#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_ACHILLES_Lineage_Results_Top_Genes	i_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	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_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	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_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	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_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	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_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	i_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
OTUD3	23252	broad.mit.edu	37	1	20232993	20232993	+	Missense_Mutation	SNP	G	G	A			TCGA-RW-A7D0-01A-11D-A35D-08	TCGA-RW-A7D0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99293d59-23c9-46cf-bdaf-00c2b51a02bf	023921e3-188f-4540-9b31-b6ebf8d992fd	g.chr1:20232993G>A	ENST00000375120.3	+	7	905	c.904G>A	c.(904-906)Ggc>Agc	p.G302S		NM_015207.1	NP_056022.1	Q5T2D3	OTUD3_HUMAN	OTU deubiquitinase 3	302					protein K11-linked deubiquitination (GO:0035871)|protein K6-linked deubiquitination (GO:0044313)		ubiquitin-specific protease activity (GO:0004843)			breast(1)|kidney(2)|large_intestine(4)|lung(1)|skin(1)	9		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000276)|Lung NSC(340;0.000338)|Breast(348;0.000812)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.12e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000142)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.000408)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		GGAGGAGGGTGGCAGTGGTGC	0.468																																						ENST00000375120.3																			0				breast(1)|kidney(2)|large_intestine(4)|lung(1)|skin(1)	9						c.(904-906)Ggc>Agc		OTU domain containing 3							101.0	108.0	106.0					1																	20232993		1997	4191	6188	SO:0001583	missense	23252							g.chr1:20232993G>A	AB007928	CCDS41279.1	1p36.13	2014-02-24	2014-02-24		ENSG00000169914	ENSG00000169914		"""OTU domain containing"""	29038	protein-coding gene	gene with protein product		611758	"""OTU domain containing 3"""			9455484, 23827681	Standard	NM_015207		Approved	KIAA0459, DUBA4	uc001bcs.4	Q5T2D3	OTTHUMG00000002696	ENST00000375120.3:c.904G>A	1.37:g.20232993G>A	ENSP00000364261:p.Gly302Ser						p.G302S	NM_015207.1	NP_056022.1	Q5T2D3	OTUD3_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.12e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000142)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.000408)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	7	905	+		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000276)|Lung NSC(340;0.000338)|Breast(348;0.000812)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)	302					O75047	Missense_Mutation	SNP	ENST00000375120.3	37	c.904G>A	CCDS41279.1	.	.	.	.	.	.	.	.	.	.	G	15.93	2.976893	0.53720	.	.	ENSG00000169914	ENST00000375120	T	0.29397	1.57	5.78	5.78	0.91487	.	0.102913	0.64402	D	0.000003	T	0.29423	0.0733	L	0.40543	1.245	0.44006	D	0.996713	B	0.25235	0.121	B	0.26310	0.068	T	0.02596	-1.1136	10	0.37606	T	0.19	.	16.7276	0.85427	0.0:0.0:1.0:0.0	.	302	Q5T2D3	OTUD3_HUMAN	S	302	ENSP00000364261:G302S	ENSP00000364261:G302S	G	+	1	0	OTUD3	20105580	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.218000	0.58554	2.729000	0.93468	0.650000	0.86243	GGC		0.468	OTUD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007655.1			5	8	0	0	0	1	0	5	8				
ZFP2	80108	broad.mit.edu	37	5	178358732	178358732	+	Missense_Mutation	SNP	A	A	G			TCGA-RW-A7D0-01A-11D-A35D-08	TCGA-RW-A7D0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99293d59-23c9-46cf-bdaf-00c2b51a02bf	023921e3-188f-4540-9b31-b6ebf8d992fd	g.chr5:178358732A>G	ENST00000361362.2	+	5	948	c.418A>G	c.(418-420)Att>Gtt	p.I140V	ZFP2_ENST00000520301.1_Missense_Mutation_p.I140V|ZFP2_ENST00000503510.2_Missense_Mutation_p.I140V|ZFP2_ENST00000523286.1_Missense_Mutation_p.I140V	NM_030613.2	NP_085116.2	Q6ZN57	ZFP2_HUMAN	ZFP2 zinc finger protein	140					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	20	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.00655)|GBM - Glioblastoma multiforme(465;0.0302)|OV - Ovarian serous cystadenocarcinoma(192;0.0615)|Epithelial(171;0.111)		GAAACACTTCATTGAACGATC	0.413																																						ENST00000361362.2																			0				NS(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	20						c.(418-420)Att>Gtt		ZFP2 zinc finger protein							59.0	63.0	62.0					5																	178358732		2203	4300	6503	SO:0001583	missense	80108				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr5:178358732A>G	AK025281	CCDS4440.1	5q35.3	2013-01-08	2012-11-27		ENSG00000198939	ENSG00000198939		"""Zinc fingers, C2H2-type"""	26138	protein-coding gene	gene with protein product			"""zinc finger protein 2 homolog (mouse)"""				Standard	NM_030613		Approved	FLJ21628, ZNF751	uc003mjn.1	Q6ZN57	OTTHUMG00000130885	ENST00000361362.2:c.418A>G	5.37:g.178358732A>G	ENSP00000354453:p.Ile140Val					ZFP2_ENST00000520301.1_Missense_Mutation_p.I140V|ZFP2_ENST00000523286.1_Missense_Mutation_p.I140V|ZFP2_ENST00000503510.2_Missense_Mutation_p.I140V	p.I140V	NM_030613.2	NP_085116.2	Q6ZN57	ZFP2_HUMAN	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.00655)|GBM - Glioblastoma multiforme(465;0.0302)|OV - Ovarian serous cystadenocarcinoma(192;0.0615)|Epithelial(171;0.111)	5	948	+	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	140					A5PLN5|B7ZM23|Q9H6Z6	Missense_Mutation	SNP	ENST00000361362.2	37	c.418A>G	CCDS4440.1	.	.	.	.	.	.	.	.	.	.	a	9.292	1.050907	0.19827	.	.	ENSG00000198939	ENST00000361362;ENST00000520301;ENST00000523286;ENST00000503510	T;T;T;T	0.05717	3.4;3.4;3.4;3.4	4.71	4.71	0.59529	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.255631	0.20520	N	0.090703	T	0.03915	0.0110	N	0.03294	-0.36	0.27513	N	0.951621	B	0.24675	0.109	B	0.30943	0.122	T	0.38134	-0.9675	10	0.38643	T	0.18	-5.6166	12.1786	0.54199	1.0:0.0:0.0:0.0	.	140	Q6ZN57	ZFP2_HUMAN	V	140	ENSP00000354453:I140V;ENSP00000430980:I140V;ENSP00000430531:I140V;ENSP00000438114:I140V	ENSP00000354453:I140V	I	+	1	0	ZFP2	178291338	0.001000	0.12720	1.000000	0.80357	0.840000	0.47671	1.373000	0.34272	1.963000	0.57068	0.482000	0.46254	ATT		0.413	ZFP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253470.2	NM_030613		25	29	0	0	0	1	0	25	29				
