#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
GNA15	2769	broad.mit.edu	37	19	3151776	3151776	+	Missense_Mutation	SNP	G	G	A			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr19:3151776G>A	ENST00000262958.3	+	4	815	c.557G>A	c.(556-558)cGc>cAc	p.R186H	AC005264.2_ENST00000587587.1_RNA	NM_002068.2	NP_002059.2	P30679	GNA15_HUMAN	guanine nucleotide binding protein (G protein), alpha 15 (Gq class)	186					activation of phospholipase C activity (GO:0007202)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)	p.R186H(1)		large_intestine(5)|lung(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;7.04e-05)|OV - Ovarian serous cystadenocarcinoma(105;5.08e-113)|Epithelial(107;6.19e-111)|all cancers(105;6.19e-103)|BRCA - Breast invasive adenocarcinoma(158;0.00145)|STAD - Stomach adenocarcinoma(1328;0.184)		CTCCGCAGCCGCATGCCCACC	0.647																																						ENST00000262958.3																			1	Substitution - Missense(1)	p.R186H(1)	lung(1)	large_intestine(5)|lung(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						c.(556-558)cGc>cAc		guanine nucleotide binding protein (G protein), alpha 15 (Gq class)							116.0	99.0	105.0					19																	3151776		2203	4300	6503	SO:0001583	missense	2769				activation of phospholipase C activity by dopamine receptor signaling pathway|activation of phospholipase C activity by muscarinic acetylcholine receptor signaling pathway|elevation of cytosolic calcium ion concentration|G-protein signaling, coupled to cAMP nucleotide second messenger|platelet activation|protein ADP-ribosylation	heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity	g.chr19:3151776G>A		CCDS12104.1	19p13.3	2008-07-16				ENSG00000060558			4383	protein-coding gene	gene with protein product		139314				1302014	Standard	NM_002068		Approved	GNA16	uc002lxf.2	P30679		ENST00000262958.3:c.557G>A	19.37:g.3151776G>A	ENSP00000262958:p.Arg186His					AC005264.2_ENST00000587587.1_RNA	p.R186H	NM_002068.2	NP_002059.2	P30679	GNA15_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (162;7.04e-05)|OV - Ovarian serous cystadenocarcinoma(105;5.08e-113)|Epithelial(107;6.19e-111)|all cancers(105;6.19e-103)|BRCA - Breast invasive adenocarcinoma(158;0.00145)|STAD - Stomach adenocarcinoma(1328;0.184)	4	815	+		Hepatocellular(1079;0.137)	186					E9KL40|E9KL47|O75247|Q53XK2	Missense_Mutation	SNP	ENST00000262958.3	37	c.557G>A	CCDS12104.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.974513	0.92919	.	.	ENSG00000060558	ENST00000262958	T	0.65916	-0.18	4.59	4.59	0.56863	G protein alpha subunit, helical insertion (1);	0.000000	0.85682	U	0.000000	D	0.84202	0.5420	H	0.94925	3.6	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.89005	0.3424	10	0.87932	D	0	.	14.9063	0.70721	0.0:0.0:1.0:0.0	.	186	P30679	GNA15_HUMAN	H	186	ENSP00000262958:R186H	ENSP00000262958:R186H	R	+	2	0	GNA15	3102776	0.993000	0.37304	1.000000	0.80357	0.946000	0.59487	5.184000	0.65070	2.093000	0.63338	0.546000	0.68486	CGC		0.647	GNA15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452320.2	NM_002068		4	166	0	0	0	1	0	4	166				
ATAD2	29028	broad.mit.edu	37	8	124361593	124361593	+	Missense_Mutation	SNP	T	T	C			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr8:124361593T>C	ENST00000287394.5	-	14	1845	c.1738A>G	c.(1738-1740)Ata>Gta	p.I580V	ATAD2_ENST00000521903.1_5'UTR|MIR548AA1_ENST00000384971.2_RNA	NM_014109.3	NP_054828.2	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	580					ATP catabolic process (GO:0006200)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|lung(16)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	48	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			GCAGGATCTATAGAATCTAGC	0.408																																						ENST00000287394.5																			0				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|lung(16)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	48						c.(1738-1740)Ata>Gta		ATPase family, AAA domain containing 2							143.0	130.0	134.0					8																	124361593		2203	4300	6503	SO:0001583	missense	29028				regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrion|nucleus	ATP binding|ATPase activity	g.chr8:124361593T>C	BC019909	CCDS6343.1	8q24.13	2014-01-21		2007-02-08	ENSG00000156802	ENSG00000156802		"""ATPases / AAA-type"""	30123	protein-coding gene	gene with protein product		611941				12477932	Standard	NM_014109		Approved	PRO2000, DKFZp667N1320, MGC5254, MGC29843, CT137	uc003yqh.4	Q6PL18	OTTHUMG00000165090	ENST00000287394.5:c.1738A>G	8.37:g.124361593T>C	ENSP00000287394:p.Ile580Val					ATAD2_ENST00000521903.1_5'UTR	p.I580V	NM_014109.3	NP_054828.2	Q6PL18	ATAD2_HUMAN	STAD - Stomach adenocarcinoma(47;0.00288)		14	1845	-	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		580					Q14CR1|Q658P2|Q68CQ0|Q6PJV6|Q8N890|Q9UHS5	Missense_Mutation	SNP	ENST00000287394.5	37	c.1738A>G	CCDS6343.1	.	.	.	.	.	.	.	.	.	.	T	27.4	4.830327	0.91036	.	.	ENSG00000156802	ENST00000287394	D	0.94184	-3.37	5.7	5.7	0.88788	ATPase, AAA-type, conserved site (1);ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.095181	0.64402	D	0.000001	D	0.94679	0.8284	L	0.43757	1.38	0.80722	D	1	D	0.69078	0.997	D	0.70227	0.968	D	0.93505	0.6848	10	0.28530	T	0.3	-23.2294	15.9666	0.79979	0.0:0.0:0.0:1.0	.	580	Q6PL18	ATAD2_HUMAN	V	580	ENSP00000287394:I580V	ENSP00000287394:I580V	I	-	1	0	ATAD2	124430774	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.040000	0.89188	2.174000	0.68829	0.482000	0.46254	ATA		0.408	ATAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381766.2	NM_014109		4	156	0	0	0	1	0	4	156				
TSSC2	650368	broad.mit.edu	37	11	3427845	3427845	+	RNA	SNP	C	C	T			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr11:3427845C>T	ENST00000529482.1	+	0	962									tumor suppressing subtransferable candidate 2 pseudogene																		CTTCAAGTGGCAGGAGCAGAA	0.587																																						ENST00000529482.1																			0																																																			0							g.chr11:3427845C>T			11p15.4	2014-06-05	2008-06-30		ENSG00000223756	ENSG00000223756			12384	pseudogene	pseudogene	"""tumor-supressing STF cDNA 2"", ""asparagine-linked glycosylation 1 homolog (yeast, beta-1,4-mannosyltransferase) (ALG1) pseudogene"""	608999	"""tumor suppressing subtransferable candidate 2"""			9403053	Standard	NR_024248		Approved				OTTHUMG00000011705		11.37:g.3427845C>T														0	962	+									RNA	SNP	ENST00000529482.1	37																																																																																						0.587	TSSC2-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000392020.1			4	72	0	0	0	1	0	4	72				
