#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
OR2G2	81470	hgsc.bcm.edu	37	1	247751788	247751788	+	Silent	SNP	T	T	C			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr1:247751788T>C	ENST00000320065.1	+	1	127	c.127T>C	c.(127-129)Ttg>Ctg	p.L43L	RP11-978I15.10_ENST00000435333.1_RNA|RP11-978I15.10_ENST00000446347.1_RNA	NM_001001915.1	NP_001001915.1	Q8NGZ5	OR2G2_HUMAN	olfactory receptor, family 2, subfamily G, member 2	43						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(4)|large_intestine(3)|lung(30)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			ACTAACTATTTTGGGGAATAC	0.408																																					p.L43L		Atlas-SNP	.											.	OR2G2	88	.	0			c.T127C						PASS	.						227.0	217.0	220.0					1																	247751788		2203	4300	6503	SO:0001819	synonymous_variant	81470	exon1			ACTATTTTGGGGA	BK004472	CCDS31092.1	1q44	2012-08-09	2008-05-23		ENSG00000177489	ENSG00000177489		"""GPCR / Class A : Olfactory receptors"""	15007	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily G, member 2"", ""olfactory receptor, family 2, subfamily G, member 2 pseudogene"""				Standard	NM_001001915		Approved		uc010pyy.2	Q8NGZ5	OTTHUMG00000040575	ENST00000320065.1:c.127T>C	chr1.hg19:g.247751788T>C		178.0	0.0	.		319.0	87.0	.	NM_001001915	Q5JQT2|Q6IEZ0	Silent	SNP	ENST00000320065.1	hg19	CCDS31092.1																																																																																			.	.	.	none		0.408	OR2G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097623.1		
CCT4	10575	hgsc.bcm.edu	37	2	62115531	62115531	+	Missense_Mutation	SNP	T	T	C	rs199542002		TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr2:62115531T>C	ENST00000394440.3	-	1	408	c.112A>G	c.(112-114)Att>Gtt	p.I38V	CCT4_ENST00000544185.1_5'UTR|CCT4_ENST00000538252.1_5'UTR|CCT4_ENST00000544079.1_Missense_Mutation_p.I38V|AC107081.5_ENST00000425779.1_RNA	NM_006430.3	NP_006421.2	P50991	TCPD_HUMAN	chaperonin containing TCP1, subunit 4 (delta)	38					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			breast(1)|large_intestine(2)|lung(6)|ovary(2)	11	Lung NSC(7;0.035)|all_lung(7;0.0691)		LUSC - Lung squamous cell carcinoma(7;6.5e-06)|Epithelial(17;0.0647)|all cancers(80;0.221)			GCGGCGGAAATGTTGCTGAAG	0.677																																					p.I38V		Atlas-SNP	.											.	CCT4	38	.	0			c.A112G						PASS	.	T	VAL/ILE	0,4404		0,0,2202	47.0	43.0	45.0		112	3.3	0.8	2		45	1,8599	1.2+/-3.3	0,1,4299	no	missense	CCT4	NM_006430.2	29	0,1,6501	CC,CT,TT		0.0116,0.0,0.0077	probably-damaging	38/540	62115531	1,13003	2202	4300	6502	SO:0001583	missense	10575	exon1			CGGAAATGTTGCT		CCDS33206.1, CCDS58711.1	2p15	2011-09-02			ENSG00000115484	ENSG00000115484		"""Heat Shock Proteins / Chaperonins"""	1617	protein-coding gene	gene with protein product		605142				9819444	Standard	NM_001256721		Approved	Cctd	uc002sbo.4	P50991	OTTHUMG00000152166	ENST00000394440.3:c.112A>G	chr2.hg19:g.62115531T>C	ENSP00000377958:p.Ile38Val	40.0	0.0	.		50.0	23.0	.	NM_001256721	B2R6I3|B7Z8B1|F5H5W3|O14870|Q53QP9|Q96C51	Missense_Mutation	SNP	ENST00000394440.3	hg19	CCDS33206.1	.	.	.	.	.	.	.	.	.	.	T	17.95	3.513788	0.64522	0.0	1.16E-4	ENSG00000115484	ENST00000394440;ENST00000544079	T;T	0.12984	2.63;2.63	4.44	3.27	0.37495	.	0.053328	0.64402	D	0.000001	T	0.14570	0.0352	L	0.36672	1.1	0.80722	D	1	P;P	0.48834	0.916;0.847	P;B	0.47134	0.539;0.399	T	0.01520	-1.1334	10	0.87932	D	0	-12.7568	9.5232	0.39149	0.1581:0.0:0.0:0.8419	.	38;38	F5H5W3;P50991	.;TCPD_HUMAN	V	38	ENSP00000377958:I38V;ENSP00000443061:I38V	ENSP00000377958:I38V	I	-	1	0	CCT4	61969035	1.000000	0.71417	0.823000	0.32752	0.746000	0.42486	5.484000	0.66844	0.722000	0.32252	0.529000	0.55759	ATT	.	T|0.998;C|0.002	0.002	weak		0.677	CCT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325548.2		