LIMS2	55679	broad.mit.edu	37	2	128412102	128412102	+	Silent	SNP	G	G	A			TCGA-RW-A7D0-01A-11D-A35D-08	TCGA-RW-A7D0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99293d59-23c9-46cf-bdaf-00c2b51a02bf	023921e3-188f-4540-9b31-b6ebf8d992fd	g.chr2:128412102G>A	ENST00000355119.4	-	4	420	c.255C>T	c.(253-255)ggC>ggT	p.G85G	LIMS2_ENST00000409455.1_Silent_p.G80G|LIMS2_ENST00000324938.5_Silent_p.G109G|LIMS2_ENST00000545738.2_Silent_p.G107G|LIMS2_ENST00000410011.1_Silent_p.G80G|LIMS2_ENST00000409808.2_Silent_p.G80G	NM_001161403.1	NP_001154875.1	Q7Z4I7	LIMS2_HUMAN	LIM and senescent cell antigen-like domains 2	85	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|negative regulation of apoptotic process (GO:0043066)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of neural precursor cell proliferation (GO:2000178)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|single organismal cell-cell adhesion (GO:0016337)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0681)		TGATGACGCGGCCAATGATGA	0.607																																						ENST00000409455.1																			0				endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						c.(238-240)ggC>ggT		LIM and senescent cell antigen-like domains 2							145.0	131.0	136.0					2																	128412102		2203	4300	6503	SO:0001819	synonymous_variant	55679				cell junction assembly	cytosol|focal adhesion|nucleus	zinc ion binding	g.chr2:128412102G>A	AF520987	CCDS2147.1, CCDS54394.1, CCDS54395.1, CCDS54396.1, CCDS58725.1	2q21.1	2008-02-05			ENSG00000072163	ENSG00000072163			16084	protein-coding gene	gene with protein product		607908					Standard	NM_017980		Approved		uc002tox.3	Q7Z4I7	OTTHUMG00000131529	ENST00000355119.4:c.255C>T	2.37:g.128412102G>A						LIMS2_ENST00000409808.2_Silent_p.G80G|LIMS2_ENST00000355119.4_Silent_p.G85G|LIMS2_ENST00000324938.5_Silent_p.G109G|LIMS2_ENST00000545738.2_Silent_p.G107G|LIMS2_ENST00000410011.1_Silent_p.G80G	p.G80G			Q7Z4I7	LIMS2_HUMAN		BRCA - Breast invasive adenocarcinoma(221;0.0681)	4	875	-	Colorectal(110;0.1)		85			LIM zinc-binding 2.		A6NLH0|B4DMV1|F5H6E6|Q7Z4I2|Q7Z4I6|Q7Z4I8|Q8NFE7|Q9HA13	Silent	SNP	ENST00000355119.4	37	c.240C>T	CCDS54395.1																																																																																				0.607	LIMS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331133.2	NM_017980		4	86	0	0	0	1	0	4	86				
PRMT1	3276	broad.mit.edu	37	19	50185323	50185323	+	Splice_Site	SNP	G	G	C			TCGA-RW-A7D0-01A-11D-A35D-08	TCGA-RW-A7D0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99293d59-23c9-46cf-bdaf-00c2b51a02bf	023921e3-188f-4540-9b31-b6ebf8d992fd	g.chr19:50185323G>C	ENST00000391851.4	+	3	423		c.e3+1		PRMT1_ENST00000454376.2_Splice_Site|MIR5088_ENST00000581740.1_RNA|PRMT1_ENST00000532489.1_Splice_Site	NM_198318.4	NP_938074.2	Q99873	ANM1_HUMAN	protein arginine methyltransferase 1						cell surface receptor signaling pathway (GO:0007166)|histone H4-R3 methylation (GO:0043985)|histone methylation (GO:0016571)|negative regulation of megakaryocyte differentiation (GO:0045653)|neuron projection development (GO:0031175)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|protein methylation (GO:0006479)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H4-R3 specific) (GO:0044020)|identical protein binding (GO:0042802)|methyltransferase activity (GO:0008168)|N-methyltransferase activity (GO:0008170)|poly(A) RNA binding (GO:0044822)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|ovary(2)	12		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00103)|GBM - Glioblastoma multiforme(134;0.012)		GGTCATCGGGGTGAGTCTCCA	0.682																																						ENST00000532489.1																			0				cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|ovary(2)	12						c.e4+1		protein arginine methyltransferase 1							36.0	39.0	38.0					19																	50185323		2202	4299	6501	SO:0001630	splice_region_variant	3276					cytoplasm	protein methyltransferase activity	g.chr19:50185323G>C	D66904	CCDS42592.1, CCDS46145.1, CCDS74425.1	19q13	2014-06-12	2006-02-16	2006-02-16	ENSG00000126457	ENSG00000126457	2.1.1.125	"""Protein arginine methyltransferases"""	5187	protein-coding gene	gene with protein product		602950	"""HMT1 (hnRNP methyltransferase, S. cerevisiae)-like 2"", ""HMT1 hnRNP methyltransferase-like 2 (S. cerevisiae)"""	HRMT1L2		9545638	Standard	NM_001207042		Approved	HCP1, ANM1	uc010enf.2	Q99873	OTTHUMG00000167568	ENST00000391851.4:c.294+1G>C	19.37:g.50185323G>C						PRMT1_ENST00000454376.2_Splice_Site|PRMT1_ENST00000391851.4_Splice_Site				Q8WUW5	Q8WUW5_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.00103)|GBM - Glioblastoma multiforme(134;0.012)	4	716	+		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)						B4E3C3|G5E9B6|Q15529|Q2VP93|Q6LEU5|Q8WUW5|Q99872|Q99874|Q9NZ04|Q9NZ05|Q9NZ06	Splice_Site	SNP	ENST00000391851.4	37		CCDS42592.1	.	.	.	.	.	.	.	.	.	.	g	14.23	2.473067	0.43942	.	.	ENSG00000126457	ENST00000529284;ENST00000532489;ENST00000527382;ENST00000534465;ENST00000391851;ENST00000449059;ENST00000454376;ENST00000524771;ENST00000529836;ENST00000526224;ENST00000527412	.	.	.	4.6	4.6	0.57074	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2955	0.73902	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PRMT1	54877135	1.000000	0.71417	1.000000	0.80357	0.464000	0.32679	9.215000	0.95146	2.560000	0.86352	0.549000	0.68633	.		0.682	PRMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395065.1	NM_001536	Intron	3	42	0	0	0	1	0	3	42				