SNHG14	104472715	broad.mit.edu	37	15	25425564	25425564	+	RNA	SNP	C	C	T			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr15:25425564C>T	ENST00000424208.1	+	0	0				SNORD115-6_ENST00000363942.1_RNA|SNHG14_ENST00000365306.1_RNA|SNORD115-5_ENST00000363633.1_RNA|SNHG14_ENST00000441592.2_RNA	NR_003305.1				small nucleolar RNA host gene 14 (non-protein coding)																		TTCCTGGCATCCTGGTCTCCT	0.597																																						ENST00000441592.2																			0																																																			0							g.chr15:25425564C>T			15q11.2	2014-01-17	2011-08-22	2011-08-22	ENSG00000224078	ENSG00000224078		"""Long non-coding RNAs"""	37462	non-coding RNA	RNA, long non-coding	"""non-protein coding RNA 214"""		"""UBE3A antisense RNA 1 (non-protein coding)"""	UBE3A-AS1		23771028	Standard			Approved	NCRNA00214, UBE3A-AS			OTTHUMG00000056661		15.37:g.25425564C>T														0	552	+									RNA	SNP	ENST00000424208.1	37																																																																																						0.597	SNHG14-002	KNOWN	basic	antisense	processed_transcript	OTTHUMT00000126729.2			38	60	0	0	0	1	0	38	60				
MAGEE1	57692	broad.mit.edu	37	X	75648746	75648746	+	Silent	SNP	G	G	A			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chrX:75648746G>A	ENST00000361470.2	+	1	701	c.423G>A	c.(421-423)ccG>ccA	p.P141P		NM_020932.2	NP_065983.1	Q9HCI5	MAGE1_HUMAN	melanoma antigen family E, 1	141	Pro-rich.					dendrite (GO:0030425)|dystrophin-associated glycoprotein complex (GO:0016010)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(12)|lung(20)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	51						CCTCCAGGCCGCCCACTTCCT	0.677																																						ENST00000361470.2																			0				breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(12)|lung(20)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	51						c.(421-423)ccG>ccA		melanoma antigen family E, 1							28.0	30.0	29.0					X																	75648746		2203	4300	6503	SO:0001819	synonymous_variant	57692					dendrite|nucleus|perinuclear region of cytoplasm|postsynaptic membrane		g.chrX:75648746G>A	AF490507	CCDS14433.1	Xq13	2008-02-05			ENSG00000198934	ENSG00000198934			24934	protein-coding gene	gene with protein product		300759				14623885	Standard	NM_020932		Approved	KIAA1587, DAMAGE	uc004ecm.2	Q9HCI5	OTTHUMG00000021879	ENST00000361470.2:c.423G>A	X.37:g.75648746G>A							p.P141P	NM_020932.2	NP_065983.1	Q9HCI5	MAGE1_HUMAN			1	701	+			141			Pro-rich.		Q5JXC7|Q86TG0|Q8TD92|Q9H216	Silent	SNP	ENST00000361470.2	37	c.423G>A	CCDS14433.1																																																																																				0.677	MAGEE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057298.1	NM_020932		3	50	0	0	0	1	0	3	50				
NCOR1P1	149934	broad.mit.edu	37	20	26084295	26084295	+	RNA	SNP	C	C	T	rs76611503		TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr20:26084295C>T	ENST00000478176.1	-	0	162					NR_003678.1		Q9H4R4	CT191_HUMAN	nuclear receptor corepressor 1 pseudogene 1									p.G41R(1)									TGTTTGCCTCCAAATGCTGGA	0.373																																						ENST00000478176.1																			1	Substitution - Missense(1)	p.G41R(1)	kidney(1)																	42.0	30.0	34.0					20																	26084295		692	1590	2282			0							g.chr20:26084295C>T	AL391119		20p11.1	2011-09-16	2011-09-16	2011-09-16	ENSG00000240108	ENSG00000240108			16724	pseudogene	pseudogene			"""chromosome 20 open reading frame 191"""	C20orf191			Standard	NR_003678		Approved	bB329D4.2	uc002wvj.5	Q9H4R4	OTTHUMG00000032145		20.37:g.26084295C>T								NR_003678.1						0	162	-								A2RUA0	RNA	SNP	ENST00000478176.1	37																																																																																						0.373	NCOR1P1-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000078478.2			3	66	0	0	0	1	0	3	66				
BRAF	673	broad.mit.edu	37	7	140453134	140453134	+	Missense_Mutation	SNP	T	T	C	rs397516897|rs121913364|rs121913226|rs121913377		TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr7:140453134T>C	ENST00000288602.6	-	15	1861	c.1801A>G	c.(1801-1803)Aaa>Gaa	p.K601E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	601	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		K -> E (in CRC). {ECO:0000269|PubMed:12198537}.|K -> Q (in CFC1). {ECO:0000269|PubMed:19206169}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.K601E(40)|p.V600_K601>E(12)|p.T599_R603>I(2)|p.K601del(1)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	CATCGAGATTTCACTGTAGCT	0.368		61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												Colon(40;35 892 2973 5743 27438)	ENST00000288602.6		61		Dom	yes		7	7q34	673	"""Mis, T, O"""	v-raf murine sarcoma viral oncogene homolog B1	yes	Cardio-facio-cutaneous syndrome	E	"""AKAP9, KIAA1549"""		"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	58	Substitution - Missense(40)|Complex - deletion inframe(17)|Deletion - In frame(1)	p.K601E(40)|p.V600_K601>E(12)|p.T599_R603>I(2)|p.K601del(1)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)	thyroid(30)|skin(15)|large_intestine(5)|ovary(2)|pancreas(2)|upper_aerodigestive_tract(1)|endometrium(1)|lung(1)|NS(1)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380						c.(1801-1803)Aaa>Gaa		v-raf murine sarcoma viral oncogene homolog B	Sorafenib(DB00398)						111.0	103.0	106.0					7																	140453134		2203	4300	6503	SO:0001583	missense	673	Cardiofaciocutaneous syndrome	Familial Cancer Database	CFC, CFCS	activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding	g.chr7:140453134T>C	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1801A>G	7.37:g.140453134T>C	ENSP00000288602:p.Lys601Glu						p.K601E	NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN			15	1861	-	Melanoma(164;0.00956)		601		K -> E (in colorectal cancer).|K -> Q (in CFC syndrome).	Protein kinase.		A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	c.1801A>G	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	23.8|23.8	4.454487|4.454487	0.84209|0.84209	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000288602|ENST00000496384	D|.	0.82711|.	-1.64|.	5.65|5.65	5.65|5.65	0.86999|0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.54464|.	0.1860|.	N|N	0.25380|0.25380	0.74|0.74	0.80722|0.80722	D|D	1|1	P|.	0.42584|.	0.784|.	P|.	0.49922|.	0.626|.	T|.	0.51108|.	-0.8747|.	10|.	0.87932|.	D|.	0|.	.|.	15.9326|15.9326	0.79675|0.79675	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	601|.	P15056|.	BRAF_HUMAN|.	E|W	601|208	ENSP00000288602:K601E|.	ENSP00000288602:K601E|.	K|X	-|-	1|3	0|0	BRAF|BRAF	140099603|140099603	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.921000|7.921000	0.87530|0.87530	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	AAA|TGA		0.368	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		43	66	0	0	0	1	0	43	66				