ZSWIM2	151112	hgsc.bcm.edu	37	2	187693177	187693177	+	Missense_Mutation	SNP	T	T	A			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr2:187693177T>A	ENST00000295131.2	-	9	1475	c.1436A>T	c.(1435-1437)aAt>aTt	p.N479I		NM_182521.2	NP_872327.2	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM-type containing 2	479					apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein polyubiquitination (GO:0000209)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(28)|ovary(2)|prostate(4)|skin(6)|urinary_tract(1)	52			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)			TTTTTTTGAATTTGAATTATC	0.299																																					p.N479I		Atlas-SNP	.											.	ZSWIM2	119	.	0			c.A1436T						PASS	.						36.0	42.0	40.0					2																	187693177		2202	4298	6500	SO:0001583	missense	151112	exon9			TTTGAATTTGAAT	AK128006	CCDS33348.1	2q32.2	2008-02-05			ENSG00000163012	ENSG00000163012		"""Zinc fingers, SWIM-type"", ""Zinc fingers, ZZ-type"""	30990	protein-coding gene	gene with protein product						12477932	Standard	NM_182521		Approved	MGC33890, ZZZ2	uc002upu.1	Q8NEG5	OTTHUMG00000154259	ENST00000295131.2:c.1436A>T	chr2.hg19:g.187693177T>A	ENSP00000295131:p.Asn479Ile	43.0	0.0	.		43.0	7.0	.	NM_182521	B3KXV6|Q53SI3|Q57ZY3	Missense_Mutation	SNP	ENST00000295131.2	hg19	CCDS33348.1	.	.	.	.	.	.	.	.	.	.	T	6.741	0.505511	0.12822	.	.	ENSG00000163012	ENST00000295131	T	0.28895	1.59	5.6	1.83	0.25207	.	1.004620	0.08011	N	0.990290	T	0.21186	0.0510	L	0.32530	0.975	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.36890	-0.9729	10	0.87932	D	0	0.0079	1.3043	0.02085	0.1451:0.1617:0.1507:0.5425	.	479	Q8NEG5	ZSWM2_HUMAN	I	479	ENSP00000295131:N479I	ENSP00000295131:N479I	N	-	2	0	ZSWIM2	187401422	0.045000	0.20229	0.035000	0.18076	0.220000	0.24768	0.733000	0.26087	0.070000	0.16634	-0.376000	0.06991	AAT	.	.	.	none		0.299	ZSWIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334565.1	NM_182521	
RCHY1	25898	hgsc.bcm.edu	37	4	76439476	76439476	+	Silent	SNP	T	T	C			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr4:76439476T>C	ENST00000324439.5	-	1	419	c.21A>G	c.(19-21)gaA>gaG	p.E7E	RCHY1_ENST00000451788.1_Silent_p.E7E|THAP6_ENST00000514480.1_5'Flank|RCHY1_ENST00000512706.1_5'UTR|THAP6_ENST00000508105.1_5'Flank|THAP6_ENST00000504190.1_5'Flank|THAP6_ENST00000502620.1_5'Flank|RCHY1_ENST00000514021.1_Intron|THAP6_ENST00000507885.1_5'Flank|THAP6_ENST00000311638.3_5'Flank|RCHY1_ENST00000380840.2_Silent_p.E7E|THAP6_ENST00000507557.1_5'Flank|THAP6_ENST00000507556.1_5'Flank|THAP6_ENST00000380837.3_5'Flank|RCHY1_ENST00000513257.1_Silent_p.E7E	NM_001278536.1|NM_001278538.1|NM_001278539.1	NP_001265465.1|NP_001265467.1|NP_001265468.1	Q96PM5	ZN363_HUMAN	ring finger and CHY zinc finger domain containing 1, E3 ubiquitin protein ligase	7					positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|p53 binding (GO:0002039)|protein homodimerization activity (GO:0042803)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(2)|pancreas(1)	3			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			TGGCGCCATCTTCCCGGGCCG	0.602																																					p.E7E		Atlas-SNP	.											.	RCHY1	17	.	0			c.A21G						PASS	.						78.0	69.0	72.0					4																	76439476		2203	4300	6503	SO:0001819	synonymous_variant	25898	exon1			GCCATCTTCCCGG	AF255666	CCDS3567.1, CCDS34012.1, CCDS63990.1, CCDS63991.1, CCDS63992.1	4q21.1-q21.3	2014-02-17	2012-02-23	2004-03-30	ENSG00000163743	ENSG00000163743		"""RING-type (C3HC4) zinc fingers"""	17479	protein-coding gene	gene with protein product	"""androgen-receptor N-terminal-interacting protein"", ""p53-induced protein with a RING-H2 domain"", ""zinc finger, CHY-type"""	607680	"""zinc finger protein 363"", ""ring finger and CHY zinc finger domain containing 1"""	ZNF363		12654245	Standard	NM_015436		Approved	CHIMP, DKFZp586C1620, PRO1996, RNF199, ARNIP, PIRH2, ZCHY	uc003hik.3	Q96PM5	OTTHUMG00000130105	ENST00000324439.5:c.21A>G	chr4.hg19:g.76439476T>C		67.0	0.0	.		74.0	12.0	.	NM_001008925	B3KRG3|C7E541|C7E542|C7E543|D3YRV2|E7EMC8|E7ETW5|J3KPI0|Q2KN33|Q59GN7|Q86X26|Q96PR5	Silent	SNP	ENST00000324439.5	hg19	CCDS3567.1																																																																																			.	.	.	none		0.602	RCHY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252411.2	NM_015436	
GPR98	84059	hgsc.bcm.edu	37	5	90052799	90052799	+	Missense_Mutation	SNP	G	G	A	rs200576500	byFrequency	TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr5:90052799G>A	ENST00000405460.2	+	57	11857	c.11761G>A	c.(11761-11763)Gct>Act	p.A3921T		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	3921	Calx-beta 26. {ECO:0000255}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		CTTAAAGGGCGCTGGGGAAGT	0.388													G|||	2	0.000399361	0.0015	0.0	5008	,	,		16046	0.0		0.0	False		,,,				2504	0.0				p.A3921T		Atlas-SNP	.											.	GPR98	605	.	0			c.G11761A						PASS	.	