PREX2	80243	broad.mit.edu	37	8	68934377	68934377	+	Splice_Site	SNP	T	T	A			TCGA-RW-A7D0-01A-11D-A35D-08	TCGA-RW-A7D0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99293d59-23c9-46cf-bdaf-00c2b51a02bf	023921e3-188f-4540-9b31-b6ebf8d992fd	g.chr8:68934377T>A	ENST00000288368.4	+	4	718		c.e4+2		PREX2_ENST00000529398.1_Splice_Site	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2						adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						TTTCTTTTGGTAAGTGTATAT	0.338																																						ENST00000288368.4																			0				NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						c.e4+2		phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2							98.0	93.0	94.0					8																	68934377		2202	4300	6502	SO:0001630	splice_region_variant	80243				G-protein coupled receptor protein signaling pathway|intracellular signal transduction	intracellular	protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity	g.chr8:68934377T>A	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"""Rho guanine nucleotide exchange factors"""	22950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 129"""	612139	"""DEP domain containing 2"""	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.441+2T>A	8.37:g.68934377T>A						PREX2_ENST00000529398.1_Splice_Site		NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN			4	718	+								B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Splice_Site	SNP	ENST00000288368.4	37		CCDS6201.1	.	.	.	.	.	.	.	.	.	.	T	16.08	3.022780	0.54683	.	.	ENSG00000046889	ENST00000288368;ENST00000396539;ENST00000354677	.	.	.	6.04	4.9	0.64082	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.6392	0.51222	0.0:0.0685:0.0:0.9315	.	.	.	.	.	-1	.	.	.	+	.	.	PREX2	69096931	1.000000	0.71417	1.000000	0.80357	0.541000	0.35023	5.950000	0.70265	2.317000	0.78254	0.460000	0.39030	.		0.338	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170	Intron	11	19	0	0	0	1	0	11	19				
SPAG4	6676	broad.mit.edu	37	20	34205716	34205716	+	Silent	SNP	C	C	T			TCGA-RW-A7D0-01A-11D-A35D-08	TCGA-RW-A7D0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99293d59-23c9-46cf-bdaf-00c2b51a02bf	023921e3-188f-4540-9b31-b6ebf8d992fd	g.chr20:34205716C>T	ENST00000374273.3	+	4	604	c.492C>T	c.(490-492)atC>atT	p.I164I	SPAG4_ENST00000462896.1_Intron	NM_003116.1	NP_003107.1	Q9NPE6	SPAG4_HUMAN	sperm associated antigen 4	164					spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|motile cilium (GO:0031514)	structural molecule activity (GO:0005198)	p.I164I(1)		NS(1)|cervix(5)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)	21	Lung NSC(9;0.0053)|all_lung(11;0.00785)		BRCA - Breast invasive adenocarcinoma(18;0.0127)			TCTGTTCCATCCGCTTCCTGT	0.637																																						ENST00000374273.3																			1	Substitution - coding silent(1)	p.I164I(1)	lung(1)	NS(1)|cervix(5)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)	21						c.(490-492)atC>atT		sperm associated antigen 4							73.0	71.0	72.0					20																	34205716		2203	4300	6503	SO:0001819	synonymous_variant	6676				spermatogenesis	cilium|flagellar axoneme|integral to membrane	structural molecule activity	g.chr20:34205716C>T	AF043344	CCDS13259.1	20q11.2	2010-04-23			ENSG00000061656	ENSG00000061656			11214	protein-coding gene	gene with protein product	"""acrosomal protein ACR55"", ""Sad1 and UNC84 domain containing 4"", ""cancer/testis antigen 127"""	603038				9691178, 10373309	Standard	NM_003116		Approved	SUN4, CT127	uc002xdb.1	Q9NPE6	OTTHUMG00000032352	ENST00000374273.3:c.492C>T	20.37:g.34205716C>T						SPAG4_ENST00000462896.1_Intron	p.I164I	NM_003116.1	NP_003107.1	Q9NPE6	SPAG4_HUMAN	BRCA - Breast invasive adenocarcinoma(18;0.0127)		4	604	+	Lung NSC(9;0.0053)|all_lung(11;0.00785)		164					O43648	Silent	SNP	ENST00000374273.3	37	c.492C>T	CCDS13259.1																																																																																				0.637	SPAG4-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078896.1	NM_003116		22	46	0	0	0	1	0	22	46				
RICTOR	253260	broad.mit.edu	37	5	38950323	38950323	+	Silent	SNP	C	C	T			TCGA-RW-A7D0-01A-11D-A35D-08	TCGA-RW-A7D0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99293d59-23c9-46cf-bdaf-00c2b51a02bf	023921e3-188f-4540-9b31-b6ebf8d992fd	g.chr5:38950323C>T	ENST00000357387.3	-	31	3657	c.3627G>A	c.(3625-3627)acG>acA	p.T1209T	RICTOR_ENST00000296782.5_Silent_p.T1209T	NM_152756.3	NP_689969.2			RPTOR independent companion of MTOR, complex 2											NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|prostate(3)|skin(5)	75	all_lung(31;0.000396)					TATGTGAGCTCGTTGAACTTT	0.393																																						ENST00000357387.3																			0				NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|prostate(3)|skin(5)	75						c.(3625-3627)acG>acA		RPTOR independent companion of MTOR, complex 2							216.0	212.0	214.0					5																	38950323		2202	4298	6500	SO:0001819	synonymous_variant	253260				actin cytoskeleton reorganization|embryo development|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of TOR signaling cascade|regulation of protein kinase B signaling cascade|T cell costimulation	cytosol|TORC2 complex	protein binding	g.chr5:38950323C>T		CCDS34148.1, CCDS68861.1	5p13.1	2009-07-09			ENSG00000164327	ENSG00000164327			28611	protein-coding gene	gene with protein product	"""rapamycin-insensitive companion of mTOR"", ""pianissimo"""	609022				12477932	Standard	XM_005248278		Approved	MGC39830, AVO3, PIA, KIAA1999	uc003jlp.2	Q6R327	OTTHUMG00000162037	ENST00000357387.3:c.3627G>A	5.37:g.38950323C>T						RICTOR_ENST00000296782.5_Silent_p.T1209T	p.T1209T	NM_152756.3	NP_689969.2	Q6R327	RICTR_HUMAN			31	3657	-	all_lung(31;0.000396)		1209						Silent	SNP	ENST00000357387.3	37	c.3627G>A	CCDS34148.1																																																																																				0.393	RICTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366985.1	NM_152756		4	178	0	0	0	1	0	4	178				
