	Missense_Mutation	SNP	ENST00000368336.5	hg19	CCDS1120.1	.	.	.	.	.	.	.	.	.	.	G	0.013	-1.629646	0.00813	.	.	ENSG00000132676	ENST00000368336;ENST00000343043;ENST00000421487;ENST00000535183	T;T;T;T	0.40756	1.03;1.03;1.06;1.02	5.65	-2.53	0.06326	.	0.680865	0.15179	N	0.276217	T	0.01835	0.0058	N	0.00114	-2.085	0.09310	N	0.999999	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.46665	-0.9175	10	0.02654	T	1	0.0	11.3623	0.49651	0.6267:0.0:0.3733:0.0	.	54;61;61;95	B4DP59;B4DY62;E7EM60;P51398	.;.;.;RT29_HUMAN	N	95;95;61;54	ENSP00000357320:S95N;ENSP00000341692:S95N;ENSP00000412605:S61N;ENSP00000445003:S54N	ENSP00000341692:S95N	S	+	2	0	DAP3	153961810	0.928000	0.31464	0.005000	0.12908	0.078000	0.17371	1.904000	0.39868	-0.315000	0.08703	-0.136000	0.14681	AGT	.	.	.	none		0.453	DAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086042.1	NM_004632	
TIPRL	261726	hgsc.bcm.edu	37	1	168168189	168168189	+	Silent	SNP	G	G	A			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr1:168168189G>A	ENST00000367833.2	+	6	790	c.645G>A	c.(643-645)acG>acA	p.T215T		NM_152902.3	NP_690866.1	O75663	TIPRL_HUMAN	TOR signaling pathway regulator	215	Interaction with PPP2CA.				DNA damage checkpoint (GO:0000077)|negative regulation of protein phosphatase type 2A activity (GO:0034048)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				breast(1)|kidney(1)|large_intestine(1)|ovary(2)|skin(1)	6	all_hematologic(923;0.215)					GAGAATATACGTCACGAGAAA	0.259																																					p.T215T		Atlas-SNP	.											.	TIPRL	16	.	0			c.G645A						PASS	.						56.0	60.0	59.0					1																	168168189		2200	4299	6499	SO:0001819	synonymous_variant	261726	exon6			ATATACGTCACGA	AB097034	CCDS1270.1, CCDS30935.1	1q23.2	2014-03-07	2014-03-07		ENSG00000143155	ENSG00000143155			30231	protein-coding gene	gene with protein product		611807	"""TIP41, TOR signaling pathway regulator-like (S. cerevisiae)"""			12761501	Standard	NM_001031800		Approved	MGC3794, dJ69E11.3, TIP41	uc001gfg.3	O75663	OTTHUMG00000034646	ENST00000367833.2:c.645G>A	chr1.hg19:g.168168189G>A		40.0	0.0	.		51.0	11.0	.	NM_152902	B2R8V3|Q5HYB2|Q8IZ86	Silent	SNP	ENST00000367833.2	hg19	CCDS1270.1																																																																																			.	.	.	none		0.259	TIPRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083822.1	NM_152902	
RFWD2	64326	hgsc.bcm.edu	37	1	175914297	175914297	+	Silent	SNP	A	A	G			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr1:175914297A>G	ENST00000367669.3	-	20	2702	c.2188T>C	c.(2188-2190)Ttg>Ctg	p.L730L	RFWD2_ENST00000308769.8_Silent_p.L706L	NM_022457.5	NP_071902.2	Q8NHY2	RFWD2_HUMAN	ring finger and WD repeat domain 2, E3 ubiquitin protein ligase	730					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|response to ionizing radiation (GO:0010212)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin protein ligase activity (GO:0061630)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(5)|lung(17)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						CTTCATACCAATTCTAGCACC	0.318																																					p.L730L	Ovarian(134;1413 1765 5706 35534 51541)	Atlas-SNP	.											.	RFWD2	67	.	0			c.T2188C						PASS	.						49.0	44.0	46.0					1																	175914297		2203	4300	6503	SO:0001819	synonymous_variant	64326	exon20			ATACCAATTCTAG	AK001278	CCDS30944.1, CCDS44279.1	1q25.1-q25.2	2013-01-09	2012-02-23		ENSG00000143207	ENSG00000143207		"""WD repeat domain containing"", ""RING-type (C3HC4) zinc fingers"""	17440	protein-coding gene	gene with protein product		608067	"""ring finger and WD repeat domain 2"""			10395541	Standard	XM_005245447		Approved	FLJ10416, COP1, RNF200	uc001gku.1	Q8NHY2	OTTHUMG00000034986	ENST00000367669.3:c.2188T>C	chr1.hg19:g.175914297A>G		52.0	0.0	.		77.0	4.0	.	NM_022457	E9PKI0|Q504W6|Q6H103|Q9H6L7|X5D9B4	Silent	SNP	ENST00000367669.3	hg19	CCDS30944.1																																																																																			.	.	.	none		0.318	RFWD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084672.2	NM_022457	
KLHDC8A	55220	hgsc.bcm.edu	37	1	205312513	205312513	+	Missense_Mutation	SNP	C	C	T			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr1:205312513C>T	ENST00000367156.3	-	5	1036	c.220G>A	c.(220-222)Gtc>Atc	p.V74I	KLHDC8A_ENST00000367155.3_Missense_Mutation_p.V74I|KLHDC8A_ENST00000539253.1_Missense_Mutation_p.V74I|KLHDC8A_ENST00000460687.1_Intron|KLHDC8A_ENST00000537168.1_Intron|KLHDC8A_ENST00000606529.1_5'Flank	NM_001271863.1	NP_001258792.1	Q8IYD2	KLD8A_HUMAN	kelch domain containing 8A	74										breast(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Breast(84;0.23)		BRCA - Breast invasive adenocarcinoma(75;0.117)			AGGGCGGTGACGGCCACCCCC	0.672																																					p.V74I		Atlas-SNP	.											.	KLHDC8A	31	.	0			c.G220A						PASS	.						61.0	64.0	63.0					1																	205312513		2203	4300	6503	SO:0001583	missense	55220	exon2			CGGTGACGGCCAC		CCDS30985.1	1q32.1	2008-02-05			ENSG00000162873	ENSG00000162873			25573	protein-coding gene	gene with protein product		614503					Standard	NM_018203		Approved	FLJ10748	uc031prx.1	Q8IYD2	OTTHUMG00000037199	ENST00000367156.3:c.220G>A	chr1.hg19:g.205312513C>T	ENSP00000356124:p.Val74Ile	172.0	0.0	.		174.0	52.0	.	NM_018203	B3KU70|Q9NVG5	Missense_Mutation	SNP	ENST00000367156.3	hg19	CCDS30985.1	.	.	.	.	.	.	.	.	.	.	C	16.14	3.040035	0.55003	.	.	ENSG00000162873	ENST00000367155;ENST00000367156;ENST00000539253	T;T;T	0.80304	-1.36;-1.36;-1.36	5.65	4.73	0.59995	Kelch-type beta propeller (1);	0.190308	0.45361	N	0.000376	T	0.78065	0.4225	M	0.72576	2.205	0.31222	N	0.697307	B	0.13594	0.008	B	0.08055	0.003	T	0.76753	-0.2843	10	0.51188	T	0.08	-18.7937	10.6433	0.45604	0.0:0.8425:0.0:0.1575	.	74	Q8IYD2	KLD8A_HUMAN	I	74	ENSP00000356123:V74I;ENSP00000356124:V74I;ENSP00000442229:V74I	ENSP00000356123:V74I	V	-	1	0	KLHDC8A	203579136	0.981000	0.34729	0.230000	0.23976	0.980000	0.70556	2.591000	0.46163	1.346000	0.45694	0.655000	0.94253	GTC	.	.	.	none		0.672	KLHDC8A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090397.1	NM_018203	
HEATR5B	54497	hgsc.bcm.edu	37	2	37267620	37267620	+	Missense_Mutation	SNP	A	A	T			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr2:37267620A>T	ENST00000233099.5	-	20	2993	c.2898T>A	c.(2896-2898)agT>agA	p.S966R	HEATR5B_ENST00000354531.2_Missense_Mutation_p.S966R	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	966						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				ACATCGGACCACTAGAATCCA	0.373																																					p.S966R		Atlas-SNP	.											.	HEATR5B	185	.	0			c.T2898A						PASS	.						107.0	92.0	97.0					2																	37267620		2203	4300	6503	SO:0001583	missense	54497	exon20			CGGACCACTAGAA	AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869			29273	protein-coding gene	gene with protein product						10718198	Standard	XM_005264379		Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.2898T>A	chr2.hg19:g.37267620A>T	ENSP00000233099:p.Ser966Arg	120.0	0.0	.		125.0	38.0	.	NM_019024	B5MDU8|Q7Z3B2|Q9NVL7	Missense_Mutation	SNP	ENST00000233099.5	hg19	CCDS33181.1	.	.	.	.	.	.	.	.	.	.	A	14.94	2.686846	0.48097	.	.	ENSG00000008869	ENST00000233099;ENST00000354531	T;T	0.06528	3.29;3.29	5.5	1.75	0.24633	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.06096	0.0158	L	0.38175	1.15	0.51767	D	0.999939	B	0.32425	0.371	B	0.32149	0.141	T	0.35599	-0.9782	10	0.52906	T	0.07	-15.7822	11.2928	0.49261	0.805:0.0:0.195:0.0	.	966	Q9P2D3	HTR5B_HUMAN	R	966	ENSP00000233099:S966R;ENSP00000346531:S966R	ENSP00000233099:S966R	S	-	3	2	HEATR5B	37121124	1.000000	0.71417	0.999000	0.59377	0.938000	0.57974	1.659000	0.37387	0.035000	0.15519	-1.139000	0.01908	AGT	.	.	.	none		0.373	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024	
UGGT1	56886	hgsc.bcm.edu	37	2	128918714	128918714	+	Silent	SNP	C	C	A			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr2:128918714C>A	ENST00000259253.6	+	25	2744	c.2697C>A	c.(2695-2697)atC>atA	p.I899I	UGGT1_ENST00000375990.3_Silent_p.I875I	NM_020120.3	NP_064505.1	Q9NYU2	UGGG1_HUMAN	UDP-glucose glycoprotein glucosyltransferase 1	899					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)|unfolded protein binding (GO:0051082)			NS(1)|breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(14)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						CTTCACAGATCATTGGGCCAC	0.478																																					p.I899I		Atlas-SNP	.											.	UGGT1	126	.	0			c.C2697A						PASS	.						96.0	95.0	95.0					2																	128918714		2203	4300	6503	SO:0001819	synonymous_variant	56886	exon25			ACAGATCATTGGG	AF227905	CCDS2154.1	2q14.3	2009-07-23	2009-07-23	2009-07-23	ENSG00000136731	ENSG00000136731			15663	protein-coding gene	gene with protein product		605897	"""UDP-glucose ceramide glucosyltransferase-like 1"""	UGCGL1		10694380	Standard	NM_020120		Approved	HUGT1	uc002tps.3	Q9NYU2	OTTHUMG00000131570	ENST00000259253.6:c.2697C>A	chr2.hg19:g.128918714C>A		135.0	0.0	.		139.0	45.0	.	NM_020120	Q53QP2|Q53SL3|Q8IW30|Q9H8I4	Silent	SNP	ENST00000259253.6	hg19	CCDS2154.1																																																																																			.	.	.	none		0.478	UGGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254435.2	NM_020120	
MGAT5	4249	hgsc.bcm.edu	37	2	135206357	135206357	+	Missense_Mutation	SNP	G	G	A			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr2:135206357G>A	ENST00000409645.1	+	17	2417	c.2165G>A	c.(2164-2166)aGg>aAg	p.R722K	MGAT5_ENST00000281923.2_Missense_Mutation_p.R722K			Q09328	MGT5A_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase	722					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity (GO:0030144)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|liver(1)|lung(18)|ovary(3)|pancreas(1)|skin(3)	36				BRCA - Breast invasive adenocarcinoma(221;0.0964)		AGGCACCAGAGGGTCTGCCCC	0.597																																					p.R722K		Atlas-SNP	.											.	MGAT5	84	.	0			c.G2165A						PASS	.						66.0	66.0	66.0					2																	135206357		2203	4300	6503	SO:0001583	missense	4249	exon16			ACCAGAGGGTCTG	D17716	CCDS2171.1	2q21	2013-02-25			ENSG00000152127	ENSG00000152127	2.4.1.155	"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	7049	protein-coding gene	gene with protein product		601774				8292036	Standard	NM_002410		Approved	GNT-V	uc002ttw.4	Q09328	OTTHUMG00000131681	ENST00000409645.1:c.2165G>A	chr2.hg19:g.135206357G>A	ENSP00000386377:p.Arg722Lys	100.0	0.0	.		113.0	36.0	.	NM_002410	D3DP70	Missense_Mutation	SNP	ENST00000409645.1	hg19	CCDS2171.1	.	.	.	.	.	.	.	.	.	.	G	34	5.389249	0.95988	.	.	ENSG00000152127	ENST00000409645;ENST00000281923	.	.	.	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	D	0.82958	0.5150	M	0.81341	2.54	0.80722	D	1	D	0.56035	0.974	D	0.70487	0.969	D	0.85213	0.1022	9	0.72032	D	0.01	-17.0654	18.7668	0.91876	0.0:0.0:1.0:0.0	.	722	Q09328	MGT5A_HUMAN	K	722	.	ENSP00000281923:R722K	R	+	2	0	MGAT5	134922827	1.000000	0.71417	0.998000	0.56505	0.896000	0.52359	9.702000	0.98712	2.523000	0.85059	0.655000	0.94253	AGG	.	.	.	none		0.597	MGAT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254584.3	NM_002410	
FMNL2	114793	hgsc.bcm.edu	37	2	153471511	153471511	+	Silent	SNP	T	T	A			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr2:153471511T>A	ENST00000288670.9	+	12	1576	c.1209T>A	c.(1207-1209)tcT>tcA	p.S403S		NM_052905.3	NP_443137.2	Q96PY5	FMNL2_HUMAN	formin-like 2	403	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				cortical actin cytoskeleton organization (GO:0030866)|cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)				central_nervous_system(2)|endometrium(3)|large_intestine(5)|liver(2)|lung(3)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	23						AAAACATTTCTCATGTAACTA	0.378																																					p.S403S		Atlas-SNP	.											.	FMNL2	75	.	0			c.T1209A						PASS	.						84.0	84.0	84.0					2																	153471511		1882	4124	6006	SO:0001819	synonymous_variant	114793	exon12			CATTTCTCATGTA	AB067489	CCDS46429.1	2q23.3	2008-02-05	2003-12-02	2003-12-03	ENSG00000157827	ENSG00000157827			18267	protein-coding gene	gene with protein product			"""formin homology 2 domain containing 2"""	FHOD2			Standard	XM_005246263		Approved	KIAA1902	uc002tye.3	Q96PY5	OTTHUMG00000154035	ENST00000288670.9:c.1209T>A	chr2.hg19:g.153471511T>A		61.0	0.0	.		106.0	38.0	.	NM_052905	B2RZH5|Q14CC9|Q4ZG52|Q8N3E0	Silent	SNP	ENST00000288670.9	hg19	CCDS46429.1																																																																																			.	.	.	none		0.378	FMNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333582.2	NM_052905	
GPD2	2820	hgsc.bcm.edu	37	2	157367411	157367411	+	Silent	SNP	C	C	T			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr2:157367411C>T	ENST00000310454.6	+	4	750	c.378C>T	c.(376-378)atC>atT	p.I126I	GPD2_ENST00000540309.1_Silent_p.I126I|GPD2_ENST00000409674.1_Silent_p.I126I|GPD2_ENST00000438166.2_Silent_p.I126I|GPD2_ENST00000409125.4_Intron	NM_001083112.2	NP_001076581.2	P43304	GPDM_HUMAN	glycerol-3-phosphate dehydrogenase 2 (mitochondrial)	126					camera-type eye development (GO:0043010)|cellular lipid metabolic process (GO:0044255)|gluconeogenesis (GO:0006094)|glycerol catabolic process (GO:0019563)|glycerol-3-phosphate metabolic process (GO:0006072)|multicellular organism growth (GO:0035264)|small molecule metabolic process (GO:0044281)	glycerol-3-phosphate dehydrogenase complex (GO:0009331)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|glycerol-3-phosphate dehydrogenase activity (GO:0004368)|sn-glycerol-3-phosphate:ubiquinone-8 oxidoreductase activity (GO:0052591)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(1)|stomach(1)	22						AGAAGGCCATCATGAAGTTGG	0.378																																					p.I126I		Atlas-SNP	.											.	GPD2	59	.	0			c.C378T						PASS	.						178.0	177.0	178.0					2																	157367411		2203	4300	6503	SO:0001819	synonymous_variant	2820	exon4			GGCCATCATGAAG		CCDS2202.1	2q24.1	2013-01-10			ENSG00000115159	ENSG00000115159	1.1.1.8	"""EF-hand domain containing"""	4456	protein-coding gene	gene with protein product		138430					Standard	NM_001083112		Approved		uc002tzd.4	P43304	OTTHUMG00000131951	ENST00000310454.6:c.378C>T	chr2.hg19:g.157367411C>T		256.0	0.0	.		277.0	76.0	.	NM_001083112	A8K4V0|B3KSA9|Q59FR1|Q9HAP9	Silent	SNP	ENST00000310454.6	hg19	CCDS2202.1																																																																																			.	.	.	none		0.378	GPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254910.3		