G	THR/ALA	5,3673		0,5,1834	77.0	75.0	76.0		11761	2.3	0.1	5		76	0,8158		0,0,4079	yes	missense	GPR98	NM_032119.3	58	0,5,5913	AA,AG,GG		0.0,0.1359,0.0422	benign	3921/6307	90052799	5,11831	1839	4079	5918	SO:0001583	missense	84059	exon57			AAGGGCGCTGGGG	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.11761G>A	chr5.hg19:g.90052799G>A	ENSP00000384582:p.Ala3921Thr	110.0	0.0	.		109.0	26.0	.	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	hg19	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	G	0.526	-0.860029	0.02610	0.001359	0.0	ENSG00000164199	ENST00000405460;ENST00000296619	T	0.27256	1.68	5.3	2.27	0.28462	Na-Ca exchanger/integrin-beta4 (1);	0.732108	0.13525	N	0.381387	T	0.11879	0.0289	N	0.14661	0.345	0.22050	N	0.999396	B;B	0.23058	0.079;0.013	B;B	0.10450	0.005;0.002	T	0.25012	-1.0144	10	0.25751	T	0.34	.	4.1082	0.10047	0.2731:0.3558:0.3711:0.0	.	3921;3921	E7ETI5;Q8WXG9	.;GPR98_HUMAN	T	3921	ENSP00000384582:A3921T	ENSP00000296619:A3921T	A	+	1	0	GPR98	90088555	0.001000	0.12720	0.090000	0.20809	0.015000	0.08874	-0.111000	0.10807	0.694000	0.31654	0.467000	0.42956	GCT	.	.	.	weak		0.388	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
KDM3B	51780	hgsc.bcm.edu	37	5	137766032	137766032	+	Missense_Mutation	SNP	A	A	G			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr5:137766032A>G	ENST00000314358.5	+	22	5188	c.4988A>G	c.(4987-4989)tAt>tGt	p.Y1663C	KDM3B_ENST00000394866.1_Missense_Mutation_p.Y1319C|KDM3B_ENST00000542866.1_Missense_Mutation_p.Y695C	NM_016604.3	NP_057688	Q7LBC6	KDM3B_HUMAN	lysine (K)-specific demethylase 3B	1663	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(15)|liver(2)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	65						AAGCGACTCTATGAGGAGTAT	0.542																																					p.Y1663C		Atlas-SNP	.											.	KDM3B	177	.	0			c.A4988G						PASS	.						146.0	136.0	140.0					5																	137766032		2203	4300	6503	SO:0001583	missense	51780	exon22			GACTCTATGAGGA	AF251039	CCDS34242.1	5q31	2011-07-01	2009-04-06	2009-04-06	ENSG00000120733	ENSG00000120733		"""Chromatin-modifying enzymes / K-demethylases"""	1337	protein-coding gene	gene with protein product		609373	"""chromosome 5 open reading frame 7"", ""jumonji domain containing 1B"""	C5orf7, JMJD1B		15138608	Standard	NM_016604		Approved	KIAA1082, NET22	uc003lcy.1	Q7LBC6	OTTHUMG00000163469	ENST00000314358.5:c.4988A>G	chr5.hg19:g.137766032A>G	ENSP00000326563:p.Tyr1663Cys	142.0	0.0	.		191.0	27.0	.	NM_016604	A6H8X7|Q9BVH6|Q9BW93|Q9BZ52|Q9NYF4|Q9UPS0	Missense_Mutation	SNP	ENST00000314358.5	hg19	CCDS34242.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.178274	0.78564	.	.	ENSG00000120733	ENST00000314358;ENST00000545151;ENST00000394866;ENST00000542866	T;T;T	0.70631	-0.5;-0.5;-0.5	5.71	4.51	0.55191	Transcription factor jumonji/aspartyl beta-hydroxylase (2);Transcription factor jumonji (1);	0.056809	0.64402	D	0.000001	T	0.72550	0.3474	L	0.41824	1.3	0.58432	D	0.999997	P;P	0.46457	0.878;0.786	P;P	0.54544	0.575;0.755	T	0.72181	-0.4368	10	0.51188	T	0.08	-12.6174	11.8878	0.52613	0.8691:0.0:0.0:0.1309	.	1319;1663	Q7LBC6-2;Q7LBC6	.;KDM3B_HUMAN	C	1663;1453;1319;695	ENSP00000326563:Y1663C;ENSP00000378335:Y1319C;ENSP00000439462:Y695C	ENSP00000326563:Y1663C	Y	+	2	0	KDM3B	137793931	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	4.941000	0.63540	0.939000	0.37446	0.533000	0.62120	TAT	.	.	.	none		0.542	KDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373597.1	NM_016604	
C6orf211	79624	hgsc.bcm.edu	37	6	151789725	151789725	+	Missense_Mutation	SNP	T	T	G			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr6:151789725T>G	ENST00000367294.3	+	5	1065	c.806T>G	c.(805-807)tTg>tGg	p.L269W	C6orf211_ENST00000545879.1_Missense_Mutation_p.L150W	NM_024573.1	NP_078849.1	Q9H993	CF211_HUMAN	chromosome 6 open reading frame 211	269										breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(7)	15			BRCA - Breast invasive adenocarcinoma(37;0.183)	OV - Ovarian serous cystadenocarcinoma(155;5.27e-11)		GCCGACTTCTTGTTGTCCTCT	0.328																																					p.L269W		Atlas-SNP	.											.	C6orf211	30	.	0			c.T806G						PASS	.						132.0	138.0	136.0					6																	151789725		2203	4300	6503	SO:0001583	missense	79624	exon5			ACTTCTTGTTGTC	AJ420548	CCDS5233.1, CCDS69224.1	6q25.1	2013-01-07			ENSG00000146476	ENSG00000146476			17872	protein-coding gene	gene with protein product							Standard	NM_001286562		Approved	FLJ12910	uc003qok.1	Q9H993	OTTHUMG00000015838	ENST00000367294.3:c.806T>G	chr6.hg19:g.151789725T>G	ENSP00000356263:p.Leu269Trp	169.0	0.0	.		