KRTAP10-8	386681	broad.mit.edu	37	21	46032334	46032334	+	Missense_Mutation	SNP	C	C	T	rs141295608	byFrequency	TCGA-RW-A7D0-01A-11D-A35D-08	TCGA-RW-A7D0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99293d59-23c9-46cf-bdaf-00c2b51a02bf	023921e3-188f-4540-9b31-b6ebf8d992fd	g.chr21:46032334C>T	ENST00000334662.2	+	1	339	c.317C>T	c.(316-318)cCg>cTg	p.P106L	TSPEAR_ENST00000323084.4_Intron	NM_198695.2	NP_941968.2	P60410	KR108_HUMAN	keratin associated protein 10-8	106	19 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|skin(1)	17						AGCTGCCAGCCGGCTTGCTGC	0.642													-|||	2	0.000399361	0.0015	0.0	5008	,	,		21158	0.0		0.0	False		,,,				2504	0.0					ENST00000334662.2																			0				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|skin(1)	17						c.(316-318)cCg>cTg		keratin associated protein 10-8		C	,LEU/PRO	6,4400	14.3+/-33.2	0,6,2197	104.0	93.0	97.0		,317	0.5	0.9	21	dbSNP_134	97	0,8600		0,0,4300	no	intron,missense	TSPEAR,KRTAP10-8	NM_144991.2,NM_198695.2	,98	0,6,6497	TT,TC,CC		0.0,0.1362,0.0461	,benign	,106/260	46032334	6,13000	2203	4300	6503	SO:0001583	missense	386681					keratin filament		g.chr21:46032334C>T	AB076355	CCDS13713.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000187766	ENSG00000187766		"""Keratin associated proteins"""	20525	protein-coding gene	gene with protein product			"""keratin associated protein 18-8"""	KRTAP18-8			Standard	NM_198695		Approved	KRTAP18.8, KAP10.8	uc002zfo.1	P60410	OTTHUMG00000057632	ENST00000334662.2:c.317C>T	21.37:g.46032334C>T	ENSP00000335565:p.Pro106Leu					TSPEAR_ENST00000323084.4_Intron	p.P106L	NM_198695.2	NP_941968.2	P60410	KR108_HUMAN			1	339	+			106			19 X 5 AA repeats of C-C-X(3).		A0JNW4	Missense_Mutation	SNP	ENST00000334662.2	37	c.317C>T	CCDS13713.1	.	.	.	.	.	.	.	.	.	.	c	10.94	1.492577	0.26774	0.001362	0.0	ENSG00000187766	ENST00000334662	T	0.01228	5.14	3.78	0.534	0.17127	.	.	.	.	.	T	0.02610	0.0079	M	0.77103	2.36	0.24354	N	0.994902	B	0.16802	0.019	B	0.10450	0.005	T	0.27502	-1.0072	9	0.59425	D	0.04	.	7.9219	0.29850	0.1596:0.7348:0.0:0.1056	.	106	P60410	KR108_HUMAN	L	106	ENSP00000335565:P106L	ENSP00000335565:P106L	P	+	2	0	KRTAP10-8	44856762	0.024000	0.19004	0.914000	0.36105	0.870000	0.49936	0.350000	0.20079	0.204000	0.20548	-1.305000	0.01319	CCG		0.642	KRTAP10-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128035.1	NM_198695		30	61	0	0	0	1	0	30	61				
FAM131B	9715	broad.mit.edu	37	7	143053779	143053779	+	Missense_Mutation	SNP	G	G	A			TCGA-RW-A7D0-01A-11D-A35D-08	TCGA-RW-A7D0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99293d59-23c9-46cf-bdaf-00c2b51a02bf	023921e3-188f-4540-9b31-b6ebf8d992fd	g.chr7:143053779G>A	ENST00000409408.1	-	6	2571	c.863C>T	c.(862-864)gCg>gTg	p.A288V	FAM131B_ENST00000409222.3_Missense_Mutation_p.A288V|FAM131B_ENST00000409346.1_Missense_Mutation_p.A288V|FAM131B_ENST00000409578.1_Missense_Mutation_p.A304V|FAM131B_ENST00000443739.2_Missense_Mutation_p.A316V			Q86XD5	F131B_HUMAN	family with sequence similarity 131, member B	288										breast(1)|endometrium(4)|large_intestine(3)|lung(13)|ovary(1)|skin(2)	24	Melanoma(164;0.205)					CCGGCATCCCGCATCCTCTTC	0.627																																						ENST00000409408.1																			0				breast(1)|endometrium(4)|large_intestine(3)|lung(13)|ovary(1)|skin(2)	24						c.(862-864)gCg>gTg		family with sequence similarity 131, member B							154.0	163.0	160.0					7																	143053779		2203	4300	6503	SO:0001583	missense	9715							g.chr7:143053779G>A	BC045611	CCDS5882.1, CCDS47734.1	7q34	2007-03-20			ENSG00000159784	ENSG00000159784			22202	protein-coding gene	gene with protein product							Standard	NM_014690		Approved	KIAA0773	uc010lpa.3	Q86XD5	OTTHUMG00000152697	ENST00000409408.1:c.863C>T	7.37:g.143053779G>A	ENSP00000387017:p.Ala288Val					FAM131B_ENST00000409578.1_Missense_Mutation_p.A304V|FAM131B_ENST00000409346.1_Missense_Mutation_p.A288V|FAM131B_ENST00000409222.3_Missense_Mutation_p.A288V|FAM131B_ENST00000443739.2_Missense_Mutation_p.A316V	p.A288V			Q86XD5	F131B_HUMAN			6	2571	-	Melanoma(164;0.205)		288					A4D2H6|A6NDW3|A8K605|B8ZZN2|D3DXE3|J3KQX2|Q7L0D6|Q86T97	Missense_Mutation	SNP	ENST00000409408.1	37	c.863C>T	CCDS5882.1	.	.	.	.	.	.	.	.	.	.	G	12.60	1.986429	0.35036	.	.	ENSG00000159784	ENST00000443739;ENST00000409578;ENST00000409346;ENST00000452076;ENST00000409408;ENST00000409222	T;T;T;T;T	0.20738	2.05;2.05;2.05;2.05;2.05	5.63	4.74	0.60224	.	0.066130	0.64402	D	0.000020	T	0.07728	0.0194	N	0.02960	-0.455	0.34853	D	0.741856	B;B	0.16802	0.009;0.019	B;B	0.08055	0.003;0.003	T	0.28586	-1.0039	10	0.14252	T	0.57	-0.1234	8.9058	0.35523	0.1855:0.0:0.8145:0.0	.	304;288	Q86XD5-2;Q86XD5	.;F131B_HUMAN	V	316;304;288;292;288;288	ENSP00000410603:A316V;ENSP00000386568:A304V;ENSP00000386984:A288V;ENSP00000387017:A288V;ENSP00000387147:A288V	ENSP00000387147:A288V	A	-	2	0	FAM131B	142763901	0.992000	0.36948	0.962000	0.40283	0.969000	0.65631	2.772000	0.47678	2.644000	0.89710	0.655000	0.94253	GCG		0.627	FAM131B-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328057.1	NM_014690		4	151	0	0	0	1	0	4	151				