TTN	7273	hgsc.bcm.edu	37	2	179575504	179575504	+	Silent	SNP	G	G	A	rs375083775		TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr2:179575504G>A	ENST00000591111.1	-	96	27593	c.27369C>T	c.(27367-27369)ggC>ggT	p.G9123G	TTN_ENST00000342992.6_Silent_p.G8196G|TTN_ENST00000460472.2_Intron|TTN_ENST00000359218.5_Intron|TTN_ENST00000589042.1_Silent_p.G9440G|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000431752.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13254	Ig-like 74.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.G8196G(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGTACTTTCCGCCACTTCGTA	0.488																																					p.G9440G		Atlas-SNP	.											TTN_ENST00000356127,rectum,carcinoma,0,1	TTN	18412	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C28320T						PASS	.	G	,,,	1,3979		0,1,1989	148.0	143.0	144.0		,24588,,	-12.3	0.4	2		144	0,8340		0,0,4170	no	intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	0,1,6159	AA,AG,GG		0.0,0.0251,0.0081	,,,	,8196/33424,,	179575504	1,12319	1990	4170	6160	SO:0001819	synonymous_variant	7273	exon98			CTTTCCGCCACTT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.27369C>T	chr2.hg19:g.179575504G>A		144.0	2.0	.		182.0	52.0	.	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	hg19																																																																																				.	.	.	weak		0.488	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ACADL	33	hgsc.bcm.edu	37	2	211081192	211081192	+	Missense_Mutation	SNP	C	C	T			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr2:211081192C>T	ENST00000233710.3	-	4	642	c.415G>A	c.(415-417)Ggt>Agt	p.G139S	AC006994.2_ENST00000412065.1_RNA	NM_001608.3	NP_001599.1	P28330	ACADL_HUMAN	acyl-CoA dehydrogenase, long chain	139					carnitine catabolic process (GO:0042413)|carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid catabolic process (GO:0044242)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|long-chain fatty acid catabolic process (GO:0042758)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of fatty acid oxidation (GO:0046322)|oxidation-reduction process (GO:0055114)|protein homotetramerization (GO:0051289)|regulation of cholesterol metabolic process (GO:0090181)|small molecule metabolic process (GO:0044281)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|fatty-acyl-CoA binding (GO:0000062)|flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)|palmitoyl-CoA oxidase activity (GO:0016401)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	14		Renal(323;0.202)		Epithelial(149;0.00631)|Lung(261;0.0438)|LUSC - Lung squamous cell carcinoma(261;0.0466)|all cancers(144;0.0621)		ATGACAATACCTGAATGAATA	0.338																																					p.G139S		Atlas-SNP	.											.	ACADL	38	.	0			c.G415A						PASS	.						107.0	101.0	103.0					2																	211081192		2202	4300	6502	SO:0001583	missense	33	exon4			CAATACCTGAATG	M74096	CCDS2389.1	2q34	2012-07-13	2010-04-30		ENSG00000115361	ENSG00000115361	1.3.99.13		88	protein-coding gene	gene with protein product		609576	"""acyl-Coenzyme A dehydrogenase, long chain"""			1774065	Standard	NM_001608		Approved	LCAD, ACAD4	uc002vdz.4	P28330	OTTHUMG00000132989	ENST00000233710.3:c.415G>A	chr2.hg19:g.211081192C>T	ENSP00000233710:p.Gly139Ser	105.0	0.0	.		112.0	44.0	.	NM_001608	B2R8T3|Q8IUN8	Missense_Mutation	SNP	ENST00000233710.3	hg19	CCDS2389.1	.	.	.	.	.	.	.	.	.	.	C	18.70	3.679212	0.68042	.	.	ENSG00000115361	ENST00000233710	D	0.99683	-6.39	5.77	4.9	0.64082	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA dehydrogenase, N-terminal (1);Acyl-CoA dehydrogenase/oxidase, N-terminal (1);	0.179938	0.64402	D	0.000017	D	0.98469	0.9490	N	0.16266	0.395	0.30365	N	0.783448	B	0.26445	0.149	B	0.34038	0.174	D	0.99899	1.1157	10	0.66056	D	0.02	.	15.4418	0.75190	0.0:0.933:0.0:0.067	.	139	P28330	ACADL_HUMAN	S	139	ENSP00000233710:G139S	ENSP00000233710:G139S	G	-	1	0	ACADL	210789437	1.000000	0.71417	0.998000	0.56505	0.919000	0.55068	5.531000	0.67148	1.578000	0.49821	0.655000	0.94253	GGT	.	.	.	none		0.338	ACADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256561.2	NM_001608	
DGKD	8527	hgsc.bcm.edu	37	2	234363455	234363455	+	Missense_Mutation	SNP	G	G	T			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr2:234363455G>T	ENST00000264057.2	+	19	2323	c.2311G>T	c.(2311-2313)Ggc>Tgc	p.G771C	DGKD_ENST00000409813.3_Missense_Mutation_p.G727C	NM_152879.2	NP_690618.2	Q16760	DGKD_HUMAN	diacylglycerol kinase, delta 130kDa	771					blood coagulation (GO:0007596)|cell growth (GO:0016049)|diacylglycerol metabolic process (GO:0046339)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|multicellular organismal development (GO:0007275)|platelet activation (GO:0030168)|protein homooligomerization (GO:0051260)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein transport (GO:0015031)|response to organic substance (GO:0010033)|second-messenger-mediated signaling (GO:0019932)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol binding (GO:0019992)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(13)|lung(15)|ovary(1)|pancreas(1)|skin(1)	38		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0538)		Epithelial(121;1.31e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000416)|Lung(119;0.00285)|LUSC - Lung squamous cell carcinoma(224;0.00655)	Phosphatidylserine(DB00144)	TTTTGGCATTGGCCTGGATGC	0.453																																					p.G771C		Atlas-SNP	.											.	DGKD	106	.	0			c.G2311T						PASS	.						168.0	145.0	153.0					2																	234363455		2203	4300	6503	SO:0001583	missense	8527	exon19			GGCATTGGCCTGG	D63479	CCDS2504.1, CCDS46546.1	2q37	2013-01-10	2002-08-29		ENSG00000077044	ENSG00000077044		"""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"""	2851	protein-coding gene	gene with protein product	"""diglyceride kinase"""	601826	"""diacylglycerol kinase, delta (130kD)"""			8626538, 12810723	Standard	NM_003648		Approved	KIAA0145, DGKdelta	uc002vui.1	Q16760	OTTHUMG00000133290	ENST00000264057.2:c.2311G>T	chr2.hg19:g.234363455G>T	ENSP00000264057:p.Gly771Cys	124.0	0.0	.		148.0	41.0	.	NM_152879	Q14158|Q6PK55|Q8NG53	Missense_Mutation	SNP	ENST00000264057.2	hg19	CCDS2504.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.405390	0.83230	.	.	ENSG00000077044	ENST00000264057;ENST00000409813	D;D	0.89270	-2.49;-2.49	3.57	3.57	0.40892	Diacylglycerol kinase, accessory domain (2);	0.000000	0.64402	D	0.000004	D	0.96324	0.8801	H	0.97077	3.935	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.97837	1.0266	10	0.87932	D	0	.	16.4941	0.84223	0.0:0.0:1.0:0.0	.	655;727;771	Q53SE4;Q16760-2;Q16760	.;.;DGKD_HUMAN	C	771;727	ENSP00000264057:G771C;ENSP00000386455:G727C	ENSP00000264057:G771C	G	+	1	0	DGKD	234028194	1.000000	0.71417	0.973000	0.42090	0.987000	0.75469	9.627000	0.98412	2.305000	0.77605	0.643000	0.83706	GGC	.	.	.	none		0.453	DGKD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257072.2	NM_003648	
CCDC13	152206	hgsc.bcm.edu	37	3	42793447	42793447	+	Missense_Mutation	SNP	T	T	G			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr3:42793447T>G	ENST00000310232.6	-	5	667	c.584A>C	c.(583-585)cAg>cCg	p.Q195P	CCDC13_ENST00000435327.2_5'UTR	NM_144719.3	NP_653320.3	Q8IYE1	CCD13_HUMAN	coiled-coil domain containing 13	195										endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	25						GTCTCCCATCTGGGCCCTCGG	0.592																																					p.Q195P		Atlas-SNP	.											.	CCDC13	71	.	0			c.A584C						PASS	.						84.0	77.0	79.0					3																	42793447		2203	4300	6503	SO:0001583	missense	152206	exon5			CCCATCTGGGCCC	AK058196	CCDS2705.1	3p22.1	2005-01-25			ENSG00000244607	ENSG00000244607			26358	protein-coding gene	gene with protein product						12477932	Standard	NM_144719		Approved	FLJ25467	uc003cly.4	Q8IYE1	OTTHUMG00000133046	ENST00000310232.6:c.584A>C	chr3.hg19:g.42793447T>G	ENSP00000309836:p.Gln195Pro	135.0	0.0	.		94.0	33.0	.	NM_144719		Missense_Mutation	SNP	ENST00000310232.6	hg19	CCDS2705.1	.	.	.	.	.	.	.	.	.	.	T	4.532	0.098801	0.08681	.	.	ENSG00000244607	ENST00000310232	T	0.24723	1.84	4.01	1.44	0.22558	.	0.735360	0.13594	N	0.376366	T	0.23451	0.0567	L	0.55103	1.725	0.20403	N	0.999901	B;B;B	0.09022	0.001;0.002;0.001	B;B;B	0.06405	0.002;0.002;0.001	T	0.21586	-1.0241	10	0.56958	D	0.05	.	8.5317	0.33337	0.0:0.0:0.4318:0.5682	.	195;195;195	B4DZD2;Q96LI1;Q8IYE1	.;.;CCD13_HUMAN	P	195	ENSP00000309836:Q195P	ENSP00000309836:Q195P	Q	-	2	0	CCDC13	42768451	0.092000	0.21681	0.182000	0.23118	0.423000	0.31445	-0.078000	0.11375	0.286000	0.22352	0.533000	0.62120	CAG	.	.	.	none		0.592	CCDC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256652.1	NM_144719	
STAB1	23166	hgsc.bcm.edu	37	3	52544437	52544437	+	Missense_Mutation	SNP	G	G	A	rs569908210		TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr3:52544437G>A	ENST00000321725.6	+	25	2777	c.2701G>A	c.(2701-2703)Gtc>Atc	p.V901I		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	901	EGF-like 7. {ECO:0000255|PROSITE- ProRule:PRU00076, ECO:0000305}.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)			breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		GGATGGCCGCGTCTGTGTGGC	0.612													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18485	0.0		0.0	False		,,,				2504	0.0				p.V901I		Atlas-SNP	.											STAB1,colon,carcinoma,0,1	STAB1	178	.	0			c.G2701A						PASS	.						95.0	86.0	89.0					3																	52544437		2203	4300	6503	SO:0001583	missense	23166	exon25			GGCCGCGTCTGTG	AJ275213	CCDS33768.1	3p21.31	2008-07-18			ENSG00000010327	ENSG00000010327			18628	protein-coding gene	gene with protein product	"""MS-1 antigen"", ""fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-1"", ""common lymphatic endothelial and vascular endothelial receptor-1"""	608560				11829752, 12077138	Standard	XM_005264973		Approved	KIAA0246, STAB-1, FEEL-1, CLEVER-1, FELE-1, FEX1	uc003dej.3	Q9NY15	OTTHUMG00000158574	ENST00000321725.6:c.2701G>A	chr3.hg19:g.52544437G>A	ENSP00000312946:p.Val901Ile	119.0	0.0	.		70.0	37.0	.	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Missense_Mutation	SNP	ENST00000321725.6	hg19	CCDS33768.1	.	.	.	.	.	.	.	.	.	.	G	11.43	1.637778	0.29157	.	.	ENSG00000010327	ENST00000321725	T	0.42131	0.98	5.86	1.84	0.25277	Epidermal growth factor-like (1);EGF-like region, conserved site (1);Epidermal growth factor-like, type 3 (1);	0.431461	0.22025	N	0.065676	T	0.29850	0.0746	L	0.37697	1.125	0.19575	N	0.999963	B	0.20988	0.05	B	0.12837	0.008	T	0.16719	-1.0393	10	0.36615	T	0.2	.	9.6284	0.39765	0.3064:0.0:0.6936:0.0	.	901	Q9NY15	STAB1_HUMAN	I	901	ENSP00000312946:V901I	ENSP00000312946:V901I	V	+	1	0	STAB1	52519477	0.886000	0.30341	0.825000	0.32803	0.923000	0.55619	1.548000	0.36201	0.322000	0.23283	-0.345000	0.07892	GTC	.	.	.	none		0.612	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136	
EPHB1	2047	hgsc.bcm.edu	37	3	134670526	134670526	+	Missense_Mutation	SNP	T	T	A			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr3:134670526T>A	ENST00000398015.3	+	3	807	c.437T>A	c.(436-438)tTc>tAc	p.F146Y	EPHB1_ENST00000488154.1_3'UTR	NM_004441.4	NP_004432.1	P54762	EPHB1_HUMAN	EPH receptor B1	146	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|camera-type eye morphogenesis (GO:0048593)|cell chemotaxis (GO:0060326)|cell-substrate adhesion (GO:0031589)|central nervous system projection neuron axonogenesis (GO:0021952)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|neural precursor cell proliferation (GO:0061351)|neurogenesis (GO:0022008)|optic nerve morphogenesis (GO:0021631)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of JNK cascade (GO:0046328)|retinal ganglion cell axon guidance (GO:0031290)	axon (GO:0030424)|early endosome membrane (GO:0031901)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(63)|ovary(8)|pancreas(2)|prostate(8)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	130						GATGAGAGCTTCTCCCAGGTG	0.493																																					p.F146Y		Atlas-SNP	.											.	EPHB1	519	.	0			c.T437A						PASS	.						154.0	151.0	152.0					3																	134670526		1972	4204	6176	SO:0001583	missense	2047	exon3			AGAGCTTCTCCCA	L40636	CCDS46921.1	3q21-q23	2013-02-11	2004-10-28			ENSG00000154928		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3392	protein-coding gene	gene with protein product		600600	"""EphB1"""	EPHT2		8666391	Standard	NM_004441		Approved	Hek6	uc003eqt.3	P54762		ENST00000398015.3:c.437T>A	chr3.hg19:g.134670526T>A	ENSP00000381097:p.Phe146Tyr	273.0	0.0	.		222.0	112.0	.	NM_004441	A8K593|B3KTB2|B5A969|O43569|O95142|O95143|Q0VG87	Missense_Mutation	SNP	ENST00000398015.3	hg19	CCDS46921.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.644684	0.87859	.	.	ENSG00000154928	ENST00000398015;ENST00000474732	T;T	0.04234	3.67;3.67	5.49	5.49	0.81192	Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	T	0.25232	0.0613	M	0.86097	2.795	0.80722	D	1	D;D	0.71674	0.998;0.997	D;D	0.91635	0.999;0.991	T	0.01725	-1.1287	9	.	.	.	.	15.6027	0.76636	0.0:0.0:0.0:1.0	.	146;146	B5A969;P54762	.;EPHB1_HUMAN	Y	146;124	ENSP00000381097:F146Y;ENSP00000418352:F124Y	.	F	+	2	0	EPHB1	136153216	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.085000	0.62840	0.533000	0.62120	TTC	.	.	.	none		0.493	EPHB1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357671.1	NM_004441	