LRP2BP	55805	broad.mit.edu	37	4	186295505	186295505	+	Silent	SNP	T	T	C			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr4:186295505T>C	ENST00000328559.7	-	4	1252	c.441A>G	c.(439-441)aaA>aaG	p.K147K	LRP2BP_ENST00000510776.1_Silent_p.K121K|LRP2BP_ENST00000505916.1_Silent_p.K147K|LRP2BP_ENST00000362004.3_Silent_p.K149K|RP11-714G18.1_ENST00000514884.1_RNA	NM_018409.3	NP_060879.2	Q9P2M1	LR2BP_HUMAN	LRP2 binding protein	147						cytoplasm (GO:0005737)				breast(1)|endometrium(2)|large_intestine(6)|lung(3)|prostate(1)|skin(2)	15		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;0.00109)|Colorectal(36;0.0215)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;2.14e-25)|Epithelial(43;1.55e-22)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-11)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.000132)|STAD - Stomach adenocarcinoma(60;0.000766)|Colorectal(24;0.00116)|LUSC - Lung squamous cell carcinoma(40;0.00904)|COAD - Colon adenocarcinoma(29;0.0101)|READ - Rectum adenocarcinoma(43;0.161)		GTTTAACACCTTTTCCTTCAT	0.383																																						ENST00000362004.3																			0				breast(1)|endometrium(2)|large_intestine(6)|lung(3)|prostate(1)|skin(2)	15						c.(445-447)aaA>aaG		LRP2 binding protein							173.0	165.0	168.0					4																	186295505		2203	4300	6503	SO:0001819	synonymous_variant	55805					cytoplasm	protein binding	g.chr4:186295505T>C	AB037746	CCDS3840.1	4q35.1	2011-05-03			ENSG00000109771	ENSG00000109771			25434	protein-coding gene	gene with protein product						10718198, 12508107	Standard	NM_018409		Approved	DKFZp761O0113	uc003ixj.2	Q9P2M1	OTTHUMG00000160460	ENST00000328559.7:c.441A>G	4.37:g.186295505T>C						LRP2BP_ENST00000328559.7_Silent_p.K147K|RP11-714G18.1_ENST00000514884.1_RNA|LRP2BP_ENST00000510776.1_Silent_p.K121K|LRP2BP_ENST00000505916.1_Silent_p.K147K	p.K149K			Q9P2M1	LR2BP_HUMAN		all cancers(43;2.14e-25)|Epithelial(43;1.55e-22)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-11)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.000132)|STAD - Stomach adenocarcinoma(60;0.000766)|Colorectal(24;0.00116)|LUSC - Lung squamous cell carcinoma(40;0.00904)|COAD - Colon adenocarcinoma(29;0.0101)|READ - Rectum adenocarcinoma(43;0.161)	4	1258	-		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;0.00109)|Colorectal(36;0.0215)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)	147					A6NJR7|A7E219|B3KX83|Q9NSN6	Silent	SNP	ENST00000328559.7	37	c.447A>G	CCDS3840.1																																																																																				0.383	LRP2BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360679.2	NM_018409		3	132	0	0	0	1	0	3	132				
LRRC1	55227	broad.mit.edu	37	6	53769225	53769225	+	Missense_Mutation	SNP	G	G	T			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr6:53769225G>T	ENST00000370888.1	+	10	1232	c.955G>T	c.(955-957)Gca>Tca	p.A319S		NM_018214.4	NP_060684.4	Q9BTT6	LRRC1_HUMAN	leucine rich repeat containing 1	319						cytoplasm (GO:0005737)|membrane (GO:0016020)				cervix(1)|endometrium(3)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20	Lung NSC(77;0.0147)			BRCA - Breast invasive adenocarcinoma(397;0.0745)		CAACTTGAATGCAGACAGAAA	0.289																																						ENST00000370888.1																			0				cervix(1)|endometrium(3)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						c.(955-957)Gca>Tca		leucine rich repeat containing 1							93.0	89.0	90.0					6																	53769225		1821	4074	5895	SO:0001583	missense	55227					cytoplasm|membrane		g.chr6:53769225G>T	AF332199	CCDS4953.2	6p12.2	2014-07-30	2003-11-19		ENSG00000137269	ENSG00000137269			14307	protein-coding gene	gene with protein product		608195	"""leucine-rich repeat-containing 1"""				Standard	NM_018214		Approved	dJ523E19.1, LANO, FLJ10775, FLJ11834	uc003pcd.1	Q9BTT6	OTTHUMG00000014885	ENST00000370888.1:c.955G>T	6.37:g.53769225G>T	ENSP00000359925:p.Ala319Ser						p.A319S	NM_018214.4	NP_060684.4	Q9BTT6	LRRC1_HUMAN		BRCA - Breast invasive adenocarcinoma(397;0.0745)	10	1232	+	Lung NSC(77;0.0147)		319					Q5TGN3|Q9HAC0|Q9NVF1	Missense_Mutation	SNP	ENST00000370888.1	37	c.955G>T	CCDS4953.2	.	.	.	.	.	.	.	.	.	.	G	17.01	3.278821	0.59758	.	.	ENSG00000137269	ENST00000370888	T	0.58210	0.35	5.5	5.5	0.81552	.	0.238434	0.43579	D	0.000554	T	0.35595	0.0937	L	0.55743	1.74	0.80722	D	1	B	0.31459	0.324	B	0.30943	0.122	T	0.45804	-0.9236	10	0.87932	D	0	.	11.8097	0.52175	0.0796:0.0:0.9204:0.0	.	319	Q9BTT6	LRRC1_HUMAN	S	319	ENSP00000359925:A319S	ENSP00000359925:A319S	A	+	1	0	LRRC1	53877184	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.181000	0.71988	2.552000	0.86080	0.650000	0.86243	GCA		0.289	LRRC1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040970.2	NM_025168		3	82	1	0	1	1	1	3	82				
ZNF169	169841	broad.mit.edu	37	9	97063304	97063304	+	Silent	SNP	C	C	T			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr9:97063304C>T	ENST00000395395.2	+	5	1554	c.1464C>T	c.(1462-1464)tgC>tgT	p.C488C	ZNF169_ENST00000340911.4_3'UTR	NM_194320.2	NP_919301.2	Q14929	ZN169_HUMAN	zinc finger protein 169	488					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(3)|lung(8)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	24		Acute lymphoblastic leukemia(62;0.136)				CTTATCTGTGCCCCAAGTGTG	0.562																																						ENST00000395395.2																			0				endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	24						c.(1462-1464)tgC>tgT		zinc finger protein 169							86.0	73.0	77.0					9																	97063304		2203	4300	6503	SO:0001819	synonymous_variant	169841					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr9:97063304C>T	U28322	CCDS6709.2	9q22.32	2014-07-30			ENSG00000175787	ENSG00000175787		"""Zinc fingers, C2H2-type"", ""-"""	12957	protein-coding gene	gene with protein product		603404				9186526, 9071574	Standard	NM_001301275		Approved	MGC51961	uc004aum.1	Q14929	OTTHUMG00000020264	ENST00000395395.2:c.1464C>T	9.37:g.97063304C>T						ZNF169_ENST00000340911.4_3'UTR	p.C488C	NM_194320.2	NP_919301.2	Q14929	ZN169_HUMAN			5	1554	+		Acute lymphoblastic leukemia(62;0.136)	488					A2AGP5|A8K127|Q6PI28	Silent	SNP	ENST00000395395.2	37	c.1464C>T	CCDS6709.2																																																																																				0.562	ZNF169-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253714.1	NM_194320		34	45	0	0	0	1	0	34	45				