NCOA3	8202	broad.mit.edu	37	20	46279860	46279860	+	Silent	SNP	G	G	A	rs151060280	byFrequency	TCGA-RW-A7D0-01A-11D-A35D-08	TCGA-RW-A7D0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99293d59-23c9-46cf-bdaf-00c2b51a02bf	023921e3-188f-4540-9b31-b6ebf8d992fd	g.chr20:46279860G>A	ENST00000371998.3	+	20	3977	c.3786G>A	c.(3784-3786)caG>caA	p.Q1262Q	NCOA3_ENST00000341724.6_Silent_p.Q1188Q|NCOA3_ENST00000372004.3_Silent_p.Q1258Q|NCOA3_ENST00000371997.3_Silent_p.Q1253Q			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	1262	Acetyltransferase.|Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.Q1262Q(1)		breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						agcagcagcagcagcaacagc	0.567																																						ENST00000372004.3																			1	Substitution - coding silent(1)	p.Q1262Q(1)	endometrium(1)	breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						c.(3772-3774)caG>caA		nuclear receptor coactivator 3		G	,,,	10,4396	11.4+/-27.6	1,8,2194	53.0	58.0	56.0		3783,3759,3774,3786	-0.1	0.1	20	dbSNP_134	56	12,8588	9.1+/-34.3	0,12,4288	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NCOA3	NM_001174087.1,NM_001174088.1,NM_006534.3,NM_181659.2	,,,	1,20,6482	AA,AG,GG		0.1395,0.227,0.1692	,,,	1261/1424,1253/1416,1258/1421,1262/1425	46279860	22,12984	2203	4300	6503	SO:0001819	synonymous_variant	8202				androgen receptor signaling pathway|cellular lipid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleoplasm	androgen receptor binding|histone acetyltransferase activity|ligand-dependent nuclear receptor binding|protein N-terminus binding|signal transducer activity|thyroid hormone receptor binding	g.chr20:46279860G>A	AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7670	protein-coding gene	gene with protein product	"""receptor-associated coactivator 3"", ""thyroid hormone receptor activator molecule 1"""	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.3786G>A	20.37:g.46279860G>A						NCOA3_ENST00000341724.6_Silent_p.Q1188Q|NCOA3_ENST00000371997.3_Silent_p.Q1253Q|NCOA3_ENST00000371998.3_Silent_p.Q1262Q	p.Q1258Q	NM_001174087.1|NM_001174088.1|NM_006534.3|NM_181659.2	NP_001167558.1|NP_001167559.1|NP_006525.2|NP_858045.1	Q9Y6Q9	NCOA3_HUMAN			20	3990	+			1262			Acetyltransferase.|Poly-Gln.		A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Silent	SNP	ENST00000371998.3	37	c.3774G>A	CCDS13407.1																																																																																				0.567	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534		6	56	0	0	0	1	0	6	56				
NF1	4763	broad.mit.edu	37	17	29528481	29528481	+	Nonsense_Mutation	SNP	C	C	G			TCGA-RW-A7D0-01A-11D-A35D-08	TCGA-RW-A7D0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99293d59-23c9-46cf-bdaf-00c2b51a02bf	023921e3-188f-4540-9b31-b6ebf8d992fd	g.chr17:29528481C>G	ENST00000358273.4	+	11	1621	c.1238C>G	c.(1237-1239)tCa>tGa	p.S413*	NF1_ENST00000356175.3_Nonsense_Mutation_p.S413*|NF1_ENST00000431387.4_Nonsense_Mutation_p.S413*	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	413					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(6)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		CTGGTAAATTCACTCCATCGA	0.294			"""D, Mis, N, F, S, O"""		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												ENST00000358273.4			yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	"""D, Mis, N, F, S, O"""	neurofibromatosis type 1 gene			O		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""	NF1/ACCN1(2)	14	Whole gene deletion(8)|Unknown(6)	p.0?(8)|p.?(6)	soft_tissue(7)|autonomic_ganglia(3)|central_nervous_system(3)|lung(1)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599						c.(1237-1239)tCa>tGa		neurofibromin 1							86.0	96.0	92.0					17																	29528481		2203	4294	6497	SO:0001587	stop_gained	4763	Neurofibromatosis, type 1	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	g.chr17:29528481C>G		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"""neurofibromatosis"", ""von Recklinghausen disease"", ""Watson disease"""	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.1238C>G	17.37:g.29528481C>G	ENSP00000351015:p.Ser413*	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)				NF1_ENST00000431387.4_Nonsense_Mutation_p.S413*|NF1_ENST00000356175.3_Nonsense_Mutation_p.S413*	p.S413*	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)	11	1621	+		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)	413					O00662|Q14284|Q14930|Q14931|Q9UMK3	Nonsense_Mutation	SNP	ENST00000358273.4	37	c.1238C>G	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.648075	0.87958	.	.	ENSG00000196712	ENST00000431387;ENST00000358273;ENST00000356175;ENST00000456735	.	.	.	5.17	4.18	0.49190	.	0.063541	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	14.9841	0.71332	0.1439:0.8561:0.0:0.0	.	.	.	.	X	413;413;413;79	.	ENSP00000348498:S413X	S	+	2	0	NF1	26552607	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.194000	0.77789	1.146000	0.42352	0.491000	0.48974	TCA		0.294	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		40	46	0	0	0	1	0	40	46				
OR10A3	26496	broad.mit.edu	37	11	7960834	7960834	+	Silent	SNP	C	C	T			TCGA-RW-A7D0-01A-11D-A35D-08	TCGA-RW-A7D0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99293d59-23c9-46cf-bdaf-00c2b51a02bf	023921e3-188f-4540-9b31-b6ebf8d992fd	g.chr11:7960834C>T	ENST00000360759.3	-	1	307	c.234G>A	c.(232-234)acG>acA	p.T78T		NM_001003745.1	NP_001003745.1	P58181	O10A3_HUMAN	olfactory receptor, family 10, subfamily A, member 3	78					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(5)|lung(12)|pancreas(1)|skin(2)	21				Epithelial(150;1.38e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		GCATTTCAGGCGTAATGACTG	0.448																																						ENST00000360759.3																			0				endometrium(1)|large_intestine(5)|lung(12)|pancreas(1)|skin(2)	21						c.(232-234)acG>acA		olfactory receptor, family 10, subfamily A, member 3							127.0	115.0	119.0					11																	7960834		2201	4296	6497	SO:0001819	synonymous_variant	26496				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:7960834C>T	BK004404	CCDS31421.1	11p15.4	2012-08-09			ENSG00000170683	ENSG00000170683		"""GPCR / Class A : Olfactory receptors"""	8162	protein-coding gene	gene with protein product						1370859	Standard	NM_001003745		Approved	HTPCRX12, HSHTPCRX12	uc010rbi.2	P58181	OTTHUMG00000165672	ENST00000360759.3:c.234G>A	11.37:g.7960834C>T							p.T78T	NM_001003745.1	NP_001003745.1	P58181	O10A3_HUMAN		Epithelial(150;1.38e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)	1	307	-			78					B9EH39|Q6IF58|Q96R11	Silent	SNP	ENST00000360759.3	37	c.234G>A	CCDS31421.1																																																																																				0.448	OR10A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385704.1	NM_001003745		13	77	0	0	0	1	0	13	77				