MED12L	116931	hgsc.bcm.edu	37	3	151078359	151078359	+	Missense_Mutation	SNP	A	A	G			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr3:151078359A>G	ENST00000474524.1	+	19	2856	c.2818A>G	c.(2818-2820)Agc>Ggc	p.S940G	MED12L_ENST00000273432.4_Missense_Mutation_p.S800G|P2RY12_ENST00000302632.3_Intron	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	940						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TGTGTCATGTAGCCACCTCAG	0.438																																					p.S940G		Atlas-SNP	.											.	MED12L	271	.	0			c.A2818G						PASS	.						211.0	195.0	201.0					3																	151078359		2203	4300	6503	SO:0001583	missense	116931	exon19			TCATGTAGCCACC	AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"""			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.2818A>G	chr3.hg19:g.151078359A>G	ENSP00000417235:p.Ser940Gly	280.0	0.0	.		239.0	125.0	.	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Missense_Mutation	SNP	ENST00000474524.1	hg19	CCDS33876.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.133418	0.77662	.	.	ENSG00000144893	ENST00000474524;ENST00000273432	T;T	0.79653	-1.29;-1.29	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	D	0.85660	0.5748	L	0.45228	1.405	0.80722	D	1	P;D;P	0.56035	0.48;0.974;0.956	B;D;D	0.67725	0.412;0.953;0.931	D	0.87163	0.2216	10	0.87932	D	0	-22.6472	15.5111	0.75782	1.0:0.0:0.0:0.0	.	800;940;940	F8WAE6;Q86YW9-4;Q86YW9	.;.;MD12L_HUMAN	G	940;800	ENSP00000417235:S940G;ENSP00000273432:S800G	ENSP00000273432:S800G	S	+	1	0	MED12L	152561049	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.649000	0.91067	2.199000	0.70637	0.533000	0.62120	AGC	.	.	.	none		0.438	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002	
NAF1	92345	hgsc.bcm.edu	37	4	164050121	164050121	+	Silent	SNP	G	G	A			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr4:164050121G>A	ENST00000274054.2	-	8	1606	c.1413C>T	c.(1411-1413)ccC>ccT	p.P471P	NAF1_ENST00000509434.1_Intron|NAF1_ENST00000422287.2_Intron	NM_138386.2	NP_612395.2	Q96HR8	NAF1_HUMAN	nuclear assembly factor 1 ribonucleoprotein	471	Pro-rich.				pseudouridine synthesis (GO:0001522)|ribosome biogenesis (GO:0042254)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(3)|large_intestine(1)|lung(10)|ovary(2)	21	all_hematologic(180;0.166)	Prostate(90;0.109)				gagggggagggggtgggggta	0.517																																					p.P471P		Atlas-SNP	.											.	NAF1	69	.	0			c.C1413T						PASS	.						10.0	11.0	10.0					4																	164050121		2191	4274	6465	SO:0001819	synonymous_variant	92345	exon8			GGGAGGGGGTGGG		CCDS3803.1, CCDS47159.1	4q32.2	2013-03-05	2013-03-05			ENSG00000145414			25126	protein-coding gene	gene with protein product			"""nuclear assembly factor 1 homolog (S. cerevisiae)"""			16618814, 16601202	Standard	NM_138386		Approved		uc003iqj.3	Q96HR8		ENST00000274054.2:c.1413C>T	chr4.hg19:g.164050121G>A		26.0	0.0	.		22.0	16.0	.	NM_138386	D3DP28|E9PAZ2	Silent	SNP	ENST00000274054.2	hg19	CCDS3803.1																																																																																			.	.	.	none		0.517	NAF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364684.2	NM_138386	
TERT	7015	hgsc.bcm.edu	37	5	1255515	1255515	+	Missense_Mutation	SNP	C	C	A			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr5:1255515C>A	ENST00000310581.5	-	14	3101	c.3044G>T	c.(3043-3045)tGt>tTt	p.C1015F	TERT_ENST00000296820.5_3'UTR|TERT_ENST00000334602.6_Missense_Mutation_p.C952F	NM_001193376.1|NM_198253.2	NP_001180305.1|NP_937983.2	O14746	TERT_HUMAN	telomerase reverse transcriptase	1015	CTE.				DNA strand elongation (GO:0022616)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|replicative senescence (GO:0090399)|telomere formation via telomerase (GO:0032203)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|telomerase holoenzyme complex (GO:0005697)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|telomerase activity (GO:0003720)|telomeric DNA binding (GO:0042162)|telomeric RNA binding (GO:0070034)|telomeric template RNA reverse transcriptase activity (GO:0003721)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(3)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	41	all_cancers(3;3.17e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.87e-10)		Epithelial(17;0.00105)|all cancers(22;0.00178)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)		Zidovudine(DB00495)	CTGCAGCACACATGCGTGAAA	0.572									TERT Mutation-Associated Haematological Disorders;Pulmonary Fibrosis, Idiopathic;Congenital Dyskeratosis																												p.C1015F		Atlas-SNP	.											.	TERT	2594	.	0			c.G3044T						PASS	.						76.0	82.0	80.0					5																	1255515		2161	4266	6427	SO:0001583	missense	7015	exon14	Familial Cancer Database	;Hamman-Rich syndrome, Fibrocystic Pulmonary Dysplasia;Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita	AGCACACATGCGT	AF015950	CCDS3861.2, CCDS54831.1	5p15.33	2014-09-17			ENSG00000164362	ENSG00000164362			11730	protein-coding gene	gene with protein product		187270				9252327	Standard	NM_198253		Approved	TRT, TP2, TCS1, hEST2, EST2	uc003jcb.1	O14746	OTTHUMG00000090357	ENST00000310581.5:c.3044G>T	chr5.hg19:g.1255515C>A	ENSP00000309572:p.Cys1015Phe	49.0	0.0	.		51.0	14.0	.	NM_198253	O14783|Q2XS35|Q8N6C3|Q8NG38|Q8NG46	Missense_Mutation	SNP	ENST00000310581.5	hg19	CCDS3861.2	.	.	.	.	.	.	.	.	.	.	c	14.17	2.454152	0.43634	.	.	ENSG00000164362	ENST00000310581;ENST00000334602	T;T	0.66815	-0.23;-0.23	4.84	4.84	0.62591	.	0.000000	0.85682	D	0.000000	D	0.83622	0.5294	M	0.88704	2.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.83650	0.0155	10	0.27082	T	0.32	-0.9462	16.718	0.85402	0.0:1.0:0.0:0.0	.	952;1015	O14746-3;O14746	.;TERT_HUMAN	F	1015;952	ENSP00000309572:C1015F;ENSP00000334346:C952F	ENSP00000309572:C1015F	C	-	2	0	TERT	1308515	1.000000	0.71417	0.180000	0.23079	0.008000	0.06430	6.534000	0.73833	2.237000	0.73441	0.655000	0.94253	TGT	.	.	.	none		0.572	TERT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206729.2		
CCNI2	645121	hgsc.bcm.edu	37	5	132084160	132084160	+	Nonsense_Mutation	SNP	C	C	A			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr5:132084160C>A	ENST00000378731.1	+	2	602	c.551C>A	c.(550-552)tCa>tAa	p.S184*	SEPT8_ENST00000481030.1_5'Flank	NM_001039780.2	NP_001034869.1	Q6ZMN8	CCNI2_HUMAN	cyclin I family, member 2	184					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)					haematopoietic_and_lymphoid_tissue(1)|prostate(1)|urinary_tract(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CTCCTGATTTCAGTGAAGGTA	0.542																																					p.S184X		Atlas-SNP	.											.	CCNI2	11	.	0			c.C551A						PASS	.						78.0	76.0	77.0					5																	132084160		2203	4300	6503	SO:0001587	stop_gained	645121	exon2			TGATTTCAGTGAA	BC132837	CCDS34236.1, CCDS75297.1	5q31.1	2014-07-03			ENSG00000205089	ENSG00000205089			33869	protein-coding gene	gene with protein product						23707792	Standard	NM_001287252		Approved	FLJ16793	uc003kxq.1	Q6ZMN8	OTTHUMG00000059737	ENST00000378731.1:c.551C>A	chr5.hg19:g.132084160C>A	ENSP00000368005:p.Ser184*	122.0	0.0	.		163.0	47.0	.	NM_001039780	B2RNE2|B7ZMB7|B7ZMB8	Nonsense_Mutation	SNP	ENST00000378731.1	hg19	CCDS34236.1	.	.	.	.	.	.	.	.	.	.	C	17.38	3.374680	0.61735	.	.	ENSG00000205089	ENST00000378731	.	.	.	4.74	2.95	0.34219	.	0.352786	0.29699	N	0.011430	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05959	T	0.93	.	10.896	0.47023	0.0:0.8799:0.0:0.1201	.	.	.	.	X	184	.	ENSP00000368005:S184X	S	+	2	0	CCNI2	132112059	0.186000	0.23225	0.002000	0.10522	0.016000	0.09150	2.489000	0.45285	0.667000	0.31107	0.651000	0.88453	TCA	.	.	.	none		0.542	CCNI2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132833.1	NM_001039780	
OR5V1	81696	hgsc.bcm.edu	37	6	29323498	29323498	+	Missense_Mutation	SNP	G	G	C			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr6:29323498G>C	ENST00000377154.1	-	4	774	c.475C>G	c.(475-477)Cat>Gat	p.H159D	OR5V1_ENST00000543825.1_Missense_Mutation_p.H159D			Q9UGF6	OR5V1_HUMAN	olfactory receptor, family 5, subfamily V, member 1	159						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(3)|large_intestine(3)|liver(1)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						AACACTGTATGCACCACTGAG	0.438																																					p.H159D	Ovarian(32;43 883 21137 32120 42650)	Atlas-SNP	.											.	OR5V1	63	.	0			c.C475G						PASS	.						88.0	85.0	86.0					6																	29323498		2203	4299	6502	SO:0001583	missense	81696	exon1			CTGTATGCACCAC		CCDS4657.1	6p22.1	2013-09-23				ENSG00000243729		"""GPCR / Class A : Olfactory receptors"""	13972	protein-coding gene	gene with protein product							Standard	NM_030876		Approved	hs6M1-21	uc011dlo.2	Q9UGF6		ENST00000377154.1:c.475C>G	chr6.hg19:g.29323498G>C	ENSP00000366359:p.His159Asp	104.0	0.0	.		67.0	37.0	.	NM_030876	A2BDZ0|B0S860|Q5SQI9|Q6NTB5|Q8IVL3	Missense_Mutation	SNP	ENST00000377154.1	hg19	CCDS4657.1	.	.	.	.	.	.	.	.	.	.	G	10.69	1.420539	0.25639	.	.	ENSG00000243729	ENST00000377154;ENST00000377151;ENST00000543825	T;T	0.00262	8.4;8.4	4.28	4.28	0.50868	GPCR, rhodopsin-like superfamily (1);	0.000000	0.34484	N	0.003929	T	0.00328	0.0010	M	0.88512	2.96	0.26396	N	0.976491	D	0.89917	1.0	D	0.91635	0.999	T	0.37291	-0.9712	10	0.51188	T	0.08	-51.5055	12.8107	0.57637	0.0:0.0:0.8357:0.1643	.	159	Q9UGF6	OR5V1_HUMAN	D	159	ENSP00000366359:H159D;ENSP00000443309:H159D	ENSP00000366356:H159D	H	-	1	0	OR5V1	29431477	0.000000	0.05858	0.876000	0.34364	0.772000	0.43724	-0.032000	0.12266	2.374000	0.81015	0.543000	0.68304	CAT	.	.	.	none		0.438	OR5V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076398.3		
RIMS1	22999	hgsc.bcm.edu	37	6	73108662	73108662	+	Missense_Mutation	SNP	T	T	G			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr6:73108662T>G	ENST00000521978.1	+	33	4726	c.4726T>G	c.(4726-4728)Tat>Gat	p.Y1576D	RIMS1_ENST00000517960.1_Missense_Mutation_p.Y1359D|RIMS1_ENST00000538414.1_Missense_Mutation_p.Y382D|RIMS1_ENST00000520567.1_Missense_Mutation_p.Y1226D|RIMS1_ENST00000518273.1_Missense_Mutation_p.Y1255D|RIMS1_ENST00000517827.1_Missense_Mutation_p.Y710D|RIMS1_ENST00000491071.2_Missense_Mutation_p.Y1365D|RIMS1_ENST00000401910.3_Missense_Mutation_p.Y896D|RIMS1_ENST00000522291.1_Missense_Mutation_p.Y1175D|RIMS1_ENST00000431478.2_3'UTR|RIMS1_ENST00000348717.5_Missense_Mutation_p.Y1359D|RIMS1_ENST00000523963.1_Missense_Mutation_p.Y701D|RIMS1_ENST00000414192.2_Missense_Mutation_p.Y103D|RIMS1_ENST00000425662.2_Missense_Mutation_p.Y644D|RIMS1_ENST00000264839.7_Missense_Mutation_p.Y1425D	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	1576	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				TTTAGCTCCATATGTCAAAGT	0.318																																					p.Y1576D		Atlas-SNP	.											.	RIMS1	278	.	0			c.T4726G						PASS	.						66.0	62.0	63.0					6																	73108662		1796	4064	5860	SO:0001583	missense	22999	exon33			GCTCCATATGTCA	AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"""Rab3-interacting molecule"""	606629	"""RAB3 interacting protein 2"""	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.4726T>G	chr6.hg19:g.73108662T>G	ENSP00000428417:p.Tyr1576Asp	57.0	0.0	.		39.0	15.0	.	NM_014989	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Missense_Mutation	SNP	ENST00000521978.1	hg19	CCDS47449.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|T	23.1|23.1|23.1	4.374106|4.374106|4.374106	0.82573|0.82573|0.82573	.|.|.	.|.|.	ENSG00000079841|ENSG00000079841|ENSG00000079841	ENST00000522211|ENST00000517433|ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000349908;ENST00000346609;ENST00000264839;ENST00000517960;ENST00000518273;ENST00000520567;ENST00000522291;ENST00000521978;ENST00000401910;ENST00000523963;ENST00000425662;ENST00000453976;ENST00000517827;ENST00000370420;ENST00000538414;ENST00000414192	.|.|T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	.|.|0.80033	.|.|-1.33;-1.33;-1.33;-1.33;-1.33;-1.33;-1.33;-1.33;-1.33;-1.33;-1.33;0.34;-1.33;-1.33;-1.33;-1.33	5.37|5.37|5.37	5.37|5.37|5.37	0.77165|0.77165|0.77165	.|.|C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	.|.|0.000000	.|.|0.56097	.|.|D	.|.|0.000022	D|D|D	0.93953|0.93953|0.93953	0.8064|0.8064|0.8064	H|H|H	0.99516|0.99516|0.99516	4.605|4.605|4.605	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|.|D;D;D;D;D;D;D;D;D;D;D;D;D	.|.|0.89917	.|.|1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.999;1.0	.|.|D;D;D;D;D;D;D;D;D;D;D;D;D	.|.|0.97110	.|.|1.0;1.0;1.0;1.0;0.999;1.0;0.999;1.0;0.999;0.999;0.999;0.994;0.999	D|D|D	0.96600|0.96600|0.96600	0.9444|0.9444|0.9444	5|5|10	.|.|0.87932	.|.|D	.|.|0	-24.6441|-24.6441|-24.6441	15.6587|15.6587|15.6587	0.77165|0.77165|0.77165	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.|.	.|.|200;382;710;701;1425;896;1175;479;1255;1359;652;1365;1576	.|.|B7Z6K9;B7Z7W2;B7Z3S3;E9PHF5;E9PHR1;E9PF48;E7EX08;Q5JY22;E7ERQ1;E7ENC2;Q5JY21;C9JNW6;Q86UR5	.|.|.;.;.;.;.;.;.;.;.;.;.;.;RIMS1_HUMAN	Q|R|D	493|921|1365;1425;1365;1359;1255;1175;1425;1359;1255;1226;1175;1576;896;701;644;741;710;624;382;103	.|.|ENSP00000430101:Y1365D;ENSP00000275037:Y1359D;ENSP00000264839:Y1425D;ENSP00000429959:Y1359D;ENSP00000430408:Y1255D;ENSP00000430502:Y1226D;ENSP00000430932:Y1175D;ENSP00000428417:Y1576D;ENSP00000385649:Y896D;ENSP00000428328:Y701D;ENSP00000411235:Y644D;ENSP00000389503:Y741D;ENSP00000428367:Y710D;ENSP00000359448:Y624D;ENSP00000439730:Y382D;ENSP00000402273:Y103D	.|.|ENSP00000264839:Y1425D	H|I|Y	+|+|+	3|2|1	2|0|0	RIMS1|RIMS1|RIMS1	73165383|73165383|73165383	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.987000|0.987000|0.987000	0.45799|0.45799|0.45799	0.938000|0.938000|0.938000	0.57974|0.57974|0.57974	7.934000|7.934000|7.934000	0.87649|0.87649|0.87649	2.157000|2.157000|2.157000	0.67596|0.67596|0.67596	0.482000|0.482000|0.482000	0.46254|0.46254|0.46254	CAT|ATA|TAT	.	.	.	none		0.318	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1		