141.0	12.0	.	NM_024573	Q96FC6|Q9UFY5	Missense_Mutation	SNP	ENST00000367294.3	hg19	CCDS5233.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.593869	0.86953	.	.	ENSG00000146476	ENST00000367294;ENST00000545879	T;T	0.23552	1.9;1.9	6.02	6.02	0.97574	Domain of unknown function DUF89 (2);	0.141422	0.45126	D	0.000394	T	0.59959	0.2232	H	0.95884	3.735	0.58432	D	0.999993	D	0.89917	1.0	D	0.85130	0.997	T	0.74682	-0.3583	10	0.87932	D	0	.	16.5494	0.84464	0.0:0.0:0.0:1.0	.	269	Q9H993	CF211_HUMAN	W	269;150	ENSP00000356263:L269W;ENSP00000444121:L150W	ENSP00000356263:L269W	L	+	2	0	C6orf211	151831418	1.000000	0.71417	0.087000	0.20705	0.990000	0.78478	7.963000	0.87922	2.299000	0.77371	0.528000	0.53228	TTG	.	.	.	none		0.328	C6orf211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042724.1	NM_024573	
COL28A1	340267	hgsc.bcm.edu	37	7	7412962	7412963	+	Missense_Mutation	DNP	CC	CC	AT			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr7:7412962_7412963CC>AT	ENST00000399429.3	-	32	2714_2715	c.2574_2575GG>AT	c.(2572-2577)aaGGat>aaATat	p.D859Y		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	859	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		TTGAAGTCATCCTTGCTGGAGA	0.515																																					p.D859Y|p.K858K		Atlas-SNP	.											.	COL28A1	113	.	0			c.G2575T|c.G2574A						PASS	.																																			SO:0001583	missense	340267	exon32			AGTCATCCTTGCT|GTCATCCTTGCTG	AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"""Collagens"""	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.2574_2575delinsAT	chr7.hg19:g.7412962_7412963delinsAT	ENSP00000382356:p.Asp859Tyr	90.0|92.0	0.0	.		114.0|116.0	23.0|25.0	.	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Missense_Mutation|Silent	SNP	ENST00000399429.3	hg19	CCDS43553.1																																																																																			.	.	.	none		0.515	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763	
SVIL	6840	hgsc.bcm.edu	37	10	29788191	29788191	+	Splice_Site	SNP	C	C	A	rs372472784		TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr10:29788191C>A	ENST00000355867.4	-	18	4270	c.3518G>T	c.(3517-3519)cGg>cTg	p.R1173L	SVIL_ENST00000535393.1_Splice_Site_p.R87L|SVIL_ENST00000375398.2_Splice_Site_p.R1173L|SVIL_ENST00000375400.3_Splice_Site_p.R747L|SVIL_ENST00000538146.1_5'Flank	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	1173					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				TTCTGTGACCCGCTGTTCATA	0.507																																					p.R1173L		Atlas-SNP	.											.	SVIL	226	.	0			c.G3518T						PASS	.						79.0	68.0	72.0					10																	29788191		2203	4300	6503	SO:0001630	splice_region_variant	6840	exon18			GTGACCCGCTGTT	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"""archvillin"""	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.3517-1G>T	chr10.hg19:g.29788191C>A		91.0	0.0	.		97.0	4.0	.	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	hg19	CCDS7164.1	.	.	.	.	.	.	.	.	.	.	C	13.17	2.156495	0.38119	.	.	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867;ENST00000535393;ENST00000535994	T;T;T;T	0.14266	2.63;2.66;2.66;2.52	4.13	2.28	0.28536	.	0.324362	0.34853	N	0.003624	T	0.17195	0.0413	M	0.68952	2.095	0.80722	D	1	B;P;B	0.41159	0.403;0.74;0.38	B;B;B	0.41374	0.119;0.355;0.274	T	0.02042	-1.1224	10	0.59425	D	0.04	-10.9371	10.3423	0.43887	0.0:0.8378:0.0:0.1622	.	87;747;1173	F5H2Q5;O95425-2;O95425	.;.;SVIL_HUMAN	L	747;1173;1173;87;127	ENSP00000364549:R747L;ENSP00000364547:R1173L;ENSP00000348128:R1173L;ENSP00000445472:R87L	ENSP00000348128:R1173L	R	-	2	0	SVIL	29828197	0.999000	0.42202	0.998000	0.56505	0.608000	0.37181	2.104000	0.41815	0.417000	0.25871	-1.100000	0.02121	CGG	.	.	.	none		0.507	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		Missense_Mutation