CADM1	23705	broad.mit.edu	37	11	115080343	115080343	+	Silent	SNP	G	G	T			TCGA-RW-A7D0-01A-11D-A35D-08	TCGA-RW-A7D0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99293d59-23c9-46cf-bdaf-00c2b51a02bf	023921e3-188f-4540-9b31-b6ebf8d992fd	g.chr11:115080343G>T	ENST00000452722.3	-	8	1049	c.1029C>A	c.(1027-1029)acC>acA	p.T343T	CADM1_ENST00000542447.2_Intron|CADM1_ENST00000536727.1_Intron|CADM1_ENST00000331581.6_Silent_p.T343T|CADM1_ENST00000537140.1_Intron|CADM1_ENST00000537058.1_Silent_p.T343T	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																																						ENST00000537058.1																			5	Substitution - coding silent(5)	p.T343T(5)	kidney(3)|lung(2)	cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(9)|ovary(2)|skin(1)	32						c.(1027-1029)acC>acA		cell adhesion molecule 1							45.0	50.0	49.0					11																	115080343		2201	4296	6497	SO:0001819	synonymous_variant	23705				adherens junction organization|apoptosis|cell differentiation|cell junction assembly|cell recognition|detection of stimulus|heterophilic cell-cell adhesion|homophilic cell adhesion|multicellular organismal development|positive regulation of cytokine secretion|spermatogenesis|susceptibility to natural killer cell mediated cytotoxicity	basolateral plasma membrane|cell-cell junction|integral to membrane	PDZ domain binding|protein C-terminus binding|protein homodimerization activity|receptor binding	g.chr11:115080343G>T	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	11.37:g.115080343G>T						CADM1_ENST00000452722.2_Silent_p.T343T|CADM1_ENST00000331581.6_Silent_p.T343T|CADM1_ENST00000537140.1_Intron|CADM1_ENST00000536727.1_Intron|CADM1_ENST00000542447.2_Intron	p.T343T			Q9BY67	CADM1_HUMAN		BRCA - Breast invasive adenocarcinoma(274;5.01e-06)|Epithelial(105;0.000305)|all cancers(92;0.00303)	8	1049	-	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)	343	PPTTIPPPTTTTTTTTTTTTTILTIIT -> TTATTEPAVH GLTQLPNSAEELDSEDLS (in Ref. 3; BAC11657).					Silent	SNP	ENST00000452722.3	37	c.1029C>A	CCDS8373.1																																																																																				0.433	CADM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398753.2	NM_014333		3	41	1	0	0.00909568	1	0.00955046	3	41				
GGT1	2678	broad.mit.edu	37	22	25016897	25016897	+	Missense_Mutation	SNP	A	A	T			TCGA-RW-A7D0-01A-11D-A35D-08	TCGA-RW-A7D0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99293d59-23c9-46cf-bdaf-00c2b51a02bf	023921e3-188f-4540-9b31-b6ebf8d992fd	g.chr22:25016897A>T	ENST00000400382.1	+	9	1348	c.593A>T	c.(592-594)gAt>gTt	p.D198V	GGT1_ENST00000248923.4_Missense_Mutation_p.D198V|GGT1_ENST00000400383.1_Missense_Mutation_p.D198V|GGT1_ENST00000406383.2_Missense_Mutation_p.D198V|GGT1_ENST00000466310.1_Intron|GGT1_ENST00000400380.1_Missense_Mutation_p.D198V			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1	198					arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|cysteine biosynthetic process (GO:0019344)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione catabolic process (GO:0006751)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|regulation of immune system process (GO:0002682)|regulation of inflammatory response (GO:0050727)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|xenobiotic metabolic process (GO:0006805)|zymogen activation (GO:0031638)	anchored component of external side of plasma membrane (GO:0031362)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			breast(1)|endometrium(2)|kidney(14)|large_intestine(2)|lung(6)|pancreas(1)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	40					Glutathione(DB00143)	TTCTGCCGGGATAGAAAGGTG	0.642																																						ENST00000400382.1																			0				breast(1)|endometrium(2)|kidney(14)|large_intestine(2)|lung(6)|pancreas(1)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	40						c.(592-594)gAt>gTt		gamma-glutamyltransferase 1	Glutathione(DB00143)						19.0	22.0	21.0					22																	25016897		1957	4130	6087	SO:0001583	missense	2678				glutathione biosynthetic process	integral to membrane	acyltransferase activity|gamma-glutamyltransferase activity|protein binding	g.chr22:25016897A>T	M24903	CCDS42992.1	22q11.23	2008-08-15			ENSG00000100031	ENSG00000100031	2.3.2.2	"""CD molecules"", ""Gamma-glutamyltransferases"""	4250	protein-coding gene	gene with protein product		612346		GGT		8104871, 18357469	Standard	NM_001288833		Approved	D22S672, D22S732, CD224	uc003aan.1	P19440	OTTHUMG00000030859	ENST00000400382.1:c.593A>T	22.37:g.25016897A>T	ENSP00000383232:p.Asp198Val					GGT1_ENST00000400383.1_Missense_Mutation_p.D198V|GGT1_ENST00000466310.1_Intron|GGT1_ENST00000248923.4_Missense_Mutation_p.D198V|GGT1_ENST00000406383.2_Missense_Mutation_p.D198V|GGT1_ENST00000400380.1_Missense_Mutation_p.D198V	p.D198V			P19440	GGT1_HUMAN			9	1348	+			198					Q08247|Q14404|Q8TBS1|Q9UMK1	Missense_Mutation	SNP	ENST00000400382.1	37	c.593A>T	CCDS42992.1	.	.	.	.	.	.	.	.	.	.	.	14.66	2.601472	0.46423	.	.	ENSG00000100031	ENST00000248923;ENST00000412658;ENST00000400382;ENST00000400383;ENST00000400380;ENST00000406383	T;T;T;T;T;T	0.10288	2.89;2.89;2.89;2.89;2.89;2.89	3.94	3.94	0.45596	.	1.078920	0.07236	U	0.863345	T	0.18676	0.0448	M	0.79123	2.44	0.21878	N	0.999495	P	0.50528	0.936	B	0.42738	0.396	T	0.23762	-1.0179	10	0.62326	D	0.03	-28.8305	8.7795	0.34783	0.9042:0.0:0.0958:0.0	.	198	P19440	GGT1_HUMAN	V	198	ENSP00000248923:D198V;ENSP00000393537:D198V;ENSP00000383232:D198V;ENSP00000383233:D198V;ENSP00000383231:D198V;ENSP00000385975:D198V	ENSP00000248923:D198V	D	+	2	0	GGT1	23346897	0.146000	0.22672	0.001000	0.08648	0.488000	0.33401	3.920000	0.56446	1.564000	0.49628	0.454000	0.30748	GAT		0.642	GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250797.1	NM_013430		3	20	0	0	0	1	0	3	20				