ANLN	54443	hgsc.bcm.edu	37	7	36445953	36445953	+	Silent	SNP	T	T	C			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr7:36445953T>C	ENST00000265748.2	+	4	872	c.651T>C	c.(649-651)aaT>aaC	p.N217N	ANLN_ENST00000396068.2_Silent_p.N217N	NM_018685.2	NP_061155.2	Q9NQW6	ANLN_HUMAN	anillin, actin binding protein	217	Nuclear localization.				hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|regulation of exit from mitosis (GO:0007096)|septin ring assembly (GO:0000921)	actin cytoskeleton (GO:0015629)|actomyosin contractile ring (GO:0005826)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	actin binding (GO:0003779)			breast(2)|endometrium(5)|kidney(5)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(2)	45						ATGATGTAAATCACTCATTTG	0.468																																					p.N217N		Atlas-SNP	.											.	ANLN	101	.	0			c.T651C						PASS	.						108.0	105.0	106.0					7																	36445953		2203	4300	6503	SO:0001819	synonymous_variant	54443	exon4			TGTAAATCACTCA	AF273437	CCDS5447.1, CCDS64628.1	7p15-p14	2013-01-10	2006-08-22		ENSG00000011426	ENSG00000011426		"""Pleckstrin homology (PH) domain containing"""	14082	protein-coding gene	gene with protein product			"""anillin (Drosophila Scraps homolog), actin binding protein"", ""anillin, actin binding protein (scraps homolog, Drosophila)"""			10931866	Standard	NM_001284301		Approved	ANILLIN, Scraps, scra	uc003tff.3	Q9NQW6	OTTHUMG00000023143	ENST00000265748.2:c.651T>C	chr7.hg19:g.36445953T>C		138.0	0.0	.		143.0	48.0	.	NM_018685	Q5CZ78|Q6NSK5|Q9H8Y4|Q9NVN9|Q9NVP0	Silent	SNP	ENST00000265748.2	hg19	CCDS5447.1																																																																																			.	.	.	none		0.468	ANLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218582.3	NM_018685	
MUC17	140453	hgsc.bcm.edu	37	7	100681165	100681165	+	Silent	SNP	T	T	C			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr7:100681165T>C	ENST00000306151.4	+	3	6532	c.6468T>C	c.(6466-6468)taT>taC	p.Y2156Y		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2156	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					CCTCAACTTATAGTGACAGAA	0.463																																					p.Y2156Y		Atlas-SNP	.											.	MUC17	804	.	0			c.T6468C						PASS	.						221.0	219.0	220.0					7																	100681165		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			AACTTATAGTGAC	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.6468T>C	chr7.hg19:g.100681165T>C		335.0	0.0	.		383.0	130.0	.	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	hg19	CCDS34711.1																																																																																			.	.	.	none		0.463	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
MET	4233	hgsc.bcm.edu	37	7	116340025	116340025	+	Missense_Mutation	SNP	T	T	C			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr7:116340025T>C	ENST00000318493.6	+	2	1074	c.887T>C	c.(886-888)cTg>cCg	p.L296P	MET_ENST00000436117.2_Missense_Mutation_p.L296P|MET_ENST00000397752.3_Missense_Mutation_p.L296P			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			GAAATGCCTCTGGAGTGTATT	0.428			Mis		"""papillary renal, head-neck squamous cell """	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.L296P		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET	412	.	0			c.T887C						PASS	.						81.0	77.0	78.0					7																	116340025		1839	4092	5931	SO:0001583	missense	4233	exon2	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	TGCCTCTGGAGTG	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"""hepatocyte growth factor receptor"""	164860	"""met proto-oncogene"""			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.887T>C	chr7.hg19:g.116340025T>C	ENSP00000317272:p.Leu296Pro	191.0	0.0	.		199.0	57.0	.	NM_000245	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	hg19	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	T	12.57	1.978979	0.34942	.	.	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000436117	T;T;T	0.17691	2.26;2.26;2.26	6.17	6.17	0.99709	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.068376	0.64402	D	0.000011	T	0.51601	0.1684	M	0.90595	3.13	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	0.998;0.999;1.0;0.999;0.999;0.999;0.999;0.999;1.0;0.996;0.999;1.0;1.0	T	0.60895	-0.7172	10	0.87932	D	0	-8.4229	16.8222	0.85835	0.0:0.0:0.0:1.0	.	296;296;296;296;296;296;296;296;296;296;296;296;296	B5A929;E7EQ94;B5A930;B5A934;B5A936;B5A937;B5A939;B5A941;B5A940;P08581-2;B5A942;P08581;A1L467	.;.;.;.;.;.;.;.;.;.;.;MET_HUMAN;.	P	296	ENSP00000380860:L296P;ENSP00000317272:L296P;ENSP00000410980:L296P	ENSP00000317272:L296P	L	+	2	0	MET	116127261	1.000000	0.71417	1.000000	0.80357	0.010000	0.07245	7.636000	0.83301	2.371000	0.80710	0.533000	0.62120	CTG	.	.	.	none		0.428	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3		
PTPRZ1	5803	hgsc.bcm.edu	37	7	121651531	121651531	+	Silent	SNP	C	C	T	rs143422308		TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr7:121651531C>T	ENST00000393386.2	+	12	2842	c.2431C>T	c.(2431-2433)Ctg>Ttg	p.L811L	PTPRZ1_ENST00000483028.1_Intron|PTPRZ1_ENST00000449182.1_Intron	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	811					axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						TGAATCCATCCTGTCTTCCTA	0.458																																					p.L811L		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.C2431T						PASS	.						281.0	232.0	249.0					7																	121651531		2203	4300	6503	SO:0001819	synonymous_variant	5803	exon12			TCCATCCTGTCTT	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.2431C>T	chr7.hg19:g.121651531C>T		344.0	0.0	.		398.0	114.0	.	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Silent	SNP	ENST00000393386.2	hg19	CCDS34740.1																																																																																			.	C|1.000;G|0.000	.	alt		0.458	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851	
WRN	7486	hgsc.bcm.edu	37	8	30938567	30938567	+	Missense_Mutation	SNP	G	G	A			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr8:30938567G>A	ENST00000298139.5	+	9	1273	c.1024G>A	c.(1024-1026)Gtt>Att	p.V342I		NM_000553.4	NP_000544.2	Q14191	WRN_HUMAN	Werner syndrome, RecQ helicase-like	342					aging (GO:0007568)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to starvation (GO:0009267)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|double-strand break repair (GO:0006302)|multicellular organismal aging (GO:0010259)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleolus to nucleoplasm transport (GO:0032066)|positive regulation of hydrolase activity (GO:0051345)|regulation of apoptotic process (GO:0042981)|regulation of growth rate (GO:0040009)|replication fork processing (GO:0031297)|replicative cell aging (GO:0001302)|response to oxidative stress (GO:0006979)|response to UV-C (GO:0010225)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	3'-5' DNA helicase activity (GO:0043138)|3'-5' exonuclease activity (GO:0008408)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|exonuclease activity (GO:0004527)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|Y-form DNA binding (GO:0000403)			central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(13)|lung(28)|ovary(3)|skin(3)|upper_aerodigestive_tract(3)	60		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)		TTTAATTCACGTTGAAGATGA	0.353			"""Mis, N, F, S"""			"""osteosarcoma, meningioma, others"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Werner syndrome																												p.V342I	Ovarian(18;161 598 2706 14834 27543)	Atlas-SNP	.	yes	Rec		Werner Syndrome	8	8p12-p11.2	7486	Werner syndrome (RECQL2)		"""L, E, M, O"""	.	WRN	116	.	0			c.G1024A						PASS	.						105.0	101.0	103.0					8																	30938567		2203	4300	6503	SO:0001583	missense	7486	exon9	Familial Cancer Database	WS, Adult Progeria	ATTCACGTTGAAG		CCDS6082.1	8p12	2014-09-17	2009-03-19		ENSG00000165392	ENSG00000165392			12791	protein-coding gene	gene with protein product		604611	"""Werner syndrome"""			9288107	Standard	NM_000553		Approved	RECQL2, RECQ3	uc003xio.4	Q14191	OTTHUMG00000163894	ENST00000298139.5:c.1024G>A	chr8.hg19:g.30938567G>A	ENSP00000298139:p.Val342Ile	114.0	0.0	.		142.0	31.0	.	NM_000553	A1KYY9	Missense_Mutation	SNP	ENST00000298139.5	hg19	CCDS6082.1	.	.	.	.	.	.	.	.	.	.	G	4.269	0.049074	0.08243	.	.	ENSG00000165392	ENST00000298139	T	0.41758	0.99	5.27	-3.21	0.05140	.	0.909998	0.09395	N	0.807993	T	0.17534	0.0421	N	0.20401	0.57	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.28427	-1.0044	10	0.10111	T	0.7	-0.4055	0.2738	0.00235	0.3113:0.1387:0.2652:0.2848	.	342	Q14191	WRN_HUMAN	I	342	ENSP00000298139:V342I	ENSP00000298139:V342I	V	+	1	0	WRN	31058109	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.336000	0.07863	-0.260000	0.09418	-0.143000	0.13931	GTT	.	.	.	none		0.353	WRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376248.1		
EMC2	9694	hgsc.bcm.edu	37	8	109489022	109489022	+	Silent	SNP	C	C	T			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr8:109489022C>T	ENST00000220853.3	+	9	638	c.603C>T	c.(601-603)acC>acT	p.T201T	EMC2_ENST00000520294.1_3'UTR	NM_014673.3	NP_055488.1	Q15006	EMC2_HUMAN	ER membrane protein complex subunit 2	201						cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|ER membrane protein complex (GO:0072546)|mitochondrion (GO:0005739)|nucleus (GO:0005634)											TTAAGTATACCCAAGGTGGAC	0.338																																					p.T201T		Atlas-SNP	.											.	.	.	.	0			c.C603T						PASS	.						100.0	100.0	100.0					8																	109489022		2203	4300	6503	SO:0001819	synonymous_variant	9694	exon9			GTATACCCAAGGT	BC021667	CCDS6309.1	8q23.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000104412	ENSG00000104412			28963	protein-coding gene	gene with protein product		607722	"""tetratricopeptide repeat domain 35"""	KIAA0103, TTC35		7788527, 22119785	Standard	NM_014673		Approved		uc003ymw.1	Q15006	OTTHUMG00000164873	ENST00000220853.3:c.603C>T	chr8.hg19:g.109489022C>T		67.0	0.0	.		85.0	27.0	.	NM_014673	Q8WUE1	Silent	SNP	ENST00000220853.3	hg19	CCDS6309.1																																																																																			.	.	.	none		0.338	EMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380717.1	NM_014673	
FAM49B	51571	hgsc.bcm.edu	37	8	130883632	130883632	+	Nonsense_Mutation	SNP	C	C	A			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr8:130883632C>A	ENST00000519824.2	-	4	457	c.184G>T	c.(184-186)Gaa>Taa	p.E62*	FAM49B_ENST00000401979.2_Nonsense_Mutation_p.E62*|FAM49B_ENST00000523509.1_Nonsense_Mutation_p.E62*|FAM49B_ENST00000522250.1_5'UTR|FAM49B_ENST00000517654.1_Nonsense_Mutation_p.E62*|FAM49B_ENST00000519540.1_Nonsense_Mutation_p.E62*|FAM49B_ENST00000522941.1_5'UTR|FAM49B_ENST00000519110.1_Nonsense_Mutation_p.E62*|FAM49B_ENST00000522746.1_Nonsense_Mutation_p.E62*|FAM49B_ENST00000518879.1_Intron|SNORA25_ENST00000363205.1_RNA	NM_016623.4	NP_057707.3	Q9NUQ9	FA49B_HUMAN	family with sequence similarity 49, member B	62						cilium (GO:0005929)|extracellular vesicular exosome (GO:0070062)		p.E62K(1)		kidney(1)|large_intestine(6)|lung(4)|prostate(1)	12	Ovarian(5;0.000567)|Esophageal squamous(12;0.00693)|Acute lymphoblastic leukemia(118;0.155)		LUAD - Lung adenocarcinoma(14;0.0989)			TCTCGTATTTCGTGGCCAGCT	0.378																																					p.E62X		Atlas-SNP	.											FAM49B,colon,carcinoma,0,1	FAM49B	36	.	1	Substitution - Missense(1)	large_intestine(1)	c.G184T						PASS	.						110.0	106.0	108.0					8																	130883632		2203	4300	6503	SO:0001587	stop_gained	51571	exon4			GTATTTCGTGGCC	AF208851	CCDS6361.1	8q24	2004-08-20				ENSG00000153310			25216	protein-coding gene	gene with protein product							Standard	NM_001256763		Approved	BM-009	uc003ysu.4	Q9NUQ9		ENST00000519824.2:c.184G>T	chr8.hg19:g.130883632C>A	ENSP00000429150:p.Glu62*	122.0	0.0	.		153.0	56.0	.	NM_016623	Q96AZ5|Q9NW21|Q9NZE7	Nonsense_Mutation	SNP	ENST00000519824.2	hg19	CCDS6361.1	.	.	.	.	.	.	.	.	.	.	C	37	6.228266	0.97394	.	.	ENSG00000153310	ENST00000522746;ENST00000523509;ENST00000401979;ENST00000519110;ENST00000519824;ENST00000517654;ENST00000519540;ENST00000519142;ENST00000520204;ENST00000518283;ENST00000523993;ENST00000520254;ENST00000519020;ENST00000518167;ENST00000517672	.	.	.	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	-18.5272	19.0946	0.93244	0.0:1.0:0.0:0.0	.	.	.	.	X	62	.	ENSP00000384880:E62X	E	-	1	0	FAM49B	130952814	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.487000	0.81328	2.745000	0.94114	0.650000	0.86243	GAA	.	.	.	none		0.378	FAM49B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380390.2	NM_016623	
PHF20L1	51105	hgsc.bcm.edu	37	8	133816926	133816926	+	Missense_Mutation	SNP	G	G	C			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr8:133816926G>C	ENST00000395386.2	+	8	1087	c.788G>C	c.(787-789)aGg>aCg	p.R263T	PHF20L1_ENST00000395376.1_Missense_Mutation_p.R268T|PHF20L1_ENST00000220847.7_5'UTR|PHF20L1_ENST00000395379.1_Missense_Mutation_p.R263T|PHF20L1_ENST00000337920.4_Missense_Mutation_p.R237T|PHF20L1_ENST00000395390.2_Missense_Mutation_p.R238T	NM_016018.4	NP_057102.4	A8MW92	P20L1_HUMAN	PHD finger protein 20-like 1	263							zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(1)|lung(10)|ovary(2)	15	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			TCAAACAAGAGGAAAAATAAT	0.378																																					p.R263T		Atlas-SNP	.											.	PHF20L1	129	.	0			c.G788C						PASS	.						106.0	100.0	102.0					8																	133816926		2203	4300	6503	SO:0001583	missense	51105	exon8			ACAAGAGGAAAAA	AF230666	CCDS6367.2, CCDS6368.1, CCDS75791.1	8q24.22	2014-03-24			ENSG00000129292	ENSG00000129292		"""Tudor domain containing"", ""Zinc fingers, PHD-type"""	24280	protein-coding gene	gene with protein product	"""tudor domain containing 20B"""					10810093, 24492612	Standard	NM_016018		Approved	CGI-72, FLJ13649, MGC64923, FLJ21615, TDRD20B	uc003ytt.3	A8MW92	OTTHUMG00000148656	ENST00000395386.2:c.788G>C	chr8.hg19:g.133816926G>C	ENSP00000378784:p.Arg263Thr	128.0	0.0	.		164.0	48.0	.	NM_016018	A8MZC9|Q86U89|Q86W43|Q96BT0|Q9H702|Q9HBK3|Q9NYR3|Q9Y381	Missense_Mutation	SNP	ENST00000395386.2	hg19	CCDS6367.2	.	.	.	.	.	.	.	.	.	.	G	23.0	4.365266	0.82463	.	.	ENSG00000129292	ENST00000395383;ENST00000395379;ENST00000361997;ENST00000395386;ENST00000315808;ENST00000337920;ENST00000395376;ENST00000395382;ENST00000395390;ENST00000395374	T;T;T;T;T;T;T;T	0.69685	-0.35;-0.18;0.1;0.49;-0.42;0.23;-0.16;0.92	5.5	5.5	0.81552	.	0.189440	0.56097	D	0.000032	T	0.75213	0.3819	L	0.32530	0.975	0.80722	D	1	D;D;D;D;D	0.89917	0.996;0.997;0.999;1.0;0.996	D;D;D;D;D	0.87578	0.99;0.993;0.997;0.998;0.99	T	0.75590	-0.3265	10	0.49607	T	0.09	-16.2918	18.372	0.90409	0.0:0.0:1.0:0.0	.	238;102;263;263;237	F8W9L8;G5E9D0;A8MW92;A8MW92-4;A8MW92-2	.;.;P20L1_HUMAN;.;.	T	267;263;238;263;263;237;268;133;238;102	ENSP00000378781:R267T;ENSP00000378777:R263T;ENSP00000355301:R238T;ENSP00000378784:R263T;ENSP00000324519:R263T;ENSP00000338269:R237T;ENSP00000378775:R268T;ENSP00000378788:R238T	ENSP00000324519:R263T	R	+	2	0	PHF20L1	133886108	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.969000	0.70422	2.596000	0.87737	0.585000	0.79938	AGG	.	.	.	none		0.378	PHF20L1-008	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308949.3	NM_016018	