ZNF844	284391	broad.mit.edu	37	19	12187275	12187275	+	Missense_Mutation	SNP	G	G	C	rs376579156	byFrequency	TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr19:12187275G>C	ENST00000439326.3	+	4	1515	c.1340G>C	c.(1339-1341)cGt>cCt	p.R447P	ZNF844_ENST00000441304.2_3'UTR	NM_001136501.1	NP_001129973.1	Q08AG5	ZN844_HUMAN	zinc finger protein 844	447					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R447P(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(1)|prostate(1)	10						GAGAGAAACCGTATGAGTGTA	0.433																																						ENST00000439326.3																			1	Substitution - Missense(1)	p.R447P(1)	lung(1)	NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(1)|prostate(1)	10						c.(1339-1341)cGt>cCt		zinc finger protein 844							60.0	54.0	56.0					19																	12187275		692	1591	2283	SO:0001583	missense	284391				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr19:12187275G>C	AL832297	CCDS45985.1	19p13.2	2013-01-08			ENSG00000223547	ENSG00000223547		"""Zinc fingers, C2H2-type"", ""-"""	25932	protein-coding gene	gene with protein product							Standard	NM_001136501		Approved	FLJ14959	uc002mtb.2	Q08AG5	OTTHUMG00000156405	ENST00000439326.3:c.1340G>C	19.37:g.12187275G>C	ENSP00000392024:p.Arg447Pro					ZNF844_ENST00000441304.2_3'UTR	p.R447P	NM_001136501.1	NP_001129973.1	Q08AG5	ZN844_HUMAN			4	1515	+			447					Q5JPI8	Missense_Mutation	SNP	ENST00000439326.3	37	c.1340G>C	CCDS45985.1	.	.	.	.	.	.	.	.	.	.	T	0.637	-0.814748	0.02776	.	.	ENSG00000223547	ENST00000439326;ENST00000541708	T	0.03717	3.83	2.88	-3.56	0.04626	.	.	.	.	.	T	0.00524	0.0017	N	0.00049	-2.415	0.51482	D	0.999921	B	0.02656	0.0	B	0.01281	0.0	T	0.45175	-0.9279	9	0.02654	T	1	.	2.6221	0.04919	0.1164:0.4107:0.122:0.3509	.	447	Q08AG5	ZN844_HUMAN	P	447	ENSP00000392024:R447P	ENSP00000392024:R447P	R	+	2	0	ZNF844	12048275	0.000000	0.05858	0.012000	0.15200	0.001000	0.01503	-7.066000	0.00045	-0.984000	0.03507	-4.296000	0.00007	CGT		0.433	ZNF844-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344086.2			4	94	0	0	0	1	0	4	94				
RPL32P3	132241	broad.mit.edu	37	3	129116000	129116000	+	RNA	SNP	A	A	G			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr3:129116000A>G	ENST00000514355.1	-	0	412				SNORA7B_ENST00000384360.1_RNA					ribosomal protein L32 pseudogene 3											lung(1)	1						GGGAAGAAGTAGCCCCAGGTG	0.542																																						ENST00000514355.1																			0				lung(1)	1																																														0							g.chr3:129116000A>G	AK096589, AL117606		3q21.3	2014-03-20			ENSG00000251474	ENSG00000251474			27024	pseudogene	pseudogene						12477932	Standard	NR_003111		Approved		uc003ema.4		OTTHUMG00000159465		3.37:g.129116000A>G														0	412	-									RNA	SNP	ENST00000514355.1	37																																																																																						0.542	RPL32P3-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000355880.1			4	179	0	0	0	1	0	4	179				
YTHDC1	91746	broad.mit.edu	37	4	69202908	69202908	+	Silent	SNP	C	C	T	rs548927284	byFrequency	TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr4:69202908C>T	ENST00000344157.4	-	4	1055	c.720G>A	c.(718-720)gaG>gaA	p.E240E	YTHDC1_ENST00000579690.1_Silent_p.E240E|YTHDC1_ENST00000355665.3_Silent_p.E240E	NM_001031732.2	NP_001026902.1	Q96MU7	YTDC1_HUMAN	YTH domain containing 1	240	Glu-rich.				mRNA splice site selection (GO:0006376)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	30						cctcctcctcctcttcctcct	0.478																																						ENST00000344157.4																			0				NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	30						c.(718-720)gaG>gaA		YTH domain containing 1							141.0	100.0	114.0					4																	69202908		2203	4300	6503	SO:0001819	synonymous_variant	91746							g.chr4:69202908C>T	AK098515	CCDS3522.2, CCDS33992.1	4q13.3	2009-01-14			ENSG00000083896	ENSG00000083896			30626	protein-coding gene	gene with protein product						12368078, 10564280	Standard	XM_005265706		Approved	YT521, KIAA1966, YT521-B	uc003hdx.3	Q96MU7	OTTHUMG00000129306	ENST00000344157.4:c.720G>A	4.37:g.69202908C>T						YTHDC1_ENST00000579690.1_Silent_p.E240E|YTHDC1_ENST00000355665.3_Silent_p.E240E	p.E240E	NM_001031732.2	NP_001026902.1	Q96MU7	YTDC1_HUMAN			4	1055	-			240			Glu-rich.		Q4W5Q3|Q7Z622|Q8TF35	Silent	SNP	ENST00000344157.4	37	c.720G>A	CCDS33992.1																																																																																				0.478	YTHDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251437.1	NM_133370		3	35	0	0	0	1	0	3	35				
FOXP4	116113	broad.mit.edu	37	6	41557797	41557797	+	Missense_Mutation	SNP	G	G	A			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr6:41557797G>A	ENST00000307972.4	+	10	1258	c.1246G>A	c.(1246-1248)Gca>Aca	p.A416T	FOXP4_ENST00000373060.1_Missense_Mutation_p.A416T|FOXP4_ENST00000409208.1_Missense_Mutation_p.A404T|FOXP4_ENST00000373057.3_Missense_Mutation_p.A414T|FOXP4_ENST00000373063.3_Missense_Mutation_p.A403T			Q8IVH2	FOXP4_HUMAN	forkhead box P4	416					embryonic foregut morphogenesis (GO:0048617)|heart development (GO:0007507)|lung secretory cell differentiation (GO:0061140)|negative regulation of lung goblet cell differentiation (GO:1901250)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)	p.A403T(2)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	16	Ovarian(28;0.0327)|Colorectal(47;0.196)					GACCTCGGCCGCAGCCCCTGT	0.672																																						ENST00000373060.1																			2	Substitution - Missense(2)	p.A403T(2)	upper_aerodigestive_tract(1)|large_intestine(1)	autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	16						c.(1246-1248)Gca>Aca		forkhead box P4							32.0	35.0	34.0					6																	41557797		2202	4300	6502	SO:0001583	missense	116113				embryonic foregut morphogenesis|heart development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding	g.chr6:41557797G>A	AB080747	CCDS4856.1, CCDS34447.1, CCDS34448.1	6p21.1	2008-02-05			ENSG00000137166	ENSG00000137166		"""Forkhead boxes"""	20842	protein-coding gene	gene with protein product		608924					Standard	XM_006714991		Approved	FLJ40908	uc003oql.3	Q8IVH2	OTTHUMG00000014679	ENST00000307972.4:c.1246G>A	6.37:g.41557797G>A	ENSP00000309823:p.Ala416Thr					FOXP4_ENST00000307972.4_Missense_Mutation_p.A416T|FOXP4_ENST00000373063.3_Missense_Mutation_p.A403T|FOXP4_ENST00000409208.1_Missense_Mutation_p.A404T|FOXP4_ENST00000373057.3_Missense_Mutation_p.A414T	p.A416T	NM_001012426.1|NM_001012427.1	NP_001012426.1|NP_001012427.1	Q8IVH2	FOXP4_HUMAN			11	1704	+	Ovarian(28;0.0327)|Colorectal(47;0.196)		416					Q5W098|Q7Z7F8|Q8IW55|Q96E19	Missense_Mutation	SNP	ENST00000307972.4	37	c.1246G>A	CCDS34447.1	.	.	.	.	.	.	.	.	.	.	G	2.788	-0.252010	0.05829	.	.	ENSG00000137166	ENST00000373060;ENST00000373063;ENST00000409208;ENST00000373057;ENST00000307972	D;D;D;D;D	0.90197	-2.63;-2.6;-2.6;-2.63;-2.63	4.12	4.12	0.48240	.	0.135387	0.49916	D	0.000133	T	0.70945	0.3282	N	0.01576	-0.805	0.49798	D	0.999825	D;B;B	0.67145	0.996;0.011;0.008	P;B;B	0.53401	0.725;0.005;0.003	T	0.75720	-0.3219	10	0.32370	T	0.25	.	5.7433	0.18106	0.2678:0.0:0.7322:0.0	.	403;414;416	Q8IW55;Q7Z7F8;Q8IVH2	.;.;FOXP4_HUMAN	T	416;403;404;414;416	ENSP00000362151:A416T;ENSP00000362154:A403T;ENSP00000386958:A404T;ENSP00000362148:A414T;ENSP00000309823:A416T	ENSP00000309823:A416T	A	+	1	0	FOXP4	41665775	1.000000	0.71417	0.701000	0.30321	0.692000	0.40212	4.127000	0.57944	2.033000	0.60031	0.455000	0.32223	GCA		0.672	FOXP4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000106767.1	NM_138457		3	49	0	0	0	1	0	3	49				