AKAP3	10566	hgsc.bcm.edu	37	12	4736579	4736579	+	Missense_Mutation	SNP	G	G	C			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr12:4736579G>C	ENST00000545990.2	-	5	2013	c.1489C>G	c.(1489-1491)Cct>Gct	p.P497A	AKAP3_ENST00000228850.1_Missense_Mutation_p.P497A|RP11-500M8.7_ENST00000536588.1_Intron	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	497					acrosome reaction (GO:0007340)|cellular component movement (GO:0006928)|protein localization (GO:0008104)|single fertilization (GO:0007338)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	acrosomal vesicle (GO:0001669)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	protein kinase A binding (GO:0051018)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|liver(1)|lung(17)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	51						ATATCTTCAGGGTACTCAAAG	0.463																																					p.P497A		Atlas-SNP	.											.	AKAP3	212	.	0			c.C1489G						PASS	.						67.0	64.0	65.0					12																	4736579		2203	4300	6503	SO:0001583	missense	10566	exon4			CTTCAGGGTACTC	U85715	CCDS8531.1	12p13.3	2009-03-12				ENSG00000111254		"""A-kinase anchor proteins"""	373	protein-coding gene	gene with protein product	"""Fibrous Sheath Protein of 95 kDa"", ""cancer/testis antigen 82"""	604689				10334916, 10319321	Standard	NM_001278309		Approved	FSP95, SOB1, AKAP110, CT82	uc001qnb.4	O75969		ENST00000545990.2:c.1489C>G	chr12.hg19:g.4736579G>C	ENSP00000440994:p.Pro497Ala	48.0	0.0	.		47.0	10.0	.	NM_006422	O75945|Q86X01|Q9UM61	Missense_Mutation	SNP	ENST00000545990.2	hg19	CCDS8531.1	.	.	.	.	.	.	.	.	.	.	G	0.811	-0.752022	0.03041	.	.	ENSG00000111254	ENST00000228850;ENST00000545990	T;T	0.11821	2.74;2.74	4.5	-1.34	0.09143	A-kinase anchor 110kDa, C-terminal (1);	0.887861	0.09758	N	0.759675	T	0.13457	0.0326	M	0.68317	2.08	0.09310	N	1	B	0.29481	0.245	B	0.32090	0.14	T	0.40194	-0.9576	10	0.72032	D	0.01	0.0048	1.207	0.01896	0.1864:0.1329:0.362:0.3187	.	497	O75969	AKAP3_HUMAN	A	497	ENSP00000228850:P497A;ENSP00000440994:P497A	ENSP00000228850:P497A	P	-	1	0	AKAP3	4606840	0.215000	0.23574	0.000000	0.03702	0.001000	0.01503	1.832000	0.39151	-0.187000	0.10516	-0.136000	0.14681	CCT	.	.	.	none		0.463	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398911.2	NM_006422	
ATXN2	6311	hgsc.bcm.edu	37	12	111923516	111923516	+	Splice_Site	SNP	C	C	A			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr12:111923516C>A	ENST00000377617.3	-	17	3099		c.e17+1		AC002395.1_ENST00000581907.1_RNA|ATXN2_ENST00000542287.2_Splice_Site|ATXN2_ENST00000389153.4_Splice_Site|ATXN2_ENST00000550104.1_Splice_Site|ATXN2_ENST00000535949.1_Splice_Site|ATXN2_ENST00000608853.1_Splice_Site	NM_002973.3	NP_002964.3	Q99700	ATX2_HUMAN	ataxin 2						cell death (GO:0008219)|cerebellar Purkinje cell differentiation (GO:0021702)|cytoplasmic mRNA processing body assembly (GO:0033962)|homeostasis of number of cells (GO:0048872)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of receptor internalization (GO:0002091)|neuromuscular process (GO:0050905)|neuron projection morphogenesis (GO:0048812)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA transport (GO:0050658)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|trans-Golgi network (GO:0005802)	epidermal growth factor receptor binding (GO:0005154)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37						CTATGACTTACTTGCACGCCT	0.438																																					.		Atlas-SNP	.											.	ATXN2	99	.	0			c.2937+1G>T						PASS	.						165.0	142.0	150.0					12																	111923516		2203	4300	6503	SO:0001630	splice_region_variant	6311	exon18			GACTTACTTGCAC	U80749	CCDS31902.1	12q23-q24.1	2014-09-17	2004-08-12	2004-08-13	ENSG00000204842	ENSG00000204842		"""Ataxins"""	10555	protein-coding gene	gene with protein product	"""trinucleotide repeat containing 13"""	601517	"""spinocerebellar ataxia 2 (olivopontocerebellar ataxia 2, autosomal dominant, ataxin 2)"""	SCA2, TNRC13		8358438, 9225980	Standard	NM_002973		Approved	ATX2	uc001tsj.3	Q99700	OTTHUMG00000133475	ENST00000377617.3:c.2937+1G>T	chr12.hg19:g.111923516C>A		67.0	0.0	.		88.0	6.0	.	NM_002973	A6NLD4|Q6ZQZ7|Q99493	Splice_Site	SNP	ENST00000377617.3	hg19	CCDS31902.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.146986	0.77888	.	.	ENSG00000204842	ENST00000389154;ENST00000389153;ENST00000377617;ENST00000550104;ENST00000542287;ENST00000535949	.	.	.	5.71	5.71	0.89125	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.8673	0.96808	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ATXN2	110407899	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.076000	0.71267	2.709000	0.92574	0.655000	0.94253	.	.	.	.	none		0.438	ATXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257351.3	NM_002973	Intron