FBXO10	26267	hgsc.bcm.edu	37	9	37537307	37537307	+	Missense_Mutation	SNP	G	G	T			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr9:37537307G>T	ENST00000432825.2	-	3	1267	c.1219C>A	c.(1219-1221)Ctg>Atg	p.L407M	RP11-613M10.8_ENST00000544475.1_5'UTR|FBXO10_ENST00000543968.1_5'Flank|FBXO10_ENST00000541829.1_Intron	NM_012166.2	NP_036298.2	Q9UK96	FBX10_HUMAN	F-box protein 10	407					apoptotic process (GO:0006915)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of apoptotic process (GO:0042981)	cytoplasm (GO:0005737)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(5)|large_intestine(11)|lung(15)|prostate(1)|upper_aerodigestive_tract(1)	34				GBM - Glioblastoma multiforme(29;0.0107)		AGTGAGTTCAGCACTAGGCAG	0.612																																					p.L407M		Atlas-SNP	.											.	FBXO10	75	.	0			c.C1219A						PASS	.						22.0	24.0	23.0					9																	37537307		2000	4176	6176	SO:0001583	missense	26267	exon3			AGTTCAGCACTAG	AF174598	CCDS47966.1	9p13.1	2014-01-29	2004-06-15		ENSG00000147912	ENSG00000147912		"""F-boxes /  ""other"""""	13589	protein-coding gene	gene with protein product		609092	"""F-box only protein 10"""			10531035, 10531037, 19300908	Standard	NM_012166		Approved	FBX10	uc004aab.3	Q9UK96	OTTHUMG00000019926	ENST00000432825.2:c.1219C>A	chr9.hg19:g.37537307G>T	ENSP00000403802:p.Leu407Met	24.0	0.0	.		32.0	11.0	.	NM_012166	Q08AL3|Q08AL4|Q5JRT8|Q9UKC3	Missense_Mutation	SNP	ENST00000432825.2	hg19	CCDS47966.1	.	.	.	.	.	.	.	.	.	.	G	16.16	3.044290	0.55110	.	.	ENSG00000147912	ENST00000432825	T	0.51071	0.72	5.46	3.59	0.41128	Carbohydrate-binding/sugar hydrolysis domain (1);	0.084546	0.50627	D	0.000114	T	0.45657	0.1353	L	0.29908	0.895	0.80722	D	1	D	0.64830	0.994	P	0.56343	0.796	T	0.42413	-0.9453	10	0.72032	D	0.01	-14.4477	7.4587	0.27283	0.1335:0.1507:0.7157:0.0	.	407	Q9UK96	FBX10_HUMAN	M	407	ENSP00000403802:L407M	ENSP00000276960:L407M	L	-	1	2	FBXO10	37527307	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.365000	0.59486	2.543000	0.85770	0.655000	0.94253	CTG	.	.	.	none		0.612	FBXO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052472.3		
KIAA1217	56243	hgsc.bcm.edu	37	10	24508666	24508666	+	Missense_Mutation	SNP	G	G	T			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr10:24508666G>T	ENST00000376454.3	+	2	212	c.182G>T	c.(181-183)cGc>cTc	p.R61L	KIAA1217_ENST00000376452.3_Missense_Mutation_p.R61L|KIAA1217_ENST00000376462.1_5'UTR|KIAA1217_ENST00000458595.1_Missense_Mutation_p.R61L	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	61					embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)				breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						AAGTCTTCCCGCAATATCCCA	0.498																																					p.R61L		Atlas-SNP	.											.	KIAA1217	235	.	0			c.G182T						PASS	.						71.0	69.0	70.0					10																	24508666		2203	4300	6503	SO:0001583	missense	56243	exon2			CTTCCCGCAATAT	BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"""sickle tail"""					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.182G>T	chr10.hg19:g.24508666G>T	ENSP00000365637:p.Arg61Leu	81.0	0.0	.		106.0	25.0	.	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Missense_Mutation	SNP	ENST00000376454.3	hg19	CCDS31165.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.029194	0.93518	.	.	ENSG00000120549	ENST00000376456;ENST00000458595;ENST00000376454;ENST00000376452	T;T;T;T	0.62788	0.0;0.0;0.0;0.0	5.77	5.77	0.91146	.	0.093558	0.39985	N	0.001204	T	0.74981	0.3788	L	0.43923	1.385	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.997;0.999;0.998	T	0.73588	-0.3935	10	0.49607	T	0.09	.	19.9927	0.97374	0.0:0.0:1.0:0.0	.	61;61;61;61	Q5T5P2-7;A6NLF3;Q5T5P2;Q5T5P2-2	.;.;SKT_HUMAN;.	L	61	ENSP00000365639:R61L;ENSP00000392625:R61L;ENSP00000365637:R61L;ENSP00000365635:R61L	ENSP00000365635:R61L	R	+	2	0	KIAA1217	24548672	1.000000	0.71417	0.997000	0.53966	0.873000	0.50193	6.115000	0.71566	2.745000	0.94114	0.655000	0.94253	CGC	.	.	.	none		0.498	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590	
EPC1	80314	hgsc.bcm.edu	37	10	32580239	32580239	+	Missense_Mutation	SNP	C	C	G			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr10:32580239C>G	ENST00000263062.8	-	6	1096	c.827G>C	c.(826-828)gGc>gCc	p.G276A	EPC1_ENST00000375110.2_Missense_Mutation_p.G226A|EPC1_ENST00000319778.6_Missense_Mutation_p.G276A	NM_025209.2	NP_079485.1	Q9H2F5	EPC1_HUMAN	enhancer of polycomb homolog 1 (Drosophila)	276					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Piccolo NuA4 histone acetyltransferase complex (GO:0032777)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(5)|urinary_tract(1)	24		Prostate(175;0.0199)				ATTGTAGTCGCCCAAATTATA	0.313																																					p.G276A		Atlas-SNP	.											.	EPC1	74	.	0			c.G827C						PASS	.						75.0	73.0	74.0					10																	32580239		2203	4300	6503	SO:0001583	missense	80314	exon6			TAGTCGCCCAAAT	AF277374	CCDS7172.1, CCDS60511.1, CCDS73083.1	10p11	2005-12-12			ENSG00000120616	ENSG00000120616			19876	protein-coding gene	gene with protein product		610999				10976108	Standard	NM_025209		Approved	Epl1	uc001iwg.2	Q9H2F5	OTTHUMG00000017925	ENST00000263062.8:c.827G>C	chr10.hg19:g.32580239C>G	ENSP00000263062:p.Gly276Ala	102.0	0.0	.		176.0	31.0	.	NM_025209	B4DSC3|D3DRX7|Q5VW54|Q5VW56|Q5VW58|Q8NAQ4|Q8NE21|Q96LF4|Q96RR6|Q9H7T7	Missense_Mutation	SNP	ENST00000263062.8	hg19	CCDS7172.1	.	.	.	.	.	.	.	.	.	.	C	13.21	2.170633	0.38315	.	.	ENSG00000120616	ENST00000375110;ENST00000319778;ENST00000263062	T;T;T	0.66099	-0.19;-0.19;-0.19	4.89	4.89	0.63831	.	0.214139	0.49305	D	0.000142	T	0.55497	0.1924	L	0.39245	1.2	0.45594	D	0.99853	B;B;B;B	0.25667	0.048;0.131;0.097;0.059	B;B;B;B	0.27380	0.015;0.019;0.079;0.008	T	0.51124	-0.8745	10	0.22109	T	0.4	-15.0295	18.3946	0.90494	0.0:1.0:0.0:0.0	.	276;226;276;276	B8XCX7;Q9H2F5-3;Q9H2F5-2;Q9H2F5	.;.;.;EPC1_HUMAN	A	226;276;276	ENSP00000364251:G226A;ENSP00000318559:G276A;ENSP00000263062:G276A	ENSP00000263062:G276A	G	-	2	0	EPC1	32620245	1.000000	0.71417	1.000000	0.80357	0.755000	0.42902	3.929000	0.56514	2.419000	0.82065	0.467000	0.42956	GGC	.	.	.	none		0.313	EPC1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047484.1		
OSBPL5	114879	hgsc.bcm.edu	37	11	3141834	3141834	+	Missense_Mutation	SNP	G	G	C			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr11:3141834G>C	ENST00000263650.7	-	6	582	c.423C>G	c.(421-423)agC>agG	p.S141R	OSBPL5_ENST00000348039.5_Intron|OSBPL5_ENST00000389989.3_Intron|OSBPL5_ENST00000525498.1_Missense_Mutation_p.S93R|OSBPL5_ENST00000542243.1_Intron	NM_020896.3	NP_065947.1	Q9H0X9	OSBL5_HUMAN	oxysterol binding protein-like 5	141	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|Golgi to plasma membrane transport (GO:0006893)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	cholesterol binding (GO:0015485)|oxysterol binding (GO:0008142)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	25		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00607)|LUSC - Lung squamous cell carcinoma(625;0.207)		GCTTGGTCCAGCTCTTCAGGG	0.677																																					p.S141R		Atlas-SNP	.											.	OSBPL5	78	.	0			c.C423G						PASS	.						53.0	49.0	51.0					11																	3141834		2202	4298	6500	SO:0001583	missense	114879	exon6			GGTCCAGCTCTTC	AF392453	CCDS31343.1, CCDS31344.1	11p15.4	2013-01-10			ENSG00000021762	ENSG00000021762		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16392	protein-coding gene	gene with protein product		606733					Standard	NM_145638		Approved	KIAA1534, ORP5	uc001lxk.2	Q9H0X9	OTTHUMG00000011702	ENST00000263650.7:c.423C>G	chr11.hg19:g.3141834G>C	ENSP00000263650:p.Ser141Arg	94.0	0.0	.		64.0	36.0	.	NM_020896	A6NDP0|A6NJS8|Q54A90|Q8N596|Q9BZB0|Q9P1Z4	Missense_Mutation	SNP	ENST00000263650.7	hg19	CCDS31344.1	.	.	.	.	.	.	.	.	.	.	G	15.20	2.763077	0.49574	.	.	ENSG00000021762	ENST00000263650;ENST00000525498	T;T	0.76186	-1.0;2.64	4.38	4.38	0.52667	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.115051	0.64402	D	0.000020	T	0.74786	0.3762	L	0.54323	1.7	0.80722	D	1	P;B;B	0.36753	0.568;0.056;0.425	B;B;B	0.44278	0.175;0.149;0.445	T	0.78091	-0.2339	10	0.72032	D	0.01	-34.5207	12.7278	0.57180	0.0829:0.0:0.9171:0.0	.	93;102;141	B4DVB0;E7EP03;Q9H0X9	.;.;OSBL5_HUMAN	R	141;93	ENSP00000263650:S141R;ENSP00000433342:S93R	ENSP00000263650:S141R	S	-	3	2	OSBPL5	3098410	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	0.883000	0.28200	2.285000	0.76669	0.555000	0.69702	AGC	.	.	.	none		0.677	OSBPL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032332.2		
OR8H3	390152	hgsc.bcm.edu	37	11	55890629	55890629	+	Missense_Mutation	SNP	A	A	G			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr11:55890629A>G	ENST00000313472.3	+	1	781	c.781A>G	c.(781-783)Aag>Gag	p.K261E		NM_001005201.1	NP_001005201.1	Q8N146	OR8H3_HUMAN	olfactory receptor, family 8, subfamily H, member 3	261						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(30)|ovary(2)|prostate(1)|skin(3)|stomach(1)	42	Esophageal squamous(21;0.00693)					TACTTACTTAAAGCCAAGAAA	0.373																																					p.K261E		Atlas-SNP	.											.	OR8H3	92	.	0			c.A781G						PASS	.						102.0	101.0	101.0					11																	55890629		2201	4296	6497	SO:0001583	missense	390152	exon1			TACTTAAAGCCAA	AB065840	CCDS31519.1	11q11	2012-08-09			ENSG00000181761	ENSG00000181761		"""GPCR / Class A : Olfactory receptors"""	15309	protein-coding gene	gene with protein product							Standard	NM_001005201		Approved		uc001nii.1	Q8N146	OTTHUMG00000166833	ENST00000313472.3:c.781A>G	chr11.hg19:g.55890629A>G	ENSP00000323928:p.Lys261Glu	168.0	0.0	.		121.0	58.0	.	NM_001005201	Q6IFB7	Missense_Mutation	SNP	ENST00000313472.3	hg19	CCDS31519.1	.	.	.	.	.	.	.	.	.	.	A	10.17	1.276100	0.23307	.	.	ENSG00000181761	ENST00000313472	T	0.37411	1.2	3.62	2.35	0.29111	GPCR, rhodopsin-like superfamily (1);	0.222186	0.32134	N	0.006528	T	0.54822	0.1882	M	0.83774	2.66	0.09310	N	1	D	0.76494	0.999	D	0.71414	0.973	T	0.40194	-0.9576	10	0.87932	D	0	.	5.4761	0.16695	0.5957:0.3026:0.1016:0.0	.	261	Q8N146	OR8H3_HUMAN	E	261	ENSP00000323928:K261E	ENSP00000323928:K261E	K	+	1	0	OR8H3	55647205	0.000000	0.05858	0.804000	0.32291	0.121000	0.20230	-0.491000	0.06474	1.415000	0.47037	0.145000	0.16022	AAG	.	.	.	none		0.373	OR8H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391541.1	NM_001005201	
CADM1	23705	hgsc.bcm.edu	37	11	115080343	115080343	+	Silent	SNP	G	G	T			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr11:115080343G>T	ENST00000452722.3	-	8	1049	c.1029C>A	c.(1027-1029)acC>acA	p.T343T	CADM1_ENST00000537058.1_Silent_p.T343T|CADM1_ENST00000331581.6_Silent_p.T343T|CADM1_ENST00000537140.1_Intron|CADM1_ENST00000542447.2_Intron|CADM1_ENST00000536727.1_Intron	NM_014333.3	NP_055148.3			cell adhesion molecule 1									p.T343T(5)		cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(9)|ovary(2)|skin(1)	32	all_hematologic(175;0.0628)	all_cancers(61;2.98e-14)|all_epithelial(67;2.64e-08)|all_hematologic(158;0.000154)|Melanoma(852;0.000952)|Acute lymphoblastic leukemia(157;0.00101)|Breast(348;0.0102)|Medulloblastoma(222;0.0429)|Prostate(24;0.145)|all_neural(223;0.237)		BRCA - Breast invasive adenocarcinoma(274;5.01e-06)|Epithelial(105;0.000305)|all cancers(92;0.00303)		tggtggtggtggttgttgtgg	0.433																																					p.T343T		Atlas-SNP	.											CADM1,NS,carcinoma,0,6	CADM1	74	.	5	Substitution - coding silent(5)	kidney(3)|lung(2)	c.C1029A						PASS	.						45.0	50.0	49.0					11																	115080343		2201	4296	6497	SO:0001819	synonymous_variant	23705	exon8			GGTGGTGGTTGTT	AB017563	CCDS8373.1, CCDS53711.1, CCDS73397.1, CCDS73398.1, CCDS73399.1	11q23.2	2013-01-29	2007-02-07	2007-02-07	ENSG00000182985	ENSG00000182985		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5951	protein-coding gene	gene with protein product	"""nectin-like 2"""	605686	"""tumor suppressor in lung cancer 1"", ""immunoglobulin superfamily, member 4"""	TSLC1, IGSF4		10610705	Standard	NM_014333		Approved	NECL2, ST17, BL2, SYNCAM, IGSF4A, Necl-2, SYNCAM1, RA175	uc001ppi.4	Q9BY67	OTTHUMG00000168202	ENST00000452722.3:c.1029C>A	chr11.hg19:g.115080343G>T		43.0	0.0	.		48.0	4.0	.	NM_014333		Silent	SNP	ENST00000452722.3	hg19	CCDS8373.1																																																																																			.	.	.	none		0.433	CADM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398753.2	NM_014333	
LMNTD1	160492	hgsc.bcm.edu	37	12	25702289	25702289	+	Missense_Mutation	SNP	C	C	A			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr12:25702289C>A	ENST00000282881.6	-	2	367	c.218G>T	c.(217-219)gGt>gTt	p.G73V	IFLTD1_ENST00000413632.2_Missense_Mutation_p.G94V|IFLTD1_ENST00000445693.1_Intron|IFLTD1_ENST00000539744.1_5'UTR|IFLTD1_ENST00000458174.2_Missense_Mutation_p.G94V	NM_152590.3	NP_689803.2	Q8N9Z9	LMTD1_HUMAN		73					cell proliferation (GO:0008283)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|nuclear envelope (GO:0005635)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22	all_lung(3;2.75e-22)|Lung NSC(3;1.77e-21)|all_hematologic(7;0.00656)|Colorectal(261;0.0847)					GGAACAGCTACCTACAGTAGC	0.353																																					p.G94V		Atlas-SNP	.											.	IFLTD1	121	.	0			c.G281T						PASS	.						55.0	50.0	52.0					12																	25702289		2203	4300	6503	SO:0001583	missense	160492	exon3			CAGCTACCTACAG																												ENST00000282881.6:c.218G>T	chr12.hg19:g.25702289C>A	ENSP00000282881:p.Gly73Val	78.0	0.0	.		70.0	19.0	.	NM_001145728	B4DL27|B4DY70|Q8IY38	Missense_Mutation	SNP	ENST00000282881.6	hg19	CCDS8704.1	.	.	.	.	.	.	.	.	.	.	C	4.838	0.155802	0.09236	.	.	ENSG00000152936	ENST00000282881;ENST00000458174;ENST00000413632;ENST00000538178;ENST00000540106;ENST00000542224	T;T;T	0.13538	2.74;2.77;2.58	3.4	-6.81	0.01704	.	.	.	.	.	T	0.03305	0.0096	N	0.04508	-0.205	0.09310	N	1	B;B;B	0.10296	0.003;0.002;0.001	B;B;B	0.09377	0.004;0.002;0.001	T	0.36915	-0.9728	9	0.06625	T	0.88	-7.9674	1.5985	0.02669	0.1745:0.4041:0.1887:0.2328	.	94;94;73	Q8N9Z9-5;Q8N9Z9-4;Q8N9Z9	.;.;ILFT1_HUMAN	V	73;94;94;48;48;48	ENSP00000282881:G73V;ENSP00000407353:G94V;ENSP00000393150:G94V	ENSP00000282881:G73V	G	-	2	0	IFLTD1	25593556	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.175000	0.01263	-1.982000	0.00988	0.460000	0.39030	GGT	.	.	.	none		0.353	IFLTD1-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402279.1		