ZMYM1	79830	broad.mit.edu	37	1	35580761	35580761	+	Silent	SNP	C	C	A			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr1:35580761C>A	ENST00000373330.1	+	11	3504	c.3330C>A	c.(3328-3330)gcC>gcA	p.A1110A	ZMYM1_ENST00000359858.4_Silent_p.A1110A|ZMYM1_ENST00000373329.1_3'UTR			Q5SVZ6	ZMYM1_HUMAN	zinc finger, MYM-type 1	1110						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(8)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				CTGGCCCAGCCCTAATGGCTG	0.383																																						ENST00000373330.1																			0				NS(1)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(8)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	31						c.(3328-3330)gcC>gcA		zinc finger, MYM-type 1							69.0	63.0	65.0					1																	35580761		1834	4098	5932	SO:0001819	synonymous_variant	79830					nucleus	nucleic acid binding|protein dimerization activity|zinc ion binding	g.chr1:35580761C>A	AK096206	CCDS41302.1	1p34.3	2008-05-02	2005-09-12		ENSG00000197056	ENSG00000197056		"""Zinc fingers, MYM type"""	26253	protein-coding gene	gene with protein product			"""zinc finger, MYM domain containing 1"""			12477932	Standard	XM_005271216		Approved	FLJ23151, MYM	uc001bym.3	Q5SVZ6	OTTHUMG00000004374	ENST00000373330.1:c.3330C>A	1.37:g.35580761C>A						ZMYM1_ENST00000373329.1_3'UTR|ZMYM1_ENST00000359858.4_Silent_p.A1110A	p.A1110A			Q5SVZ6	ZMYM1_HUMAN			11	3504	+		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)	1110					D3DPR7|Q7Z3Q4	Silent	SNP	ENST00000373330.1	37	c.3330C>A	CCDS41302.1																																																																																				0.383	ZMYM1-001	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012705.1	NM_024772		3	74	1	0	0.115264	1	0.119875	3	74				
GFI1	2672	broad.mit.edu	37	1	92941764	92941764	+	Splice_Site	SNP	C	C	T			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr1:92941764C>T	ENST00000370332.1	-	7	1409	c.1091G>A	c.(1090-1092)gGt>gAt	p.G364D	GFI1_ENST00000427103.1_Splice_Site_p.G364D|GFI1_ENST00000294702.5_Splice_Site_p.G364D	NM_001127215.1	NP_001120687.1	Q99684	GFI1_HUMAN	growth factor independent 1 transcription repressor	364					auditory receptor cell differentiation (GO:0042491)|cell fate commitment (GO:0045165)|cellular response to lipopolysaccharide (GO:0071222)|inner ear morphogenesis (GO:0042472)|mechanosensory behavior (GO:0007638)|negative regulation of calcidiol 1-monooxygenase activity (GO:0010956)|negative regulation of cell fate specification (GO:0009996)|negative regulation of neuron projection development (GO:0010977)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vitamin D biosynthetic process (GO:0010957)|positive regulation of cell fate specification (GO:0042660)|positive regulation of interleukin-6-mediated signaling pathway (GO:0070105)|regulation of toll-like receptor signaling pathway (GO:0034121)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|viral process (GO:0016032)	nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	15		all_lung(203;0.00292)|Lung NSC(277;0.0115)|all_neural(321;0.185)|Glioma(108;0.203)		OV - Ovarian serous cystadenocarcinoma(397;9.04e-07)|Epithelial(280;1.17e-05)|all cancers(265;5.61e-05)|GBM - Glioblastoma multiforme(16;0.0191)		AGGCTTCTCACCTGTGGGGAT	0.582																																						ENST00000370332.1																			0				autonomic_ganglia(1)|endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	15						c.e7-1		growth factor independent 1 transcription repressor							45.0	41.0	43.0					1																	92941764		2203	4300	6503	SO:0001630	splice_region_variant	2672				negative regulation of calcidiol 1-monooxygenase activity|negative regulation of NF-kappaB transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|regulation of transcription involved in G1/S phase of mitotic cell cycle|transcription, DNA-dependent|viral reproduction	nucleus	protein binding|transcription regulatory region DNA binding|zinc ion binding	g.chr1:92941764C>T	U67369	CCDS30773.1	1p22	2014-09-17	2007-10-04		ENSG00000162676	ENSG00000162676		"""Zinc fingers, C2H2-type"""	4237	protein-coding gene	gene with protein product		600871	"""growth factor independent 1"""	ZNF163		7789186	Standard	NM_005263		Approved	GFI1A, GFI-1	uc001dov.4	Q99684	OTTHUMG00000010897	ENST00000370332.1:c.1091-1G>A	1.37:g.92941764C>T						GFI1_ENST00000294702.5_Splice_Site_p.G364_splice|GFI1_ENST00000427103.1_Splice_Site_p.G364_splice	p.G364_splice	NM_001127215.1	NP_001120687.1	Q99684	GFI1_HUMAN		OV - Ovarian serous cystadenocarcinoma(397;9.04e-07)|Epithelial(280;1.17e-05)|all cancers(265;5.61e-05)|GBM - Glioblastoma multiforme(16;0.0191)	7	1409	-		all_lung(203;0.00292)|Lung NSC(277;0.0115)|all_neural(321;0.185)|Glioma(108;0.203)	364					Q8N564	Splice_Site	SNP	ENST00000370332.1	37	c.1090_splice	CCDS30773.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.226795	0.79576	.	.	ENSG00000162676	ENST00000370332;ENST00000427103;ENST00000294702	T;T;T	0.26660	1.72;1.72;1.72	5.33	5.33	0.75918	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.41534	0.1163	L	0.53671	1.685	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.34378	-0.9831	10	0.87932	D	0	.	19.0241	0.92926	0.0:1.0:0.0:0.0	.	364	Q99684	GFI1_HUMAN	D	364	ENSP00000359357:G364D;ENSP00000399719:G364D;ENSP00000294702:G364D	ENSP00000294702:G364D	G	-	2	0	GFI1	92714352	1.000000	0.71417	1.000000	0.80357	0.523000	0.34469	7.773000	0.85462	2.485000	0.83878	0.655000	0.94253	GGT		0.582	GFI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030054.1	NM_005263	Missense_Mutation	4	21	0	0	0	1	0	4	21				