PTPN11	5781	hgsc.bcm.edu	37	12	112892458	112892458	+	Silent	SNP	T	T	C	rs78376169		TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr12:112892458T>C	ENST00000351677.2	+	5	814	c.616T>C	c.(616-618)Ttg>Ctg	p.L206L	PTPN11_ENST00000392597.1_Silent_p.L206L	NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	206	SH2 2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				abortive mitotic cell cycle (GO:0033277)|activation of MAPK activity (GO:0000187)|atrioventricular canal development (GO:0036302)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage checkpoint (GO:0000077)|ephrin receptor signaling pathway (GO:0048013)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|genitalia development (GO:0048806)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|hormone metabolic process (GO:0042445)|hormone-mediated signaling pathway (GO:0009755)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|multicellular organismal reproductive process (GO:0048609)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cortisol secretion (GO:0051463)|negative regulation of growth hormone secretion (GO:0060125)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ growth (GO:0035265)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of hormone secretion (GO:0046887)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of multicellular organism growth (GO:0040014)|regulation of protein export from nucleus (GO:0046825)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	insulin receptor binding (GO:0005158)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|SH3/SH2 adaptor activity (GO:0005070)	p.L206L(1)		NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(406)|kidney(2)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(3)|stomach(3)	451						GGTGGAAACATTGGGTACAGT	0.373			Mis		"""JMML, AML, MDS"""		Noonan Syndrome		Noonan syndrome																												p.L206L		Atlas-SNP	.		Dom	yes		12	12q24.1	5781	"""protein tyrosine phosphatase, non-receptor type 11"""	yes	L	PTPN11,NS,carcinoma,0,2	PTPN11	623	.	1	Substitution - coding silent(1)	stomach(1)	c.T616C						PASS	.						87.0	82.0	84.0					12																	112892458		2203	4300	6503	SO:0001819	synonymous_variant	5781	exon5	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	GAAACATTGGGTA	D13540	CCDS9163.1, CCDS58280.1	12q24.1	2014-09-17	2008-07-31		ENSG00000179295	ENSG00000179295		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"", ""SH2 domain containing"""	9644	protein-coding gene	gene with protein product		176876	"""Noonan syndrome 1"""	NS1		7894486, 1280823	Standard	NM_080601		Approved	BPTP3, SH-PTP2, SHP-2, PTP2C, SHP2	uc001ttx.3	Q06124	OTTHUMG00000134334	ENST00000351677.2:c.616T>C	chr12.hg19:g.112892458T>C		49.0	0.0	.		68.0	3.0	.	NM_080601	A8K1D9|Q96HD7	Silent	SNP	ENST00000351677.2	hg19	CCDS9163.1																																																																																			.	.	.	weak		0.373	PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259496.2		
FLII	2314	hgsc.bcm.edu	37	17	18149935	18149935	+	Silent	SNP	G	G	A			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr17:18149935G>A	ENST00000327031.4	-	23	3249	c.3024C>T	c.(3022-3024)ttC>ttT	p.F1008F	FLII_ENST00000545457.2_Silent_p.F953F|FLII_ENST00000579294.1_Silent_p.F997F|FLII_ENST00000578558.1_Intron|FLII_ENST00000379450.4_Silent_p.F922F	NM_002018.3	NP_002009.1	Q13045	FLII_HUMAN	flightless I homolog (Drosophila)	1008					multicellular organismal development (GO:0007275)|muscle contraction (GO:0006936)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)	actin binding (GO:0003779)			central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32	all_neural(463;0.228)					AGAGGCTCTCGAACTTCTTTT	0.627																																					p.F1008F		Atlas-SNP	.											.	FLII	79	.	0			c.C3024T						PASS	.						60.0	53.0	56.0					17																	18149935		2203	4300	6503	SO:0001819	synonymous_variant	2314	exon23			GCTCTCGAACTTC	U01184	CCDS11192.1, CCDS58521.1, CCDS58522.1	17p11.2	2008-07-18	2001-11-28		ENSG00000177731	ENSG00000177731			3750	protein-coding gene	gene with protein product		600362	"""flightless I (Drosophila) homolog"""			7825574	Standard	NM_002018		Approved	FLI, FLIL, Fli1, MGC39265	uc002gsr.2	Q13045	OTTHUMG00000059389	ENST00000327031.4:c.3024C>T	chr17.hg19:g.18149935G>A		19.0	0.0	.		52.0	13.0	.	NM_002018	B4DIL0|F5H407|J3QLG3	Silent	SNP	ENST00000327031.4	hg19	CCDS11192.1																																																																																			.	.	.	none		0.627	FLII-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132032.2	NM_002018	