ALG10B	144245	hgsc.bcm.edu	37	12	38714192	38714192	+	Missense_Mutation	SNP	T	T	C			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr12:38714192T>C	ENST00000308742.4	+	3	915	c.599T>C	c.(598-600)gTc>gCc	p.V200A	ALG10B_ENST00000551464.1_Intron|AC117372.1_ENST00000401168.2_RNA	NM_001013620.3	NP_001013642.1	Q5I7T1	AG10B_HUMAN	ALG10B, alpha-1,2-glucosyltransferase	200					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transferase activity, transferring hexosyl groups (GO:0016758)			breast(2)|kidney(3)|large_intestine(7)|lung(8)|ovary(4)|skin(1)	25	Esophageal squamous(101;0.187)	Lung NSC(34;0.204)|all_lung(34;0.235)				GCAGGGAATGTCATTGCACAA	0.388																																					p.V200A		Atlas-SNP	.											.	ALG10B	58	.	0			c.T599C						PASS	.						167.0	169.0	168.0					12																	38714192		2203	4300	6503	SO:0001583	missense	144245	exon3			GGAATGTCATTGC	AY845858	CCDS31772.1	12q12	2013-03-04	2013-03-04		ENSG00000175548	ENSG00000175548	2.4.1.256		31088	protein-coding gene	gene with protein product	"""potassium channel regulator 1"", ""dolichyl-P-Glc:Glc(2)Man(9)GlcNAc(2)-PP-dolichol alpha-1,2- glucosyltransferase"""		"""asparagine-linked glycosylation 10, alpha-1,2-glucosyltransferase homolog B (yeast)"""				Standard	NM_001013620		Approved	KCR1	uc001rln.4	Q5I7T1	OTTHUMG00000169298	ENST00000308742.4:c.599T>C	chr12.hg19:g.38714192T>C	ENSP00000310120:p.Val200Ala	418.0	0.0	.		442.0	140.0	.	NM_001013620	B2RPF4	Missense_Mutation	SNP	ENST00000308742.4	hg19	CCDS31772.1	.	.	.	.	.	.	.	.	.	.	N	7.218	0.596709	0.13875	.	.	ENSG00000175548	ENST00000308742	T	0.55760	0.5	3.24	3.24	0.37175	.	0.332405	0.30771	N	0.008920	T	0.35219	0.0924	L	0.31420	0.93	0.80722	D	1	B	0.15719	0.014	B	0.10450	0.005	T	0.10941	-1.0608	10	0.12103	T	0.63	.	10.1623	0.42860	0.0:0.0:0.0:1.0	.	200	Q5I7T1	AG10B_HUMAN	A	200	ENSP00000310120:V200A	ENSP00000310120:V200A	V	+	2	0	ALG10B	37000459	0.999000	0.42202	0.009000	0.14445	0.383000	0.30230	5.798000	0.69095	1.719000	0.51432	0.448000	0.29417	GTC	.	.	.	none		0.388	ALG10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403349.1	NM_001013620	
KMT2D	8085	hgsc.bcm.edu	37	12	49427714	49427714	+	Missense_Mutation	SNP	T	T	C	rs372758101		TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr12:49427714T>C	ENST00000301067.7	-	39	10773	c.10774A>G	c.(10774-10776)Atg>Gtg	p.M3592V	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	3592	Gln-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										TATTCTGCCATGAGATTAGTG	0.582																																					p.M3592V		Atlas-SNP	.											.	MLL2	1173	.	0			c.A10774G						PASS	.	T	VAL/MET	1,4325		0,1,2162	14.0	13.0	14.0		10774	5.4	1.0	12		14	0,8464		0,0,4232	no	missense	MLL2	NM_003482.3	21	0,1,6394	CC,CT,TT		0.0,0.0231,0.0078	benign	3592/5538	49427714	1,12789	2163	4232	6395	SO:0001583	missense	8085	exon39			CTGCCATGAGATT	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7133	protein-coding gene	gene with protein product		602113	"""trinucleotide repeat containing 21"", ""myeloid/lymphoid or mixed-lineage leukemia 2"""	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.10774A>G	chr12.hg19:g.49427714T>C	ENSP00000301067:p.Met3592Val	0.0	0.0	.		9.0	5.0	.	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	hg19	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	T	9.346	1.064224	0.20067	2.31E-4	0.0	ENSG00000167548	ENST00000301067	T	0.39056	1.1	5.38	5.38	0.77491	.	0.000000	0.44688	D	0.000428	T	0.25791	0.0628	N	0.08118	0	0.31092	N	0.71073	B	0.26483	0.15	B	0.19946	0.027	T	0.30563	-0.9974	10	0.87932	D	0	.	14.6888	0.69068	0.0:0.0:0.0:1.0	.	3592	O14686	MLL2_HUMAN	V	3592	ENSP00000301067:M3592V	ENSP00000301067:M3592V	M	-	1	0	MLL2	47713981	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.118000	0.71583	2.189000	0.69895	0.460000	0.39030	ATG	.	.	.	weak		0.582	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
GCN1L1	10985	hgsc.bcm.edu	37	12	120582190	120582190	+	Silent	SNP	G	G	T			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr12:120582190G>T	ENST00000300648.6	-	42	5427	c.5415C>A	c.(5413-5415)atC>atA	p.I1805I		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	1805					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CGTACATGGAGATAACCCGCT	0.597																																					p.I1805I		Atlas-SNP	.											.	GCN1L1	207	.	0			c.C5415A						PASS	.						58.0	63.0	61.0					12																	120582190		2058	4197	6255	SO:0001819	synonymous_variant	10985	exon42			CATGGAGATAACC	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"""GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"""			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.5415C>A	chr12.hg19:g.120582190G>T		75.0	0.0	.		93.0	29.0	.	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Silent	SNP	ENST00000300648.6	hg19	CCDS41847.1																																																																																			.	.	.	none		0.597	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1		
PROSER1	80209	hgsc.bcm.edu	37	13	39596542	39596542	+	Nonsense_Mutation	SNP	A	A	T			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr13:39596542A>T	ENST00000352251.3	-	9	1484	c.651T>A	c.(649-651)taT>taA	p.Y217*	PROSER1_ENST00000484434.3_Intron|PROSER1_ENST00000350125.3_Nonsense_Mutation_p.Y195*	NM_025138.4	NP_079414.3	Q86XN7	PRSR1_HUMAN	proline and serine rich 1	217	Pro-rich.																CTGCATTGTTATAAGCACCTA	0.378																																					p.Y217X		Atlas-SNP	.											.	.	.	.	0			c.T651A						PASS	.						132.0	130.0	131.0					13																	39596542		2203	4300	6503	SO:0001587	stop_gained	80209	exon9			ATTGTTATAAGCA	AK022723	CCDS9368.2	13q13.2	2011-08-09	2011-08-09	2011-08-09	ENSG00000120685	ENSG00000120685			20291	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 23"""	C13orf23			Standard	NM_025138		Approved	bA50D16.2, FLJ12661	uc001uwy.4	Q86XN7	OTTHUMG00000016764	ENST00000352251.3:c.651T>A	chr13.hg19:g.39596542A>T	ENSP00000332034:p.Tyr217*	139.0	0.0	.		145.0	72.0	.	NM_025138	A6NJ97|Q6P2S2|Q7Z3X5|Q8N3D2|Q8N3P1|Q9H9M1	Nonsense_Mutation	SNP	ENST00000352251.3	hg19	CCDS9368.2	.	.	.	.	.	.	.	.	.	.	A	44	11.133907	0.99521	.	.	ENSG00000120685	ENST00000352251;ENST00000350125	.	.	.	5.69	-5.32	0.02722	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-7.1752	17.3861	0.87416	0.267:0.0:0.733:0.0	.	.	.	.	X	217;195	.	.	Y	-	3	2	PROSER1	38494542	0.996000	0.38824	0.817000	0.32601	0.961000	0.63080	0.263000	0.18478	-1.201000	0.02659	-0.250000	0.11733	TAT	.	.	.	none		0.378	PROSER1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044607.5	NM_025138	
TRIM9	114088	hgsc.bcm.edu	37	14	51475908	51475908	+	Missense_Mutation	SNP	T	T	C			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr14:51475908T>C	ENST00000298355.3	-	5	2317	c.1196A>G	c.(1195-1197)cAg>cGg	p.Q399R	TRIM9_ENST00000360392.4_Missense_Mutation_p.Q399R|TRIM9_ENST00000338969.5_Missense_Mutation_p.Q399R	NM_015163.5	NP_055978.4	Q9C026	TRIM9_HUMAN	tripartite motif containing 9	399	COS. {ECO:0000255|PROSITE- ProRule:PRU00586}.				negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of SNARE complex assembly (GO:0035544)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|synaptic vesicle (GO:0008021)	ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|liver(1)|lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_epithelial(31;0.00418)|Breast(41;0.148)					TTTACCCCACTGATCCTCAGT	0.488																																					p.Q399R		Atlas-SNP	.											.	TRIM9	188	.	0			c.A1196G						PASS	.						179.0	132.0	148.0					14																	51475908		2203	4300	6503	SO:0001583	missense	114088	exon5			CCCCACTGATCCT	AF220036	CCDS9703.1, CCDS45105.1	14q21.3	2013-02-11	2011-01-25		ENSG00000100505	ENSG00000100505		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"", ""Fibronectin type III domain containing"""	16288	protein-coding gene	gene with protein product		606555	"""tripartite motif-containing 9"""			11331580, 11524423	Standard	NM_015163		Approved	SPRING, RNF91	uc001wyx.4	Q9C026	OTTHUMG00000140291	ENST00000298355.3:c.1196A>G	chr14.hg19:g.51475908T>C	ENSP00000298355:p.Gln399Arg	105.0	0.0	.		149.0	49.0	.	NM_052978	D3DSB7|D3DSB8|Q92557|Q96D24|Q96NI4|Q9C025|Q9C027	Missense_Mutation	SNP	ENST00000298355.3	hg19	CCDS9703.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.412686	0.83340	.	.	ENSG00000100505	ENST00000298355;ENST00000338969;ENST00000360392	T;T;T	0.70986	-0.37;-0.53;0.54	5.94	5.94	0.96194	B-box, C-terminal (1);COS domain (1);	0.000000	0.85682	D	0.000000	T	0.80722	0.4677	M	0.62723	1.935	0.54753	D	0.99998	D;D;P	0.61697	0.986;0.99;0.901	D;D;P	0.67382	0.951;0.941;0.482	T	0.77872	-0.2426	10	0.26408	T	0.33	.	15.5887	0.76506	0.0:0.0:0.0:1.0	.	399;399;399	Q9C026-5;Q9C026-4;Q9C026	.;.;TRIM9_HUMAN	R	399	ENSP00000298355:Q399R;ENSP00000342970:Q399R;ENSP00000353561:Q399R	ENSP00000298355:Q399R	Q	-	2	0	TRIM9	50545658	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.997000	0.88414	2.275000	0.75901	0.528000	0.53228	CAG	.	.	.	none		0.488	TRIM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276874.1	NM_015163	
EARS2	124454	hgsc.bcm.edu	37	16	23540828	23540828	+	Silent	SNP	C	C	T			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr16:23540828C>T	ENST00000563459.1	-	7	1353	c.1347G>A	c.(1345-1347)gtG>gtA	p.V449V	EARS2_ENST00000564501.1_Silent_p.V449V|EARS2_ENST00000563232.1_Silent_p.V449V|EARS2_ENST00000449606.1_Silent_p.V449V|EARS2_ENST00000564987.1_5'UTR			Q5JPH6	SYEM_HUMAN	glutamyl-tRNA synthetase 2, mitochondrial	449					gene expression (GO:0010467)|glutamyl-tRNA aminoacylation (GO:0006424)|tRNA aminoacylation for mitochondrial protein translation (GO:0070127)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|glutamate-tRNA ligase activity (GO:0004818)|glutamate-tRNA(Gln) ligase activity (GO:0050561)|tRNA binding (GO:0000049)			central_nervous_system(1)|endometrium(1)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	8				GBM - Glioblastoma multiforme(48;0.0353)		CTCACCCCAGCACACGCTTGG	0.607																																					p.V449V		Atlas-SNP	.											.	EARS2	26	.	0			c.G1347A						PASS	.						38.0	42.0	41.0					16																	23540828		2124	4249	6373	SO:0001819	synonymous_variant	124454	exon7			CCCCAGCACACGC	AB075850	CCDS42132.1	16p12.2	2014-05-06	2012-10-26		ENSG00000103356	ENSG00000103356	6.1.1.17	"""Aminoacyl tRNA synthetases / Class I"""	29419	protein-coding gene	gene with protein product	"""glutamate tRNA ligase 2, mitochondrial"""	612799	"""glutamyl-tRNA synthetase 2, mitochondrial (putative)"""			15779907, 19805282, 22492562	Standard	NM_001083614		Approved	KIAA1970, MSE1	uc002dlt.4	Q5JPH6	OTTHUMG00000177018	ENST00000563459.1:c.1347G>A	chr16.hg19:g.23540828C>T		47.0	0.0	.		46.0	13.0	.	NM_001083614	B3KTT2|D3DWF1|Q86YH3|Q8TF31	Silent	SNP	ENST00000563459.1	hg19	CCDS42132.1																																																																																			.	.	.	none		0.607	EARS2-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434844.1	NM_133451	
RNF166	115992	hgsc.bcm.edu	37	16	88765421	88765421	+	Silent	SNP	C	C	A			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr16:88765421C>A	ENST00000312838.4	-	4	593	c.498G>T	c.(496-498)gtG>gtT	p.V166V	RNF166_ENST00000537718.2_Silent_p.V57V|RNF166_ENST00000568683.1_Silent_p.V57V|RNF166_ENST00000541206.2_Silent_p.V57V|RNF166_ENST00000567844.1_Silent_p.V85V|RP5-1142A6.5_ENST00000561699.1_RNA|RNF166_ENST00000562499.1_5'Flank	NM_178841.3	NP_849163.1	Q96A37	RN166_HUMAN	ring finger protein 166	166							zinc ion binding (GO:0008270)			endometrium(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0476)		CACAGTGCTTCACCAGCTCCT	0.677																																					p.V166V		Atlas-SNP	.											.	RNF166	3	.	0			c.G498T						PASS	.						52.0	49.0	50.0					16																	88765421		2191	4293	6484	SO:0001819	synonymous_variant	115992	exon4			GTGCTTCACCAGC	AK057106	CCDS10969.1, CCDS54056.1, CCDS54057.1	16q24.3	2013-01-09			ENSG00000158717	ENSG00000158717		"""RING-type (C3HC4) zinc fingers"""	28856	protein-coding gene	gene with protein product						12477932	Standard	NM_178841		Approved	MGC2647, MGC14381	uc002flk.3	Q96A37	OTTHUMG00000137863	ENST00000312838.4:c.498G>T	chr16.hg19:g.88765421C>A		14.0	0.0	.		14.0	8.0	.	NM_178841	B3KQ03|D3DX75|H3BTU8|Q96DM0	Silent	SNP	ENST00000312838.4	hg19	CCDS10969.1																																																																																			.	.	.	none		0.677	RNF166-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269544.1	NM_178841	