FLT1	2321	broad.mit.edu	37	13	28919665	28919665	+	Nonsense_Mutation	SNP	C	C	A			TCGA-RW-A7D0-01A-11D-A35D-08	TCGA-RW-A7D0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99293d59-23c9-46cf-bdaf-00c2b51a02bf	023921e3-188f-4540-9b31-b6ebf8d992fd	g.chr13:28919665C>A	ENST00000282397.4	-	16	2523	c.2272G>T	c.(2272-2274)Gag>Tag	p.E758*	FLT1_ENST00000540678.1_5'UTR	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1	758					blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	GTGATCAGCTCCAGATTAGAC	0.403																																						ENST00000282397.4																			0				NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115						c.(2272-2274)Gag>Tag		fms-related tyrosine kinase 1	Sunitinib(DB01268)						62.0	62.0	62.0					13																	28919665		2203	4300	6503	SO:0001587	stop_gained	2321				cell differentiation|female pregnancy|positive regulation of vascular endothelial growth factor receptor signaling pathway	extracellular space|Golgi apparatus|integral to plasma membrane|nucleus	ATP binding|growth factor binding|vascular endothelial growth factor receptor activity	g.chr13:28919665C>A	AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3763	protein-coding gene	gene with protein product	"""vascular endothelial growth factor receptor 1"", ""vascular permeability factor receptor"""	165070	"""fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"""	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.2272G>T	13.37:g.28919665C>A	ENSP00000282397:p.Glu758*					FLT1_ENST00000540678.1_5'UTR	p.E758*	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	16	2523	-	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	758					A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Nonsense_Mutation	SNP	ENST00000282397.4	37	c.2272G>T	CCDS9330.1	.	.	.	.	.	.	.	.	.	.	C	44	11.088426	0.99514	.	.	ENSG00000102755	ENST00000282397	.	.	.	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	.	19.4283	0.94754	0.0:1.0:0.0:0.0	.	.	.	.	X	758	.	ENSP00000282397:E758X	E	-	1	0	FLT1	27817665	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.972000	0.70448	2.590000	0.87494	0.555000	0.69702	GAG		0.403	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1			4	15	1	0	1	1	1	4	15				
HSD17B7P2	158160	broad.mit.edu	37	10	38654432	38654432	+	RNA	SNP	A	A	G	rs2257765		TCGA-RW-A7D0-01A-11D-A35D-08	TCGA-RW-A7D0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99293d59-23c9-46cf-bdaf-00c2b51a02bf	023921e3-188f-4540-9b31-b6ebf8d992fd	g.chr10:38654432A>G	ENST00000494540.1	+	0	599					NR_003086.1				hydroxysteroid (17-beta) dehydrogenase 7 pseudogene 2																		TCATCTCGCAATGCAAGGAAA	0.453																																						ENST00000494540.1																			0																																																			158160							g.chr10:38654432A>G			10p11.1	2011-06-29			ENSG00000099251	ENSG00000099251			28120	pseudogene	pseudogene						10544267	Standard	NR_003086		Approved	HSD17B7, bA291L22.1	uc010qex.1		OTTHUMG00000017993		10.37:g.38654432A>G								NR_003086.1						0	599	+									RNA	SNP	ENST00000494540.1	37																																																																																						0.453	HSD17B7P2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000047631.2	NR_003086		5	44	0	0	0	1	0	5	44				
ZNF761	388561	broad.mit.edu	37	19	53958826	53958826	+	RNA	SNP	G	G	A			TCGA-RW-A7D0-01A-11D-A35D-08	TCGA-RW-A7D0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99293d59-23c9-46cf-bdaf-00c2b51a02bf	023921e3-188f-4540-9b31-b6ebf8d992fd	g.chr19:53958826G>A	ENST00000454407.1	+	0	1518							Q86XN6	ZN761_HUMAN	zinc finger protein 761						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	30				GBM - Glioblastoma multiforme(134;0.00786)		AACCTTACAAGTGTAATGAGT	0.418																																						ENST00000454407.1																			0				endometrium(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	30								zinc finger protein 761							152.0	151.0	151.0					19																	53958826		2203	4300	6503			388561				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr19:53958826G>A	AB107355		19q13.42	2007-10-05	2006-08-11	2006-08-11	ENSG00000160336	ENSG00000160336		"""Zinc fingers, C2H2-type"""	23179	protein-coding gene	gene with protein product							Standard	NM_001008401		Approved	KIAA2033, FLJ16231, FLJ35333	uc010eqp.3	Q86XN6	OTTHUMG00000156999		19.37:g.53958826G>A										Q86XN6	ZN761_HUMAN		GBM - Glioblastoma multiforme(134;0.00786)	0	1518	+								Q6ZNB9	RNA	SNP	ENST00000454407.1	37																																																																																						0.418	ZNF761-203	KNOWN	basic	processed_transcript	processed_transcript		NM_001008401		4	135	0	0	0	1	0	4	135				