FDXR	2232	hgsc.bcm.edu	37	17	72860612	72860612	+	Missense_Mutation	SNP	G	G	C			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr17:72860612G>C	ENST00000293195.5	-	8	870	c.792C>G	c.(790-792)gaC>gaG	p.D264E	FDXR_ENST00000420580.2_Missense_Mutation_p.D224E|FDXR_ENST00000583917.1_Intron|FDXR_ENST00000442102.2_Missense_Mutation_p.D307E|FDXR_ENST00000455107.2_Missense_Mutation_p.D220E|GRIN2C_ENST00000578159.1_5'Flank|FDXR_ENST00000581969.1_5'Flank|FDXR_ENST00000544854.1_Missense_Mutation_p.D212E|FDXR_ENST00000413947.2_Missense_Mutation_p.D295E|FDXR_ENST00000581530.1_Missense_Mutation_p.D270E|FDXR_ENST00000582944.1_Missense_Mutation_p.D256E	NM_001258014.1|NM_004110.3|NM_024417.2	NP_001244943.1|NP_004101.2|NP_077728.2	P22570	ADRO_HUMAN	ferredoxin reductase	264					cholesterol metabolic process (GO:0008203)|generation of precursor metabolites and energy (GO:0006091)|NADPH oxidation (GO:0070995)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ferredoxin-NADP+ reductase activity (GO:0004324)|NADPH binding (GO:0070402)|NADPH-adrenodoxin reductase activity (GO:0015039)			central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	16	all_lung(278;0.172)|Lung NSC(278;0.207)				Flavin adenine dinucleotide(DB03147)	CCTTGATCTTGTCCTGGAGAC	0.612											OREG0024720	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D307E		Atlas-SNP	.											.	FDXR	68	.	0			c.C921G						PASS	.						42.0	47.0	45.0					17																	72860612		2203	4300	6503	SO:0001583	missense	2232	exon8			GATCTTGTCCTGG	J03826	CCDS11707.1, CCDS58591.1, CCDS58592.1, CCDS58593.1, CCDS58594.1, CCDS58595.1, CCDS58596.1	17q25.1	2013-06-18			ENSG00000161513	ENSG00000161513	1.18.1.6		3642	protein-coding gene	gene with protein product	"""adrenodoxin-NADP(+) reductase"", ""adrenodoxin reductase"""	103270		ADXR		2969697	Standard	NM_001258014		Approved		uc010wrl.2	P22570	OTTHUMG00000179026	ENST00000293195.5:c.792C>G	chr17.hg19:g.72860612G>C	ENSP00000293195:p.Asp264Glu	50.0	0.0	.	1140	88.0	7.0	.	NM_001258012	B4DDI7|B4DHX5|B4DQQ4|B4DX24|B7Z7G2|E7EQC1|Q13716|Q4PJI0|Q9BU12	Missense_Mutation	SNP	ENST00000293195.5	hg19	CCDS58593.1	.	.	.	.	.	.	.	.	.	.	G	0.015	-1.556819	0.00910	.	.	ENSG00000161513	ENST00000420580;ENST00000544854;ENST00000293195;ENST00000455107;ENST00000442102;ENST00000413947	T;T;T;T;T	0.16324	2.35;2.35;2.35;2.35;2.35	4.65	2.43	0.29744	.	0.279368	0.40554	N	0.001071	T	0.04724	0.0128	N	0.04162	-0.26	0.33484	D	0.587776	B;B;B;B;B;B;B;B;B	0.06786	0.001;0.001;0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B;B;B	0.09377	0.004;0.003;0.0;0.0;0.0;0.0;0.0;0.0;0.0	T	0.31613	-0.9937	10	0.05351	T	0.99	-16.3668	2.2561	0.04055	0.1249:0.3442:0.3522:0.1788	.	224;307;295;262;212;264;256;264;270	B4DQQ4;B4DHX5;E7EQC1;B4DDI9;B7Z7G2;Q6GSK2;B4DX24;P22570;P22570-2	.;.;.;.;.;.;.;ADRO_HUMAN;.	E	224;212;270;220;307;295	ENSP00000414172:D224E;ENSP00000445432:D212E;ENSP00000390875:D220E;ENSP00000416515:D307E;ENSP00000408595:D295E	ENSP00000293195:D270E	D	-	3	2	FDXR	70372207	0.964000	0.33143	1.000000	0.80357	0.295000	0.27426	0.151000	0.16283	0.910000	0.36722	0.561000	0.74099	GAC	.	.	.	none		0.612	FDXR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000444449.1	NM_004110	
NLRP7	199713	hgsc.bcm.edu	37	19	55452315	55452315	+	Silent	SNP	C	C	T			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr19:55452315C>T	ENST00000590030.1	-	2	376	c.336G>A	c.(334-336)tcG>tcA	p.S112S	NLRP7_ENST00000446217.1_Silent_p.S140S|NLRP7_ENST00000592784.1_Silent_p.S112S|NLRP7_ENST00000448121.2_Silent_p.S112S|NLRP7_ENST00000588756.1_Silent_p.S112S|NLRP7_ENST00000340844.2_Silent_p.S112S|NLRP7_ENST00000328092.5_Silent_p.S112S			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	112							ATP binding (GO:0005524)			autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(17)|liver(1)|lung(33)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	73				GBM - Glioblastoma multiforme(193;0.0325)		TTGCTAACTCCGAGTCTTCTT	0.433																																					p.S112S		Atlas-SNP	.											.	NLRP7	411	.	0			c.G336A						PASS	.						239.0	189.0	206.0					19																	55452315		2203	4300	6503	SO:0001819	synonymous_variant	199713	exon3			TAACTCCGAGTCT	AF464765	CCDS12912.1, CCDS33109.1, CCDS46183.1	19q13.42	2008-02-05	2006-12-08	2006-12-08		ENSG00000167634		"""Nucleotide-binding domain and leucine rich repeat containing"""	22947	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 7"""	609661	"""NACHT, leucine rich repeat and PYD containing 7"""	NALP7		12563287, 12019269	Standard	NM_139176		Approved	PYPAF3, NOD12, PAN7, CLR19.4	uc002qii.4	Q8WX94		ENST00000590030.1:c.336G>A	chr19.hg19:g.55452315C>T		215.0	0.0	.		255.0	60.0	.	NM_001127255	E9PE16|Q32MH8|Q7RTR1	Silent	SNP	ENST00000590030.1	hg19	CCDS33109.1																																																																																			.	.	.	none		0.433	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176	