IDO1	3620	broad.mit.edu	37	8	39775722	39775722	+	Missense_Mutation	SNP	G	G	A	rs200244502		TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr8:39775722G>A	ENST00000518237.1	+	3	938	c.299G>A	c.(298-300)cGt>cAt	p.R100H	RP11-44K6.3_ENST00000517623.1_RNA|IDO1_ENST00000522495.1_Missense_Mutation_p.R100H|RP11-44K6.4_ENST00000522970.1_RNA|RP11-44K6.2_ENST00000520185.1_RNA	NM_002164.5	NP_002155.1	P14902	I23O1_HUMAN	indoleamine 2,3-dioxygenase 1	100					cellular nitrogen compound metabolic process (GO:0034641)|cytokine production involved in inflammatory response (GO:0002534)|female pregnancy (GO:0007565)|kynurenic acid biosynthetic process (GO:0034276)|multicellular organismal response to stress (GO:0033555)|negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of T cell apoptotic process (GO:0070233)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chronic inflammatory response (GO:0002678)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of T cell tolerance induction (GO:0002666)|positive regulation of type 2 immune response (GO:0002830)|response to lipopolysaccharide (GO:0032496)|small molecule metabolic process (GO:0044281)|swimming behavior (GO:0036269)|tryptophan catabolic process (GO:0006569)|tryptophan catabolic process to kynurenine (GO:0019441)	cytosol (GO:0005829)|smooth muscle contractile fiber (GO:0030485)|stereocilium bundle (GO:0032421)	electron carrier activity (GO:0009055)|heme binding (GO:0020037)|indoleamine 2,3-dioxygenase activity (GO:0033754)|metal ion binding (GO:0046872)|tryptophan 2,3-dioxygenase activity (GO:0004833)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(2)	12					L-Tryptophan(DB00150)|Melatonin(DB01065)	GGAGATGTCCGTAAGGTTTGG	0.393																																						ENST00000518237.1																			0				central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(2)	12						c.(298-300)cGt>cAt		indoleamine 2,3-dioxygenase 1	L-Tryptophan(DB00150)	G	HIS/ARG	0,3838		0,0,1919	117.0	110.0	112.0		299	1.4	0.0	8		112	1,8277		0,1,4138	yes	missense	IDO1	NM_002164.5	29	0,1,6057	AA,AG,GG		0.0121,0.0,0.0083	probably-damaging	100/404	39775722	1,12115	1919	4139	6058	SO:0001583	missense	3620				female pregnancy|tryptophan catabolic process	cytosol	electron carrier activity|heme binding|indoleamine 2,3-dioxygenase activity|tryptophan 2,3-dioxygenase activity	g.chr8:39775722G>A	M34455	CCDS47847.1	8p12-p11	2009-01-07	2009-01-07	2009-01-07		ENSG00000131203	1.13.11.52		6059	protein-coding gene	gene with protein product		147435	"""indoleamine-pyrrole 2,3 dioxygenase"""	IDO, INDO		2109605, 8404046	Standard	NM_002164		Approved		uc003xnm.3	P14902		ENST00000518237.1:c.299G>A	8.37:g.39775722G>A	ENSP00000430950:p.Arg100His					RP11-44K6.4_ENST00000522970.1_RNA|IDO1_ENST00000522495.1_Missense_Mutation_p.R100H|RP11-44K6.3_ENST00000517623.1_RNA	p.R100H	NM_002164.5	NP_002155.1	P14902	I23O1_HUMAN			3	938	+			100					Q540B4	Missense_Mutation	SNP	ENST00000518237.1	37	c.299G>A	CCDS47847.1	.	.	.	.	.	.	.	.	.	.	G	14.05	2.420693	0.42918	0.0	1.21E-4	ENSG00000131203	ENST00000519154;ENST00000522495;ENST00000518237	T;T;T	0.45276	0.9;0.9;0.9	5.65	1.44	0.22558	.	0.907386	0.09317	N	0.818769	T	0.43255	0.1239	M	0.79475	2.455	0.09310	N	1	D	0.54047	0.964	P	0.45377	0.478	T	0.44360	-0.9333	9	.	.	.	-1.485	1.7288	0.02928	0.1757:0.2276:0.4465:0.1502	.	100	P14902	I23O1_HUMAN	H	100	ENSP00000428716:R100H;ENSP00000430505:R100H;ENSP00000430950:R100H	.	R	+	2	0	IDO1	39894879	0.000000	0.05858	0.003000	0.11579	0.237000	0.25408	0.234000	0.17930	0.751000	0.32900	0.585000	0.79938	CGT		0.393	IDO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376987.1	NM_002164		4	111	0	0	0	1	0	4	111				
MOV10	4343	broad.mit.edu	37	1	113234306	113234306	+	Nonsense_Mutation	SNP	G	G	T			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr1:113234306G>T	ENST00000413052.2	+	6	1246	c.856G>T	c.(856-858)Gag>Tag	p.E286*	MOV10_ENST00000369644.1_Nonsense_Mutation_p.E230*|RP11-426L16.3_ENST00000421943.1_RNA|MOV10_ENST00000369645.1_Nonsense_Mutation_p.E286*|MOV10_ENST00000357443.2_Nonsense_Mutation_p.E286*|MOV10_ENST00000468624.1_3'UTR	NM_001130079.1|NM_020963.3	NP_001123551.1|NP_066014.1	Q9HCE1	MOV10_HUMAN	Mov10 RISC complex RNA helicase	286					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(3)	38	Lung SC(450;0.246)	all_cancers(81;3.31e-11)|all_epithelial(167;5.69e-10)|all_lung(203;3.73e-05)|Breast(1374;0.000525)|Lung NSC(69;0.000954)|Ovarian(761;0.0367)|Lung SC(238;0.114)		OV - Ovarian serous cystadenocarcinoma(397;3.99e-67)|all cancers(265;1e-62)|Epithelial(280;4.78e-61)|Lung(183;0.0234)|Colorectal(144;0.0686)|READ - Rectum adenocarcinoma(129;0.0929)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|BRCA - Breast invasive adenocarcinoma(282;0.24)		CTATGACCTGGAGTTAAGTAT	0.557																																						ENST00000369644.1																			0				breast(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(3)	38						c.(688-690)Gag>Tag		Mov10, Moloney leukemia virus 10, homolog (mouse)							133.0	137.0	135.0					1																	113234306		2203	4300	6503	SO:0001587	stop_gained	4343				mRNA cleavage involved in gene silencing by miRNA|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body	ATP binding|helicase activity|protein binding|RNA binding	g.chr1:113234306G>T	AL833353	CCDS853.1, CCDS65615.1	1p13.2	2014-07-02	2014-07-02		ENSG00000155363	ENSG00000155363			7200	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 113"""	610742	"""Mov10 (Moloney leukemia virus 10, mouse) homolog"", ""Mov10, Moloney leukemia virus 10, homolog (mouse)"""			12226669	Standard	NM_001286072		Approved	gb110, MGC2948, fSAP113	uc001eck.3	Q9HCE1	OTTHUMG00000011906	ENST00000413052.2:c.856G>T	1.37:g.113234306G>T	ENSP00000399797:p.Glu286*					MOV10_ENST00000369645.1_Nonsense_Mutation_p.E286*|MOV10_ENST00000468624.1_3'UTR|MOV10_ENST00000357443.2_Nonsense_Mutation_p.E286*|MOV10_ENST00000413052.2_Nonsense_Mutation_p.E286*	p.E230*			Q9HCE1	MOV10_HUMAN		OV - Ovarian serous cystadenocarcinoma(397;3.99e-67)|all cancers(265;1e-62)|Epithelial(280;4.78e-61)|Lung(183;0.0234)|Colorectal(144;0.0686)|READ - Rectum adenocarcinoma(129;0.0929)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|BRCA - Breast invasive adenocarcinoma(282;0.24)	7	1717	+	Lung SC(450;0.246)	all_cancers(81;3.31e-11)|all_epithelial(167;5.69e-10)|all_lung(203;3.73e-05)|Breast(1374;0.000525)|Lung NSC(69;0.000954)|Ovarian(761;0.0367)|Lung SC(238;0.114)	286					Q5JR03|Q8TEF0|Q9BSY3|Q9BUJ9	Nonsense_Mutation	SNP	ENST00000413052.2	37	c.688G>T	CCDS853.1	.	.	.	.	.	.	.	.	.	.	G	46	12.447184	0.99668	.	.	ENSG00000155363	ENST00000413052;ENST00000369645;ENST00000285733;ENST00000369644;ENST00000357443;ENST00000369648	.	.	.	5.01	4.1	0.47936	.	0.296733	0.41001	D	0.000969	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.16896	T	0.51	-23.5734	9.4576	0.38764	0.096:0.0:0.904:0.0	.	.	.	.	X	286;286;286;230;286;224	.	ENSP00000285733:E286X	E	+	1	0	MOV10	113035829	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	2.898000	0.48672	1.495000	0.48549	0.561000	0.74099	GAG		0.557	MOV10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032906.1	NM_020963		66	79	1	0	7.05995e-25	1	7.64828e-25	66	79				