UNC13D	201294	hgsc.bcm.edu	37	17	73837041	73837041	+	Missense_Mutation	SNP	A	A	T			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr17:73837041A>T	ENST00000207549.4	-	7	990	c.611T>A	c.(610-612)aTg>aAg	p.M204K	UNC13D_ENST00000587504.1_5'UTR|UNC13D_ENST00000412096.2_Missense_Mutation_p.M204K	NM_199242.2	NP_954712.1	Q70J99	UN13D_HUMAN	unc-13 homolog D (C. elegans)	204	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				defense response to virus (GO:0051607)|germinal center formation (GO:0002467)|granuloma formation (GO:0002432)|natural killer cell degranulation (GO:0043320)|phagocytosis (GO:0006909)|positive regulation of exocytosis (GO:0045921)|regulation of mast cell degranulation (GO:0043304)	endosome (GO:0005768)|exocytic vesicle (GO:0070382)|lysosome (GO:0005764)|membrane (GO:0016020)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29			all cancers(21;2.11e-06)|Epithelial(20;2.32e-06)|BRCA - Breast invasive adenocarcinoma(9;0.000618)|LUSC - Lung squamous cell carcinoma(166;0.154)			CACTCACCACATGTCCAGATG	0.592									Familial Hemophagocytic Lymphohistiocytosis																												p.M204K		Atlas-SNP	.											.	UNC13D	68	.	0			c.T611A						PASS	.						250.0	240.0	243.0					17																	73837041		2203	4300	6503	SO:0001583	missense	201294	exon7	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	CACCACATGTCCA	AK024474	CCDS11730.1	17q25.3	2014-09-17				ENSG00000092929			23147	protein-coding gene	gene with protein product		608897					Standard	NM_199242		Approved	Munc13-4	uc002jpp.3	Q70J99		ENST00000207549.4:c.611T>A	chr17.hg19:g.73837041A>T	ENSP00000207549:p.Met204Lys	451.0	0.0	.		474.0	146.0	.	NM_199242	B4DWG9|Q9H7K5	Missense_Mutation	SNP	ENST00000207549.4	hg19	CCDS11730.1	.	.	.	.	.	.	.	.	.	.	A	19.45	3.830248	0.71258	.	.	ENSG00000092929	ENST00000207549;ENST00000412096;ENST00000448606	T;T	0.39406	1.08;1.08	4.44	4.44	0.53790	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.059897	0.64402	D	0.000004	T	0.61887	0.2383	M	0.82323	2.585	0.80722	D	1	D;B	0.53312	0.959;0.132	P;B	0.57244	0.816;0.207	T	0.69544	-0.5117	10	0.87932	D	0	.	13.7049	0.62631	1.0:0.0:0.0:0.0	.	204;204	B4DTQ6;Q70J99	.;UN13D_HUMAN	K	204	ENSP00000207549:M204K;ENSP00000388093:M204K	ENSP00000207549:M204K	M	-	2	0	UNC13D	71348636	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	8.339000	0.90041	1.650000	0.50662	0.460000	0.39030	ATG	.	.	.	none		0.592	UNC13D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448847.2	XM_113950	
QRICH2	84074	hgsc.bcm.edu	37	17	74288035	74288035	+	Nonsense_Mutation	SNP	G	G	A			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr17:74288035G>A	ENST00000262765.5	-	4	2454	c.2275C>T	c.(2275-2277)Cag>Tag	p.Q759*		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	759	Gln-rich.									breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(2)|stomach(4)	62						GGATCTGCCTGAGGTTGCACC	0.522																																					p.Q759X		Atlas-SNP	.											.	QRICH2	143	.	0			c.C2275T						PASS	.						181.0	166.0	171.0					17																	74288035		2203	4300	6503	SO:0001587	stop_gained	84074	exon4			CTGCCTGAGGTTG	AK058102	CCDS32741.1	17q25.1	2009-03-19			ENSG00000129646	ENSG00000129646			25326	protein-coding gene	gene with protein product							Standard	NM_032134		Approved	DKFZP434P0316	uc002jrd.1	Q9H0J4	OTTHUMG00000167578	ENST00000262765.5:c.2275C>T	chr17.hg19:g.74288035G>A	ENSP00000262765:p.Gln759*	223.0	0.0	.		219.0	74.0	.	NM_032134	A2RRE1|Q96LM3	Nonsense_Mutation	SNP	ENST00000262765.5	hg19	CCDS32741.1	.	.	.	.	.	.	.	.	.	.	g	38	6.650945	0.97734	.	.	ENSG00000129646	ENST00000262765;ENST00000301613	.	.	.	4.21	0.735	0.18300	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	-0.4735	11.7828	0.52023	0.0:0.4377:0.5623:0.0	.	.	.	.	X	759	.	ENSP00000262765:Q759X	Q	-	1	0	QRICH2	71799630	0.000000	0.05858	0.003000	0.11579	0.066000	0.16364	-1.577000	0.02127	0.500000	0.27991	-0.537000	0.04273	CAG	.	.	.	none		0.522	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134	
TAF4B	6875	hgsc.bcm.edu	37	18	23865865	23865865	+	Missense_Mutation	SNP	G	G	A			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr18:23865865G>A	ENST00000269142.5	+	7	1990	c.992G>A	c.(991-993)cGa>cAa	p.R331Q	TAF4B_ENST00000578121.1_Missense_Mutation_p.R331Q|TAF4B_ENST00000400466.2_Missense_Mutation_p.R331Q	NM_005640.1	NP_005631.1	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa	331	TAFH. {ECO:0000255|PROSITE- ProRule:PRU00440}.				gene expression (GO:0010467)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|NF-kappaB binding (GO:0051059)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|prostate(1)|skin(1)	29	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)			GTTGCCTTACGACAACTTCTG	0.408																																					p.R331Q		Atlas-SNP	.											.	TAF4B	71	.	0			c.G992A						PASS	.						117.0	105.0	108.0					18																	23865865		1933	4147	6080	SO:0001583	missense	6875	exon7			CCTTACGACAACT	Y09321	CCDS42421.1	18q11.1	2008-08-01	2002-08-29	2001-12-07		ENSG00000141384			11538	protein-coding gene	gene with protein product	"""TATA box binding protein (TBP)-associated factor 4B"""	601689	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, C2, 105kD"""	TAF2C2		8858156, 10849440	Standard	XM_005258339		Approved	TAFII105	uc002kvu.4	Q92750		ENST00000269142.5:c.992G>A	chr18.hg19:g.23865865G>A	ENSP00000269142:p.Arg331Gln	234.0	0.0	.		197.0	104.0	.	NM_005640	Q29YA4|Q29YA5	Missense_Mutation	SNP	ENST00000269142.5	hg19	CCDS42421.1	.	.	.	.	.	.	.	.	.	.	g	15.30	2.793145	0.50102	.	.	ENSG00000141384	ENST00000418698;ENST00000269142;ENST00000400466	T;T;T	0.49720	0.77;0.77;0.77	5.72	4.83	0.62350	TAFH/NHR1 (3);	0.124363	0.56097	D	0.000033	T	0.62768	0.2455	L	0.58428	1.81	0.54753	D	0.999986	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.961	T	0.58907	-0.7553	10	0.16420	T	0.52	-9.2264	15.6095	0.76704	0.0:0.0:0.861:0.139	.	331;331	Q92750;A4PBF7	TAF4B_HUMAN;.	Q	331	ENSP00000389365:R331Q;ENSP00000269142:R331Q;ENSP00000383314:R331Q	ENSP00000269142:R331Q	R	+	2	0	TAF4B	22119863	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.418000	0.80167	1.388000	0.46506	0.558000	0.71614	CGA	.	.	.	none		0.408	TAF4B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000446260.3	NM_005640	
PLPPR3	79948	hgsc.bcm.edu	37	19	814747	814747	+	Missense_Mutation	SNP	T	T	C			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr19:814747T>C	ENST00000520876.3	-	6	680	c.602A>G	c.(601-603)aAg>aGg	p.K201R	MIR3187_ENST00000583431.1_RNA|LPPR3_ENST00000359894.2_Missense_Mutation_p.K201R	NM_001270366.1	NP_001257295.1	Q6T4P5	LPPR3_HUMAN		201						integral component of membrane (GO:0016021)	phosphatidate phosphatase activity (GO:0008195)										CGGGAAGGTCTTCCTGTAAGA	0.667																																					p.K201R		Atlas-SNP	.											.	.	.	.	0			c.A602G						PASS	.						40.0	33.0	35.0					19																	814747		2187	4296	6483	SO:0001583	missense	0	exon6			AAGGTCTTCCTGT																												ENST00000520876.3:c.602A>G	chr19.hg19:g.814747T>C	ENSP00000430297:p.Lys201Arg	34.0	0.0	.		36.0	11.0	.	NM_001270366	Q86XQ4|Q96EH1|Q9BQF9|Q9HAJ4	Missense_Mutation	SNP	ENST00000520876.3	hg19	CCDS58636.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.010930	0.75046	.	.	ENSG00000129951	ENST00000300947;ENST00000359894;ENST00000520876	T;T	0.48201	0.82;0.82	4.77	4.77	0.60923	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.53110	0.1776	L	0.46567	1.45	0.39303	D	0.964943	P;P;D	0.56746	0.918;0.933;0.977	P;P;P	0.55871	0.596;0.718;0.786	T	0.54370	-0.8304	10	0.35671	T	0.21	-24.8006	12.0107	0.53286	0.0:0.0:0.0:1.0	.	202;201;201	Q6T4P5-2;Q6T4P5;Q6T4P5-3	.;LPPR3_HUMAN;.	R	202;201;201	ENSP00000352962:K201R;ENSP00000430297:K201R	ENSP00000300947:K202R	K	-	2	0	AC006273.1	765747	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	4.722000	0.61958	1.780000	0.52325	0.454000	0.30748	AAG	.	.	.	none		0.667	LPPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379096.3		
ZNF607	84775	hgsc.bcm.edu	37	19	38190209	38190209	+	Missense_Mutation	SNP	G	G	T			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr19:38190209G>T	ENST00000355202.4	-	5	1418	c.823C>A	c.(823-825)Cat>Aat	p.H275N	CTD-2528L19.4_ENST00000586606.2_Intron|ZNF607_ENST00000395835.3_Missense_Mutation_p.H274N	NM_032689.4	NP_116078.4	Q96SK3	ZN607_HUMAN	zinc finger protein 607	275					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|lung(8)|urinary_tract(1)	27			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)			TCTCCAGTATGAATACTCTGA	0.423																																					p.H275N		Atlas-SNP	.											.	ZNF607	82	.	0			c.C823A						PASS	.						48.0	48.0	48.0					19																	38190209		2203	4300	6503	SO:0001583	missense	84775	exon5			CAGTATGAATACT	AK127464	CCDS33006.1, CCDS54259.1	19q13.1	2013-01-08				ENSG00000198182		"""Zinc fingers, C2H2-type"", ""-"""	28192	protein-coding gene	gene with protein product						14702039	Standard	NM_032689		Approved	MGC13071, FLJ14802	uc002ohc.2	Q96SK3		ENST00000355202.4:c.823C>A	chr19.hg19:g.38190209G>T	ENSP00000347338:p.His275Asn	103.0	0.0	.		119.0	49.0	.	NM_032689	F5H141|Q6ZMN2|Q6ZMN4|Q96C40	Missense_Mutation	SNP	ENST00000355202.4	hg19	CCDS33006.1	.	.	.	.	.	.	.	.	.	.	G	15.02	2.708084	0.48412	.	.	ENSG00000198182	ENST00000355202;ENST00000395835	T;T	0.67345	-0.26;-0.26	2.27	2.27	0.28462	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.84005	0.5377	M	0.92923	3.36	0.33659	D	0.609455	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.88981	0.3408	9	0.87932	D	0	.	11.6009	0.51001	0.0:0.0:1.0:0.0	.	275;274	Q96SK3;F5H141	ZN607_HUMAN;.	N	275;274	ENSP00000347338:H275N;ENSP00000438015:H274N	ENSP00000347338:H275N	H	-	1	0	ZNF607	42882049	1.000000	0.71417	0.991000	0.47740	0.731000	0.41821	7.908000	0.87438	1.255000	0.44051	0.561000	0.74099	CAT	.	.	.	none		0.423	ZNF607-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459502.2	NM_032689	
SIPA1L3	23094	hgsc.bcm.edu	37	19	38621370	38621370	+	Missense_Mutation	SNP	A	A	C			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr19:38621370A>C	ENST00000222345.6	+	10	3610	c.3101A>C	c.(3100-3102)aAg>aCg	p.K1034T		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	1034	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				hematopoietic progenitor cell differentiation (GO:0002244)|regulation of small GTPase mediated signal transduction (GO:0051056)	extracellular space (GO:0005615)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			GTCACTGTGAAGGTGGTCATC	0.627																																					p.K1034T		Atlas-SNP	.											.	SIPA1L3	150	.	0			c.A3101C						PASS	.						67.0	60.0	62.0					19																	38621370		2203	4300	6503	SO:0001583	missense	23094	exon10			CTGTGAAGGTGGT	AB011117	CCDS33007.1	19q13.13	2008-02-05			ENSG00000105738	ENSG00000105738			23801	protein-coding gene	gene with protein product							Standard	XM_005258671		Approved	KIAA0545	uc002ohk.3	O60292	OTTHUMG00000073727	ENST00000222345.6:c.3101A>C	chr19.hg19:g.38621370A>C	ENSP00000222345:p.Lys1034Thr	87.0	0.0	.		92.0	28.0	.	NM_015073	Q2TV87	Missense_Mutation	SNP	ENST00000222345.6	hg19	CCDS33007.1	.	.	.	.	.	.	.	.	.	.	A	17.63	3.437903	0.62955	.	.	ENSG00000105738	ENST00000222345	T	0.62788	0.0	5.33	5.33	0.75918	PDZ/DHR/GLGF (2);	0.108901	0.64402	D	0.000008	T	0.33673	0.0871	N	0.00972	-1.085	0.58432	D	0.999992	B	0.33212	0.402	B	0.33846	0.171	T	0.42999	-0.9418	10	0.28530	T	0.3	-40.8953	14.5799	0.68282	1.0:0.0:0.0:0.0	.	1034	O60292	SI1L3_HUMAN	T	1034	ENSP00000222345:K1034T	ENSP00000222345:K1034T	K	+	2	0	SIPA1L3	43313210	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	3.751000	0.55165	2.148000	0.66965	0.533000	0.62120	AAG	.	.	.	none		0.627	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278	
ZNF780B	163131	hgsc.bcm.edu	37	19	40540344	40540344	+	Missense_Mutation	SNP	G	G	A			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr19:40540344G>A	ENST00000434248.1	-	5	2487	c.2422C>T	c.(2422-2424)Cct>Tct	p.P808S	ZNF780B_ENST00000221355.6_Missense_Mutation_p.P660S	NM_001005851.2	NP_001005851.1	Q9Y6R6	Z780B_HUMAN	zinc finger protein 780B	808					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	23	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					ACATTCAAAGGGTTTCTCACC	0.393																																					p.P808S		Atlas-SNP	.											.	ZNF780B	143	.	0			c.C2422T						PASS	.						59.0	64.0	62.0					19																	40540344		2188	4297	6485	SO:0001583	missense	163131	exon5			TCAAAGGGTTTCT	AK127063	CCDS46077.1	19q13.2	2013-01-08	2006-08-15	2006-08-15	ENSG00000128000	ENSG00000128000		"""Zinc fingers, C2H2-type"", ""-"""	33109	protein-coding gene	gene with protein product			"""zinc finger protein 779"""	ZNF779			Standard	NM_001005851		Approved		uc002omu.3	Q9Y6R6	OTTHUMG00000155118	ENST00000434248.1:c.2422C>T	chr19.hg19:g.40540344G>A	ENSP00000391641:p.Pro808Ser	63.0	0.0	.		100.0	38.0	.	NM_001005851	B9EH00	Missense_Mutation	SNP	ENST00000434248.1	hg19	CCDS46077.1	.	.	.	.	.	.	.	.	.	.	G	10.62	1.400412	0.25291	.	.	ENSG00000128000	ENST00000434248;ENST00000221355	T;T	0.06142	3.55;3.34	2.24	1.16	0.20824	Zinc finger, C2H2 (1);	.	.	.	.	T	0.06050	0.0157	L	0.41906	1.305	0.20926	N	0.999822	B	0.02656	0.0	B	0.04013	0.001	T	0.34153	-0.9840	9	0.59425	D	0.04	.	6.6373	0.22889	0.1624:0.0:0.8376:0.0	.	808	Q9Y6R6	Z780B_HUMAN	S	808;660	ENSP00000391641:P808S;ENSP00000221355:P660S	ENSP00000221355:P660S	P	-	1	0	ZNF780B	45232184	0.008000	0.16893	0.148000	0.22405	0.135000	0.20990	0.773000	0.26661	0.135000	0.18707	-0.448000	0.05591	CCT	.	.	.	none		0.393	ZNF780B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338466.1	NM_001005851	
CLPTM1	1209	hgsc.bcm.edu	37	19	45495628	45495628	+	Missense_Mutation	SNP	G	G	A	rs369873479		TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr19:45495628G>A	ENST00000337392.5	+	13	1843	c.1693G>A	c.(1693-1695)Gtt>Att	p.V565I	CLPTM1_ENST00000541297.2_Missense_Mutation_p.V551I|CLPTM1_ENST00000546079.1_Missense_Mutation_p.V463I	NM_001282175.1|NM_001282176.1|NM_001294.2	NP_001269104.1|NP_001269105.1|NP_001285.1	O96005	CLPT1_HUMAN	cleft lip and palate associated transmembrane protein 1	565					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of T cell differentiation in thymus (GO:0033081)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00354)|Epithelial(262;0.187)		CAAGATGCCCGTTATGTACCG	0.627																																					p.V565I		Atlas-SNP	.											.	CLPTM1	109	.	0			c.G1693A						PASS	.	G	ILE/VAL	0,4406		0,0,2203	203.0	182.0	190.0		1693	4.2	0.4	19		190	1,8599	1.2+/-3.3	0,1,4299	no	missense	CLPTM1	NM_001294.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	565/670	45495628	1,13005	2203	4300	6503	SO:0001583	missense	1209	exon13			ATGCCCGTTATGT	AF037339	CCDS12651.1, CCDS74394.1, CCDS74395.1	19q13.3	2008-02-05				ENSG00000104853			2087	protein-coding gene	gene with protein product		604783				9828125	Standard	NM_001294		Approved		uc002pai.3	O96005		ENST00000337392.5:c.1693G>A	chr19.hg19:g.45495628G>A	ENSP00000336994:p.Val565Ile	282.0	0.0	.		261.0	100.0	.	NM_001294	B3KQH2|B4DDS3|B4E2X9|B7Z9X9|F5H8J3|Q53ET6|Q9BSS5	Missense_Mutation	SNP	ENST00000337392.5	hg19	CCDS12651.1	.	.	.	.	.	.	.	.	.	.	G	13.28	2.191286	0.38707	0.0	1.16E-4	ENSG00000104853	ENST00000546079;ENST00000541297;ENST00000337392;ENST00000347493	.	.	.	5.21	4.17	0.49024	.	0.186290	0.46758	D	0.000276	T	0.11836	0.0288	N	0.02916	-0.46	0.31931	N	0.612128	P;P	0.40602	0.723;0.602	B;B	0.30316	0.114;0.053	T	0.10636	-1.0621	9	0.17369	T	0.5	-31.7339	9.7828	0.40658	0.0929:0.0:0.9071:0.0	.	551;565	F5H8J3;O96005	.;CLPT1_HUMAN	I	463;551;565;565	.	ENSP00000336994:V565I	V	+	1	0	CLPTM1	50187468	1.000000	0.71417	0.352000	0.25734	0.978000	0.69477	6.750000	0.74888	1.443000	0.47586	0.650000	0.86243	GTT	.	.	.	weak		0.627	CLPTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453267.1	NM_001294	