HELZ2	85441	hgsc.bcm.edu	37	20	62198513	62198513	+	Missense_Mutation	SNP	C	C	T			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr20:62198513C>T	ENST00000467148.1	-	6	2267	c.2198G>A	c.(2197-2199)cGg>cAg	p.R733Q	HELZ2_ENST00000427522.2_Missense_Mutation_p.R164Q|HELZ2_ENST00000479540.1_5'Flank	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	733	Interaction with THRAP3.				cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										GCGGCTCTGCCGCGCCACCTC	0.662																																					p.R733Q		Atlas-SNP	.											.	.	.	.	0			c.G2198A						PASS	.						42.0	45.0	44.0					20																	62198513		2201	4296	6497	SO:0001583	missense	85441	exon7			CTCTGCCGCGCCA	AB201715	CCDS13527.1, CCDS33508.1	20q13.33	2012-09-26			ENSG00000130589	ENSG00000130589			30021	protein-coding gene	gene with protein product	"""peroxisomal proliferator activated receptor A interacting complex 285"", ""PPARG-DBD-interacting protein 1"""	611265				11214970, 12189208, 16239304	Standard	NM_001037335		Approved	PDIP1, PRIC285, KIAA1769	uc002yfm.2	Q9BYK8	OTTHUMG00000032969	ENST00000467148.1:c.2198G>A	chr20.hg19:g.62198513C>T	ENSP00000417401:p.Arg733Gln	91.0	0.0	.		156.0	9.0	.	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	hg19	CCDS33508.1	.	.	.	.	.	.	.	.	.	.	C	0.028	-1.354760	0.01256	.	.	ENSG00000130589	ENST00000427522;ENST00000467148	D;D	0.92199	-2.99;-2.99	5.06	-10.1	0.00402	.	1.876900	0.02583	N	0.099118	T	0.75027	0.3794	N	0.04880	-0.145	0.09310	N	1	B;B	0.16603	0.018;0.014	B;B	0.06405	0.002;0.001	T	0.70296	-0.4911	10	0.05959	T	0.93	-12.0678	6.0815	0.19944	0.1162:0.2139:0.0711:0.5987	.	733;164	Q9BYK8;Q9BYK8-2	PR285_HUMAN;.	Q	164;733	ENSP00000393257:R164Q;ENSP00000417401:R733Q	ENSP00000393257:R164Q	R	-	2	0	RP4-697K14.7	61668957	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.789000	0.04609	-1.726000	0.01370	-1.028000	0.02416	CGG	.	.	.	none		0.662	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335	
RNMT	8731	hgsc.bcm.edu	37	18	13731629	13731630	+	Frame_Shift_Ins	INS	-	-	T			TCGA-BQ-5887-01A-11D-1961-08	TCGA-BQ-5887-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	1bd98e6b-f43c-424d-9d69-f2653ae70618	84765358-2446-4447-ab14-94b835dc736b	g.chr18:13731629_13731630insT	ENST00000383314.2	+	3	353_354	c.113_114insT	c.(112-117)gcttctfs	p.S39fs	RNMT_ENST00000592764.1_Frame_Shift_Ins_p.S39fs|RNMT_ENST00000262173.3_Frame_Shift_Ins_p.S39fs|RNMT_ENST00000589866.1_Frame_Shift_Ins_p.S39fs|RNMT_ENST00000535051.1_Intron|RNMT_ENST00000543302.2_Frame_Shift_Ins_p.S39fs			O43148	MCES_HUMAN	RNA (guanine-7-) methyltransferase	39					7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|RNA (guanine-N7)-methylation (GO:0036265)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	mRNA cap binding complex (GO:0005845)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|receptor complex (GO:0043235)	mRNA (guanine-N7-)-methyltransferase activity (GO:0004482)|RNA binding (GO:0003723)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|skin(2)	18						AACACAACAGCTTCTGGGACTG	0.371																																					p.A38fs	GBM(29;474 594 19092 36647 41529)	Atlas-INDEL	.											.	RNMT	42	.	0			c.113_114insT						PASS	.																																			SO:0001589	frameshift_variant	8731	exon3			.	AF067791	CCDS11867.1	18p11.21	2008-05-14			ENSG00000101654	ENSG00000101654	2.1.1.56		10075	protein-coding gene	gene with protein product		603514				9828141, 9705270	Standard	NM_003799		Approved	RG7MT1	uc002ksl.1	O43148	OTTHUMG00000131718	ENST00000383314.2:c.115dupT	chr18.hg19:g.13731631_13731631dupT	ENSP00000372804:p.Ser39fs	222.0	0.0	0		140.0	31.0	0.221429	NM_003799	B0YJ90|D3DUJ5|O94996|Q9UIJ9	Frame_Shift_Ins	INS	ENST00000383314.2	hg19	CCDS11867.1																																																																																			.	.	.	none		0.371	RNMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254636.1	NM_003799	