GBF1	8729	broad.mit.edu	37	10	104139192	104139192	+	Splice_Site	SNP	G	G	A			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr10:104139192G>A	ENST00000369983.3	+	34	4902		c.e34+1			NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1						COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		TTACTGCAGGGTAAACCAGGA	0.582																																						ENST00000369983.3																			0				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71						c.e34+1		golgi brefeldin A resistant guanine nucleotide exchange factor 1							53.0	50.0	51.0					10																	104139192		2203	4300	6503	SO:0001630	splice_region_variant	8729				COPI coating of Golgi vesicle|post-Golgi vesicle-mediated transport|regulation of ARF protein signal transduction|retrograde vesicle-mediated transport, Golgi to ER	Golgi membrane	ARF guanyl-nucleotide exchange factor activity|protein binding	g.chr10:104139192G>A	D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"""golgi-specific brefeldin A resistance factor 1"""			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.4642+1G>A	10.37:g.104139192G>A								NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)	34	4902	+		Colorectal(252;0.0236)						Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Splice_Site	SNP	ENST00000369983.3	37		CCDS7533.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.220155	0.79464	.	.	ENSG00000107862	ENST00000369983	.	.	.	5.03	5.03	0.67393	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.5757	0.91154	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	GBF1	104129182	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	9.456000	0.97628	2.614000	0.88457	0.561000	0.74099	.		0.582	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1		Intron	3	55	0	0	0	1	0	3	55				
XRCC6	2547	broad.mit.edu	37	22	42052945	42052945	+	Missense_Mutation	SNP	A	A	G			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr22:42052945A>G	ENST00000359308.4	+	9	1985	c.1330A>G	c.(1330-1332)Agg>Ggg	p.R444G	XRCC6_ENST00000402580.3_Missense_Mutation_p.R403G|XRCC6_ENST00000428575.2_Missense_Mutation_p.R311G|XRCC6_ENST00000405506.1_Missense_Mutation_p.R394G|XRCC6_ENST00000405878.1_Missense_Mutation_p.R444G|XRCC6_ENST00000360079.3_Missense_Mutation_p.R444G			P12956	XRCC6_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 6	444	Ku.				brain development (GO:0007420)|cellular hyperosmotic salinity response (GO:0071475)|cellular response to X-ray (GO:0071481)|DNA duplex unwinding (GO:0032508)|DNA ligation (GO:0006266)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|innate immune response (GO:0045087)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|telomere maintenance (GO:0000723)|transcription, DNA-templated (GO:0006351)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	cytosol (GO:0005829)|Ku70:Ku80 complex (GO:0043564)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nuclear telomere cap complex (GO:0000783)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	5'-deoxyribose-5-phosphate lyase activity (GO:0051575)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|telomeric DNA binding (GO:0042162)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|liver(2)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	31						TGATGATAAAAGGAAGATGCC	0.418								Non-homologous end-joining																														ENST00000359308.4																			0				central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|liver(2)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	31						c.(1330-1332)Agg>Ggg	Non-homologous end-joining	X-ray repair complementing defective repair in Chinese hamster cells 6							81.0	77.0	79.0					22																	42052945		2203	4300	6503	SO:0001583	missense	2547				DNA ligation|double-strand break repair via nonhomologous end joining|initiation of viral infection|negative regulation of transcription, DNA-dependent|positive regulation of transcription from RNA polymerase II promoter|provirus integration|telomere maintenance|transcription, DNA-dependent	DNA-dependent protein kinase-DNA ligase 4 complex|Ku70:Ku80 complex|membrane fraction|nuclear telomere cap complex|transcription factor complex	5'-deoxyribose-5-phosphate lyase activity|ATP binding|ATP-dependent DNA helicase activity|double-stranded DNA binding|protein C-terminus binding|transcription regulatory region DNA binding	g.chr22:42052945A>G	J04607	CCDS14021.1, CCDS74870.1, CCDS74871.1	22q13.2	2011-09-12	2008-07-31	2005-05-06	ENSG00000196419	ENSG00000196419			4055	protein-coding gene	gene with protein product	"""Ku autoantigen, 70kDa"""	152690	"""thyroid autoantigen 70kD (Ku antigen)"", ""thyroid autoantigen 70kDa (Ku antigen)"""	G22P1		9200330, 9223317	Standard	NM_001469		Approved	D22S731, D22S671, KU70, ML8	uc003bao.1	P12956	OTTHUMG00000151190	ENST00000359308.4:c.1330A>G	22.37:g.42052945A>G	ENSP00000352257:p.Arg444Gly					XRCC6_ENST00000405506.1_Missense_Mutation_p.R394G|XRCC6_ENST00000402580.3_Missense_Mutation_p.R403G|XRCC6_ENST00000428575.2_Missense_Mutation_p.R311G|XRCC6_ENST00000360079.3_Missense_Mutation_p.R444G|XRCC6_ENST00000405878.1_Missense_Mutation_p.R444G	p.R444G			P12956	XRCC6_HUMAN			9	1985	+			444			Ku.		B1AHC8|Q6FG89|Q9UCQ2|Q9UCQ3	Missense_Mutation	SNP	ENST00000359308.4	37	c.1330A>G	CCDS14021.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.950063	0.73787	.	.	ENSG00000196419	ENST00000360079;ENST00000402580;ENST00000428575;ENST00000359308;ENST00000405878;ENST00000402409;ENST00000405506	.	.	.	5.46	3.29	0.37713	Spen Paralogue and Orthologue SPOC, C-terminal-like (1);DNA helicase, ATP-dependent, Ku type (2);Ku70/Ku80 C-terminal arm (1);	0.000000	0.85682	D	0.000000	D	0.84352	0.5453	M	0.91038	3.17	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.997;0.999;0.989;0.997	D	0.88326	0.2965	9	0.87932	D	0	-11.2454	14.1857	0.65605	0.2822:0.7178:0.0:0.0	.	394;444;403;444	B1AHC9;B1AHC7;B1AHC8;P12956	.;.;.;XRCC6_HUMAN	G	444;403;311;444;444;444;394	.	ENSP00000352257:R444G	R	+	1	2	XRCC6	40382891	0.962000	0.33011	1.000000	0.80357	0.941000	0.58515	2.246000	0.43142	1.286000	0.44565	-0.213000	0.12676	AGG		0.418	XRCC6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321688.1	NM_001469		3	69	0	0	0	1	0	3	69				