NLRP2	55655	hgsc.bcm.edu	37	19	55493701	55493701	+	Missense_Mutation	SNP	A	A	T			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr19:55493701A>T	ENST00000543010.1	+	6	778	c.635A>T	c.(634-636)tAt>tTt	p.Y212F	NLRP2_ENST00000339757.7_Missense_Mutation_p.Y190F|NLRP2_ENST00000448584.2_Missense_Mutation_p.Y212F|NLRP2_ENST00000427260.2_Missense_Mutation_p.Y189F|NLRP2_ENST00000263437.6_Missense_Mutation_p.Y209F|NLRP2_ENST00000391721.4_Missense_Mutation_p.Y188F|NLRP2_ENST00000538819.1_Missense_Mutation_p.Y188F|NLRP2_ENST00000537859.1_Missense_Mutation_p.Y190F	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	212	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|Pyrin domain binding (GO:0032090)			large_intestine(4)|liver(1)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	11			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		GTGGTGCTGTATGGTCCTGCA	0.527																																					p.Y212F		Atlas-SNP	.											.	NLRP2	161	.	0			c.A635T						PASS	.						78.0	79.0	79.0					19																	55493701		2203	4300	6503	SO:0001583	missense	55655	exon6			TGCTGTATGGTCC	AK000517	CCDS12913.1, CCDS54318.1, CCDS54319.1	19q13.42	2008-02-05	2006-12-08	2006-12-08	ENSG00000022556	ENSG00000022556		"""Nucleotide-binding domain and leucine rich repeat containing"""	22948	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2"""	609364	"""NACHT, leucine rich repeat and PYD containing 2"""	NALP2		12563287, 11270363	Standard	NM_001174081		Approved	FLJ20510, PYPAF2, NBS1, PAN1, CLR19.9	uc021vbq.1	Q9NX02	OTTHUMG00000167763	ENST00000543010.1:c.635A>T	chr19.hg19:g.55493701A>T	ENSP00000445135:p.Tyr212Phe	113.0	0.0	.		135.0	53.0	.	NM_017852	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Missense_Mutation	SNP	ENST00000543010.1	hg19	CCDS12913.1	.	.	.	.	.	.	.	.	.	.	A	9.855	1.194818	0.22037	.	.	ENSG00000022556	ENST00000543010;ENST00000391721;ENST00000339757;ENST00000448584;ENST00000537859;ENST00000427260;ENST00000538819;ENST00000263437	D;D;D;D;D;D;D;D	0.82893	-1.66;-1.66;-1.66;-1.66;-1.66;-1.66;-1.66;-1.66	1.62	0.524	0.17066	NACHT nucleoside triphosphatase (1);	1.825070	0.03631	N	0.237909	T	0.71913	0.3396	N	0.10972	0.075	0.09310	N	1	B;B;B;B;P	0.35433	0.213;0.284;0.332;0.284;0.501	B;B;B;B;B	0.41412	0.356;0.128;0.295;0.195;0.295	T	0.63193	-0.6692	10	0.48119	T	0.1	.	4.2437	0.10662	0.6116:0.0:0.3884:0.0	.	189;190;209;188;212	B4DZL7;Q9NX02-2;A8K9G6;Q9NX02-4;Q9NX02	.;.;.;.;NALP2_HUMAN	F	212;188;190;212;190;189;188;209	ENSP00000445135:Y212F;ENSP00000375601:Y188F;ENSP00000344074:Y190F;ENSP00000409370:Y212F;ENSP00000440601:Y190F;ENSP00000402474:Y189F;ENSP00000441133:Y188F;ENSP00000263437:Y209F	ENSP00000263437:Y209F	Y	+	2	0	NLRP2	60185513	0.000000	0.05858	0.009000	0.14445	0.001000	0.01503	0.117000	0.15583	0.085000	0.17107	0.402000	0.26972	TAT	.	.	.	none		0.527	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852	
RPL3	6122	hgsc.bcm.edu	37	22	39714484	39714484	+	Missense_Mutation	SNP	C	C	A			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr22:39714484C>A	ENST00000216146.4	-	2	290	c.117G>T	c.(115-117)aaG>aaT	p.K39N	SNORD43_ENST00000583861.1_RNA|RPL3_ENST00000465618.1_5'UTR|RPL3_ENST00000401609.1_5'UTR	NM_000967.3|NM_001033853.1	NP_000958.1|NP_001029025.1	P39023	RL3_HUMAN	ribosomal protein L3	39					cellular protein metabolic process (GO:0044267)|cellular response to interleukin-4 (GO:0071353)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			breast(1)|kidney(4)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	12	Melanoma(58;0.04)				Homoharringtonine(DB04865)	GGTGGACCGGCTTGGACGGGT	0.592																																					p.K39N		Atlas-SNP	.											.	RPL3	29	.	0			c.G117T						PASS	.						58.0	54.0	55.0					22																	39714484		2203	4298	6501	SO:0001583	missense	6122	exon2			GACCGGCTTGGAC	AB007166	CCDS13988.1	22q13	2011-04-06			ENSG00000100316	ENSG00000100316		"""L ribosomal proteins"""	10332	protein-coding gene	gene with protein product		604163				2891103, 9582194	Standard	NM_000967		Approved	L3	uc003axi.3	P39023	OTTHUMG00000151079	ENST00000216146.4:c.117G>T	chr22.hg19:g.39714484C>A	ENSP00000346001:p.Lys39Asn	68.0	0.0	.		55.0	13.0	.	NM_001033853	B2RDV9|Q15548|Q5I0G0	Missense_Mutation	SNP	ENST00000216146.4	hg19	CCDS13988.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.63|16.63	3.175374|3.175374	0.57692|0.57692	.|.	.|.	ENSG00000100316|ENSG00000100316	ENST00000427905|ENST00000216146;ENST00000453303	.|T;T	.|0.49720	.|1.38;0.77	4.5|4.5	3.48|3.48	0.39840|0.39840	.|Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.61123|0.61123	0.2322|0.2322	M|M	0.88842|0.88842	2.985|2.985	0.80722|0.80722	D|D	1|1	.|D;P	.|0.57899	.|0.981;0.715	.|P;P	.|0.48982	.|0.597;0.477	T|T	0.69982|0.69982	-0.4997|-0.4997	5|10	.|0.72032	.|D	.|0.01	.|.	12.3136|12.3136	0.54942|0.54942	0.0:0.9173:0.0:0.0827|0.0:0.9173:0.0:0.0827	.|.	.|39;39	.|P39023;B3KS36	.|RL3_HUMAN;.	S|N	71|39;66	.|ENSP00000346001:K39N;ENSP00000415198:K66N	.|ENSP00000346001:K39N	A|K	-|-	1|3	0|2	RPL3|RPL3	38044430|38044430	1.000000|1.000000	0.71417|0.71417	0.787000|0.787000	0.31911|0.31911	0.431000|0.431000	0.31685|0.31685	2.393000|2.393000	0.44442|0.44442	0.884000|0.884000	0.36064|0.36064	0.455000|0.455000	0.32223|0.32223	GCC|AAG	.	.	.	none		0.592	RPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321196.1	NM_000967	
YY2	404281	hgsc.bcm.edu	37	X	21875588	21875588	+	Missense_Mutation	SNP	G	G	A			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chrX:21875588G>A	ENST00000429584.2	+	1	1484	c.986G>A	c.(985-987)cGc>cAc	p.R329H	MBTPS2_ENST00000365779.2_Intron|MBTPS2_ENST00000379484.5_Intron|MBTPS2_ENST00000465888.1_3'UTR	NM_206923.3	NP_996806.2	O15391	TYY2_HUMAN	YY2 transcription factor	329	Mediates transcriptional repression.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|skin(2)	19						TTCAATTTGCGCACACACTTG	0.532																																					p.R329H		Atlas-SNP	.											.	YY2	43	.	0			c.G986A						PASS	.						182.0	181.0	181.0					X																	21875588		2203	4300	6503	SO:0001583	missense	404281	exon1			ATTTGCGCACACA	AK091850	CCDS14202.1	Xp22.2-p22.1	2011-02-11			ENSG00000230797	ENSG00000230797		"""Zinc fingers, C2H2-type"""	31684	protein-coding gene	gene with protein product	"""transcription factor yin yang 2"""	300570				14702039	Standard	NM_206923		Approved	ZNF631	uc011mjp.2	O15391	OTTHUMG00000021236	ENST00000429584.2:c.986G>A	chrX.hg19:g.21875588G>A	ENSP00000389381:p.Arg329His	253.0	0.0	.		289.0	203.0	.	NM_206923	B2RP10|Q6Q1S4	Missense_Mutation	SNP	ENST00000429584.2	hg19	CCDS14202.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.787837	0.90367	.	.	ENSG00000230797	ENST00000429584	T	0.41400	1.0	4.6	4.6	0.57074	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	U	0.000000	T	0.52273	0.1724	L	0.35288	1.05	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.53222	-0.8469	10	0.52906	T	0.07	.	14.034	0.64634	0.0:0.0:1.0:0.0	.	329	O15391	TYY2_HUMAN	H	329	ENSP00000389381:R329H	ENSP00000389381:R329H	R	+	2	0	YY2	21785509	1.000000	0.71417	0.992000	0.48379	0.757000	0.42996	7.776000	0.85560	2.276000	0.75962	0.544000	0.68410	CGC	.	.	.	none		0.532	YY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056025.1	NM_206923	
DAP3	7818	hgsc.bcm.edu	37	1	155695184	155695185	+	Frame_Shift_Ins	INS	-	-	A			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr1:155695184_155695185insA	ENST00000368336.5	+	5	406_407	c.282_283insA	c.(283-285)agtfs	p.S95fs	DAP3_ENST00000535183.1_Frame_Shift_Ins_p.S54fs|DAP3_ENST00000496863.1_3'UTR|DAP3_ENST00000471642.2_Frame_Shift_Ins_p.S54fs|DAP3_ENST00000421487.2_Frame_Shift_Ins_p.S61fs|MSTO1_ENST00000538143.1_Intron|MSTO1_ENST00000452804.2_Intron|DAP3_ENST00000343043.3_Frame_Shift_Ins_p.S95fs	NM_001199849.1|NM_004632.3	NP_001186778.1|NP_004623.1	P51398	RT29_HUMAN	death associated protein 3	95					apoptotic mitochondrial changes (GO:0008637)|apoptotic signaling pathway (GO:0097190)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|small ribosomal subunit (GO:0015935)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	24	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)					TGAAGACATTCAGTGAAGCTTG	0.45																																					p.F94fs		Atlas-INDEL	.											.	DAP3	46	.	0			c.282_283insA						PASS	.																																			SO:0001589	frameshift_variant	7818	exon5			.	X83544	CCDS1120.1, CCDS55646.1, CCDS55647.1	1q22	2012-11-14			ENSG00000132676	ENSG00000132676		"""Mitochondrial ribosomal proteins / small subunits"""	2673	protein-coding gene	gene with protein product	"""mitochondrial 28S ribosomal protein S29"""	602074				7499268, 9284927	Standard	NM_004632		Approved	MRPS29, DAP-3, MRP-S29, bMRP-10, MGC126058, MGC126059, DKFZp686G12159	uc001flr.3	P51398	OTTHUMG00000035439	ENST00000368336.5:c.283dupA	chr1.hg19:g.155695185_155695185dupA	ENSP00000357320:p.Ser95fs	163.0	0.0	0		178.0	63.0	0.353933	NM_033657	B4DP59|B4DY62|E7EM60|Q13044|Q68CT7|Q96Q20	Frame_Shift_Ins	INS	ENST00000368336.5	hg19	CCDS1120.1																																																																																			.	.	.	none		0.450	DAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086042.1	NM_004632	
RTL1	388015	hgsc.bcm.edu	37	14	101348358	101348358	+	Frame_Shift_Del	DEL	T	T	-			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr14:101348358delT	ENST00000534062.1	-	1	2826	c.2768delA	c.(2767-2769)aagfs	p.K923fs	MIR127_ENST00000384876.1_RNA|MIR431_ENST00000385266.1_RNA|MIR433_ENST00000384837.1_RNA|MIR136_ENST00000385207.1_RNA|MIR432_ENST00000606207.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	923					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)				breast(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(5)|pancreas(1)|prostate(2)|skin(2)	21						TGGAAGAATCTTCATCTCCGC	0.537																																					p.K923fs		Atlas-INDEL	.											.	RTL1	120	.	0			c.2769delG						PASS	.						38.0	37.0	37.0					14																	101348358		1568	3582	5150	SO:0001589	frameshift_variant	388015	exon1			.		CCDS53910.1	14q32.2	2012-04-18			ENSG00000254656	ENSG00000254656			14665	protein-coding gene	gene with protein product		611896				16155747, 15854907, 12796779	Standard	NM_001134888		Approved	PEG11, MART1, Mar1	uc010txj.1	A6NKG5	OTTHUMG00000167573	ENST00000534062.1:c.2768delA	chr14.hg19:g.101348358delT	ENSP00000435342:p.Lys923fs	42.0	0.0	0		53.0	17.0	0.320755	NM_001134888	E9PKS8	Frame_Shift_Del	DEL	ENST00000534062.1	hg19	CCDS53910.1																																																																																			.	.	.	none		0.537	RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888	
CCDC13	152206	hgsc.bcm.edu	37	3	42793437	42793438	+	Frame_Shift_Ins	INS	-	-	TC			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr3:42793437_42793438insTC	ENST00000310232.6	-	5	676_677	c.593_594insGA	c.(592-594)gacfs	p.D198fs	CCDC13_ENST00000435327.2_5'UTR	NM_144719.3	NP_653320.3	Q8IYE1	CCD13_HUMAN	coiled-coil domain containing 13	198										endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	25						CCAATGCTCTGTCTCCCATCTG	0.609																																					p.D198fs		Atlas-INDEL	.											.	CCDC13	71	.	0			c.594_595insGA						PASS	.																																			SO:0001589	frameshift_variant	152206	exon5			.	AK058196	CCDS2705.1	3p22.1	2005-01-25			ENSG00000244607	ENSG00000244607			26358	protein-coding gene	gene with protein product						12477932	Standard	NM_144719		Approved	FLJ25467	uc003cly.4	Q8IYE1	OTTHUMG00000133046	ENST00000310232.6:c.592_593dupGA	chr3.hg19:g.42793440_42793441dupTC	ENSP00000309836:p.Asp198fs	124.0	0.0	0		83.0	25.0	0.301205	NM_144719		Frame_Shift_Ins	INS	ENST00000310232.6	hg19	CCDS2705.1																																																																																			.	.	.	none		0.609	CCDC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256652.1	NM_144719	
EFCAB6	64800	hgsc.bcm.edu	37	22	44107398	44107399	+	Frame_Shift_Ins	INS	-	-	A			TCGA-BQ-5882-01A-11D-1589-08	TCGA-BQ-5882-11A-01D-1589-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	f65963b3-cd4d-4c08-afc0-15bce361cd03	b04cfca5-40a2-4035-b650-45bc55651c71	g.chr22:44107398_44107399insA	ENST00000262726.7	-	10	1240_1241	c.987_988insT	c.(985-990)tttgtafs	p.V330fs	EFCAB6_ENST00000358439.4_Frame_Shift_Ins_p.V224fs|EFCAB6_ENST00000396231.2_Frame_Shift_Ins_p.V178fs	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	330	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(16)|lung(25)|ovary(4)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68		Ovarian(80;0.0247)|all_neural(38;0.025)				ATTTGGTATACAAAAGTGTCGA	0.381																																					p.V330fs		Atlas-INDEL	.											.	EFCAB6	177	.	0			c.988_989insT						PASS	.																																			SO:0001589	frameshift_variant	64800	exon10			.	Z82201	CCDS14049.1, CCDS14050.1	22q13.2	2013-01-10			ENSG00000186976	ENSG00000186976		"""EF-hand domain containing"""	24204	protein-coding gene	gene with protein product						11258795, 12612053	Standard	NM_022785		Approved	FLJ23588, DJBP, HSCBCIP1, KIAA1672, dJ185D5.1	uc003bdy.2	Q5THR3	OTTHUMG00000150522	ENST00000262726.7:c.988dupT	chr22.hg19:g.44107402_44107402dupA	ENSP00000262726:p.Val330fs	74.0	0.0	0		88.0	25.0	0.284091	NM_022785	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Frame_Shift_Ins	INS	ENST00000262726.7	hg19	CCDS14049.1																																																																																			.	.	.	none		0.381	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785	