CSRNP1	64651	broad.mit.edu	37	3	39188103	39188105	+	In_Frame_Del	DEL	GAG	GAG	-			TCGA-RW-A7D0-01A-11D-A35D-08	TCGA-RW-A7D0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99293d59-23c9-46cf-bdaf-00c2b51a02bf	023921e3-188f-4540-9b31-b6ebf8d992fd	g.chr3:39188103_39188105delGAG	ENST00000273153.5	-	2	246_248	c.69_71delCTC	c.(67-72)tcctct>tct	p.23_24SS>S	CSRNP1_ENST00000514182.1_In_Frame_Del_p.23_24SS>S	NM_033027.3	NP_149016.2	Q96S65	CSRN1_HUMAN	cysteine-serine-rich nuclear protein 1	23	Ser-rich.				apoptotic process (GO:0006915)|face morphogenesis (GO:0060325)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|skeletal system morphogenesis (GO:0048705)	nucleus (GO:0005634)	RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(3)|endometrium(4)|kidney(1)|large_intestine(5)|lung(3)|ovary(5)|skin(3)	24						CCCAGAGGAAGAGGAGGAGGAGG	0.616																																						ENST00000273153.5																			0				central_nervous_system(3)|endometrium(4)|kidney(1)|large_intestine(5)|lung(3)|ovary(5)|skin(3)	24						c.(67-72)tct>tc		cysteine-serine-rich nuclear protein 1																																				SO:0001651	inframe_deletion	64651				apoptosis|positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity	g.chr3:39188103_39188105delGAG	AB053121	CCDS2682.1	3p22	2009-04-17	2009-04-17	2009-04-17	ENSG00000144655	ENSG00000144655			14300	protein-coding gene	gene with protein product		606458	"""AXIN1 up-regulated 1"""	AXUD1		11526492, 17726538	Standard	NM_033027		Approved	URAX1, DKFZp566F164, FAM130B, TAIP-3	uc003cjg.3	Q96S65	OTTHUMG00000131293	ENST00000273153.5:c.69_71delCTC	3.37:g.39188112_39188114delGAG	ENSP00000273153:p.Ser26del					CSRNP1_ENST00000514182.1_In_Frame_Del_p.SS25del	p.SS25del	NM_033027.3	NP_149016.2	Q96S65	CSRN1_HUMAN			2	246_248	-			25			Ser-rich.		Q69YY5	In_Frame_Del	DEL	ENST00000273153.5	37	c.69_71delCTC	CCDS2682.1																																																																																				0.616	CSRNP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254061.1	NM_033027		2	4						2	4	---	---	---	---
CPSF7	79869	broad.mit.edu	37	11	61183138	61183148	+	Splice_Site	DEL	CTGCACTGGCT	CTGCACTGGCT	-	rs200619739		TCGA-RW-A7D0-01A-11D-A35D-08	TCGA-RW-A7D0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99293d59-23c9-46cf-bdaf-00c2b51a02bf	023921e3-188f-4540-9b31-b6ebf8d992fd	g.chr11:61183138_61183148delCTGCACTGGCT	ENST00000394888.4	-	7	1246_1256	c.1074_1084delAGCCAGTGCAG	c.(1072-1086)ggagccagtgcaggg>gggg	p.GASAG358fs	CPSF7_ENST00000340437.4_Splice_Site_p.GASAG401fs|CPSF7_ENST00000448745.1_Splice_Site_p.GASAG349fs|CPSF7_ENST00000439958.3_Splice_Site_p.GASAG349fs	NM_001136040.2	NP_001129512.1	Q8N684	CPSF7_HUMAN	cleavage and polyadenylation specific factor 7, 59kDa	358					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|protein tetramerization (GO:0051262)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)|mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	22						ACTGAGTTACCTGCACTGGCTCCAGATACTG	0.436																																						ENST00000340437.4																			0				breast(3)|central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	22						c.e7+1		cleavage and polyadenylation specific factor 7, 59kDa																																				SO:0001630	splice_region_variant	79869				mRNA 3'-end processing|nuclear mRNA splicing, via spliceosome|protein tetramerization|termination of RNA polymerase II transcription	mRNA cleavage factor complex	nucleotide binding|protein binding|RNA binding	g.chr11:61183138_61183148delCTGCACTGGCT		CCDS8006.2, CCDS44619.1, CCDS44620.1	11q12.2	2013-06-18			ENSG00000149532	ENSG00000149532		"""RNA binding motif (RRM) containing"""	30098	protein-coding gene	gene with protein product	"""pre mRNA cleavage factor I, 59 kDa subunit"", ""cleavage factor Im complex 59 kDa subunit"""					12477932	Standard	NM_024811		Approved	FLJ12529	uc001nrp.3	Q8N684	OTTHUMG00000168198	ENST00000394888.4:c.1084+1AGCCAGTGCAG>-	11.37:g.61183138_61183148delCTGCACTGGCT						CPSF7_ENST00000448745.1_Splice_Site_p.GASAG349_splice|CPSF7_ENST00000394888.4_Splice_Site_p.GASAG358_splice|CPSF7_ENST00000439958.3_Splice_Site_p.GASAG349_splice	p.GASAG401_splice	NM_024811.3	NP_079087.3	Q8N684	CPSF7_HUMAN			7	1283_1293	-			358					B3KU04|C9K0Q4|Q7Z3H9|Q9H025|Q9H9V1	Splice_Site	DEL	ENST00000394888.4	37	c.1213_splice	CCDS44619.1																																																																																				0.436	CPSF7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347835.2	NM_024811	Frame_Shift_Del	10	28						10	28	---	---	---	---
RP11-44F14.1	0	broad.mit.edu	37	16	53404542	53404543	+	RNA	INS	-	-	A			TCGA-RW-A7D0-01A-11D-A35D-08	TCGA-RW-A7D0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99293d59-23c9-46cf-bdaf-00c2b51a02bf	023921e3-188f-4540-9b31-b6ebf8d992fd	g.chr16:53404542_53404543insA	ENST00000565421.1	-	0	410																											TCTCCTTTCTCAAACTTAACCT	0.327																																						ENST00000565421.1																			0																																																			0							g.chr16:53404542_53404543insA																													16.37:g.53404545_53404545dupA														0	410	-									RNA	INS	ENST00000565421.1	37																																																																																						0.327	RP11-44F14.1-002	KNOWN	basic	retained_intron	pseudogene	OTTHUMT00000422364.2			8	31						8	31	---	---	---	---
BAHCC1	57597	broad.mit.edu	37	17	79423466	79423467	+	Frame_Shift_Ins	INS	-	-	G	rs200506858	byFrequency	TCGA-RW-A7D0-01A-11D-A35D-08	TCGA-RW-A7D0-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	99293d59-23c9-46cf-bdaf-00c2b51a02bf	023921e3-188f-4540-9b31-b6ebf8d992fd	g.chr17:79423466_79423467insG	ENST00000307745.7	+	20	4713_4714	c.4713_4714insG	c.(4714-4716)gggfs	p.G1572fs																								AGGCTACCCCCGGGGGGCGCAT	0.683																																						ENST00000307745.7																			0											c.(4711-4716)ccggggfs																																						SO:0001589	frameshift_variant	57597							g.chr17:79423466_79423467insG																												ENST00000307745.7:c.4719dupG	17.37:g.79423472_79423472dupG	ENSP00000303486:p.Gly1572fs						p.PG1571fs							20	4713_4714	+									Frame_Shift_Ins	INS	ENST00000307745.7	37	c.4713_4714insG																																																																																					0.683	RP11-1055B8.7-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				2	4						2	4	---	---	---	---