CXCL5	6374	broad.mit.edu	37	4	74864215	74864217	+	In_Frame_Del	DEL	CAG	CAG	-	rs139966143	byFrequency	TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr4:74864215_74864217delCAG	ENST00000296027.4	-	1	279_281	c.82_84delCTG	c.(82-84)ctgdel	p.L28del		NM_002994.3	NP_002985.1	P42830	CXCL5_HUMAN	chemokine (C-X-C motif) ligand 5	28					cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|chemotaxis (GO:0006935)|immune response (GO:0006955)|positive regulation of cell proliferation (GO:0008284)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemokine activity (GO:0008009)			endometrium(3)|large_intestine(2)|lung(3)|urinary_tract(1)	9	Breast(15;0.00136)		all cancers(17;0.00273)|Lung(101;0.196)			CTGGCTGCGTCAGCAGCAGCAGC	0.7																																						ENST00000296027.4																			0				endometrium(3)|large_intestine(2)|lung(3)|urinary_tract(1)	9						c.(82-84)del		chemokine (C-X-C motif) ligand 5				159,4049		24,111,1969						-0.9	0.4			15	307,7843		42,223,3810	no	coding	CXCL5	NM_002994.3		66,334,5779	A1A1,A1R,RR		3.7669,3.7785,3.7708				466,11892				SO:0001651	inframe_deletion	6374				cell-cell signaling|chemotaxis|immune response|positive regulation of cell proliferation|signal transduction	extracellular space	chemokine activity	g.chr4:74864215_74864217delCAG	X78686	CCDS34006.1	4q13.3	2013-02-25	2002-08-22	2002-08-23		ENSG00000163735		"""Endogenous ligands"""	10642	protein-coding gene	gene with protein product		600324	"""small inducible cytokine subfamily B (Cys-X-Cys), member 5 (epithelial-derived neutrophil-activating peptide 78)"""	SCYB5		7929219	Standard	NM_002994		Approved	ENA-78	uc003hhk.4	P42830		ENST00000296027.4:c.82_84delCTG	4.37:g.74864224_74864226delCAG	ENSP00000296027:p.Leu28del						p.L28del	NM_002994.3	NP_002985.1	P42830	CXCL5_HUMAN	all cancers(17;0.00273)|Lung(101;0.196)		1	279_281	-	Breast(15;0.00136)		28					Q96QE1	In_Frame_Del	DEL	ENST00000296027.4	37	c.82_84delCTG	CCDS34006.1																																																																																				0.700	CXCL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362749.1	NM_002994		2	4						2	4	---	---	---	---
TPTE2	93492	broad.mit.edu	37	13	20041394	20041394	+	Frame_Shift_Del	DEL	A	A	-			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr13:20041394delA	ENST00000400230.2	-	7	527	c.483delT	c.(481-483)tttfs	p.F161fs	TPTE2_ENST00000400103.2_Intron|TPTE2_ENST00000390680.2_Intron|TPTE2_ENST00000382975.4_Intron|TPTE2_ENST00000255310.6_Intron|TPTE2_ENST00000382977.4_Frame_Shift_Del_p.F161fs|TPTE2_ENST00000382978.1_Intron|TPTE2_ENST00000457266.2_Intron			Q6XPS3	TPTE2_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	161					phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		ACTTAATGTCAAAAAAAATGT	0.303																																						ENST00000400230.2																			0				NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						c.(481-483)ttfs		transmembrane phosphoinositide 3-phosphatase and tensin homolog 2			,,	4,21,4229		0,0,4,1,19,2103	46.0	51.0	49.0		,,	2.4	0.0	13		49	5,25,8188		0,1,4,4,16,4084	no	codingComplex,intron,intron	TPTE2	NM_199254.2,NM_130785.3,NM_001141968.1	,,	0,1,8,5,35,6187	A1A1,A1A2,A1R,A2A2,A2R,RR		0.3651,0.5877,0.441	,,	,,	20041394	9,46,12417	2200	4283	6483	SO:0001589	frameshift_variant	93492					endoplasmic reticulum membrane|integral to membrane	ion channel activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	g.chr13:20041394delA	AJ421032	CCDS9285.1, CCDS45013.1, CCDS45014.1	13q12.11	2012-12-10			ENSG00000132958	ENSG00000132958		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	17299	protein-coding gene	gene with protein product		606791				11716755, 12717346, 15057823	Standard	NM_130785		Approved	TPIP	uc001umd.3	Q6XPS3	OTTHUMG00000016493	ENST00000400230.2:c.483delT	13.37:g.20041394delA	ENSP00000383089:p.Phe161fs					TPTE2_ENST00000382977.4_Frame_Shift_Del_p.F161fs|TPTE2_ENST00000382978.1_Intron|TPTE2_ENST00000255310.6_Intron|TPTE2_ENST00000457266.2_Intron|TPTE2_ENST00000382975.4_Intron|TPTE2_ENST00000400103.2_Intron|TPTE2_ENST00000390680.2_Intron	p.F161fs			Q6XPS3	TPTE2_HUMAN		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)	7	527	-		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)	161					A1A4X0|A1A4X1|A8MX64|B1AQ16|B4DWZ2|Q5VUH2|Q8WWL4|Q8WWL5	Frame_Shift_Del	DEL	ENST00000400230.2	37	c.483delT	CCDS45014.1																																																																																				0.303	TPTE2-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_199254		7	114						7	114	---	---	---	---
IGHV1OR21-1	390530	broad.mit.edu	37	21	10862646	10862646	+	RNA	DEL	T	T	-			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr21:10862646delT	ENST00000559480.1	+	0	25							A6NJS3	IV1U1_HUMAN	immunoglobulin heavy variable 1/OR21-1 (non-functional)							extracellular region (GO:0005576)				breast(1)|endometrium(1)|kidney(3)|lung(20)|urinary_tract(1)	26						GAGGATCCTGTTTTTGGTGGT	0.512																																						ENST00000559480.1																			0				breast(1)|endometrium(1)|kidney(3)|lung(20)|urinary_tract(1)	26															352.0	330.0	337.0					21																	10862646		1950	4148	6098			0							g.chr21:10862646delT			21p11.2	2014-05-06	2010-11-09		ENSG00000169861	ENSG00000277282		"""Immunoglobulins / IGH orphons"""	38040	other	immunoglobulin gene			"""immunoglobulin heavy variable 1/OR21-1 pseudogene"""				Standard	NG_011680		Approved	IGHV1/OR21-1		A6NJS3	OTTHUMG00000188295		21.37:g.10862646delT														0	25	+									RNA	DEL	ENST00000559480.1	37																																																																																						0.512	IGHV1OR21-1-201	KNOWN	basic|appris_principal	IG_V_gene	IG_V_gene		NG_011680		7	719						7	719	---	---	---	---
CRYBB2P1	1416	broad.mit.edu	37	22	25855683	25855684	+	RNA	DEL	GT	GT	-			TCGA-EM-A3O8-01A-11D-A21Z-08	TCGA-EM-A3O8-10A-01D-A21Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	273fa499-61f1-44ac-b537-3f6d7fbba63a	dfb338fd-ead0-4819-9fb3-5e701e5cf53d	g.chr22:25855683_25855684delGT	ENST00000609084.1	+	0	0									crystallin, beta B2 pseudogene 1																		CTGGCAGCTGgtgtgtgtgtgt	0.525																																						ENST00000354451.2																			0																																																			0							g.chr22:25855683_25855684delGT	M18441		22q11.2-q12.1	2012-02-29			ENSG00000100058	ENSG00000100058			2399	pseudogene	pseudogene				CRYB2B			Standard	NR_033733		Approved		uc003abu.4		OTTHUMG00000150874		22.37:g.25855693_25855694delGT														0	366	+									RNA	DEL	ENST00000609084.1	37																																																																																						0.525	CRYBB2P1-006	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000472347.1			4	3						4	3	---	---	---	---
