#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
PRTG	283659	broad.mit.edu	37	15	55933315	55933315	+	Silent	SNP	G	G	A	rs201795095	byFrequency	TCGA-P7-A5NY-05A-11D-A35D-08	TCGA-P7-A5NY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d	87bae02a-0994-4ce5-a27b-72494a4a1b5f	g.chr15:55933315G>A	ENST00000389286.4	-	12	2180	c.2133C>T	c.(2131-2133)tgC>tgT	p.C711C		NM_173814.4	NP_776175.2			protogenin											breast(1)|endometrium(6)|kidney(4)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	41				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)		ACTTACACACGCATCCTGGAG	0.448													G|||	3	0.000599042	0.0	0.0014	5008	,	,		17280	0.0		0.001	False		,,,				2504	0.001					ENST00000389286.4																			0				breast(1)|endometrium(6)|kidney(4)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	41						c.(2131-2133)tgC>tgT		protogenin		G		0,3994		0,0,1997	122.0	119.0	120.0		2133	-7.8	0.5	15		120	5,8341		0,5,4168	no	coding-synonymous	PRTG	NM_173814.4		0,5,6165	AA,AG,GG		0.0599,0.0,0.0405		711/1151	55933315	5,12335	1997	4173	6170	SO:0001819	synonymous_variant	283659				multicellular organismal development	integral to membrane		g.chr15:55933315G>A	AK098622	CCDS42040.1	15q21.3	2013-02-11	2010-06-24		ENSG00000166450	ENSG00000166450		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	26373	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 5"""	613261	"""protogenin homolog (Gallus gallus)"""				Standard	NM_173814		Approved	FLJ25756, IGDCC5	uc002adg.3	Q2VWP7		ENST00000389286.4:c.2133C>T	15.37:g.55933315G>A							p.C711C	NM_173814.4	NP_776175.2	Q2VWP7	PRTG_HUMAN		all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)	12	2180	-			711						Silent	SNP	ENST00000389286.4	37	c.2133C>T	CCDS42040.1																																																																																				0.448	PRTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419357.1	NM_173814		3	26	0	0	0	1	0	3	26				
BTN2A3P	54718	broad.mit.edu	37	6	26422353	26422353	+	RNA	SNP	C	C	T	rs571530750	byFrequency	TCGA-P7-A5NY-05A-11D-A35D-08	TCGA-P7-A5NY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d	87bae02a-0994-4ce5-a27b-72494a4a1b5f	g.chr6:26422353C>T	ENST00000466808.2	+	0	7							Q96KV6	BT2A3_HUMAN	butyrophilin, subfamily 2, member A3, pseudogene							integral component of membrane (GO:0016021)		p.P3S(2)									GCTCATGGAACCAGCTGCTGC	0.622													C|||	7	0.00139776	0.0023	0.0	5008	,	,		16376	0.001		0.0	False		,,,				2504	0.0031					ENST00000466808.2																			2	Substitution - Missense(2)	p.P3S(2)	endometrium(1)|kidney(1)																																																54718							g.chr6:26422353C>T	AL021917		6p22.1	2014-01-14	2011-09-06	2011-09-06	ENSG00000124549	ENSG00000124549		"""Butyrophilins"""	13229	pseudogene	pseudogene		613592	"""butyrophilin, subfamily 2, member A3"""	BTN2A3			Standard	NR_027795		Approved	BTN2.3	uc011dkl.1	Q96KV6	OTTHUMG00000014453		6.37:g.26422353C>T														0	7	+								A6NEF4	RNA	SNP	ENST00000466808.2	37																																																																																						0.622	BTN2A3P-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000040118.4	NR_027795		4	90	0	0	0	1	0	4	90				
TRPS1	7227	broad.mit.edu	37	8	116599567	116599567	+	Silent	SNP	G	G	A			TCGA-P7-A5NY-05A-11D-A35D-08	TCGA-P7-A5NY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d	87bae02a-0994-4ce5-a27b-72494a4a1b5f	g.chr8:116599567G>A	ENST00000220888.5	-	4	2481	c.2322C>T	c.(2320-2322)gaC>gaT	p.D774D	TRPS1_ENST00000519076.1_Silent_p.D528D|TRPS1_ENST00000520276.1_Silent_p.D778D|TRPS1_ENST00000519674.1_Silent_p.D774D|TRPS1_ENST00000395715.3_Silent_p.D787D			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	774	Mediates interaction with GLI3.				chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			CTTTGAGCCCGTCCTTCTCTT	0.507									Langer-Giedion syndrome																													ENST00000395715.3																			0				autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111						c.(2359-2361)gaC>gaT		trichorhinophalangeal syndrome I							291.0	299.0	297.0					8																	116599567		1953	4139	6092	SO:0001819	synonymous_variant	7227	Langer-Giedion syndrome	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr8:116599567G>A	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447		"""GATA zinc finger domain containing"", ""Zinc fingers, C2H2-type"""	12340	protein-coding gene	gene with protein product		604386				8530105, 10615131, 10647898	Standard	NM_001282903		Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000220888.5:c.2322C>T	8.37:g.116599567G>A						TRPS1_ENST00000220888.5_Silent_p.D774D|TRPS1_ENST00000519076.1_Silent_p.D528D|TRPS1_ENST00000519674.1_Silent_p.D774D|TRPS1_ENST00000520276.1_Silent_p.D778D	p.D787D	NM_014112.2	NP_054831.2	Q9UHF7	TRPS1_HUMAN	Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)		5	2938	-	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		774			Mediates interaction with GLI3.		B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Silent	SNP	ENST00000220888.5	37	c.2361C>T																																																																																					0.507	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112		4	179	0	0	0	1	0	4	179				
CRAT	1384	broad.mit.edu	37	9	131860910	131860910	+	Missense_Mutation	SNP	G	G	A			TCGA-P7-A5NY-05A-11D-A35D-08	TCGA-P7-A5NY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d	87bae02a-0994-4ce5-a27b-72494a4a1b5f	g.chr9:131860910G>A	ENST00000318080.2	-	9	1399	c.1105C>T	c.(1105-1107)Cgg>Tgg	p.R369W	RP11-247A12.1_ENST00000434250.1_RNA	NM_000755.3|NM_001257363.1	NP_000746|NP_001244292.1	P43155	CACP_HUMAN	carnitine O-acetyltransferase	369					carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carnitine O-acetyltransferase activity (GO:0004092)|receptor binding (GO:0005102)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(4)|skin(1)|urinary_tract(2)	13				UCEC - Uterine corpus endometrioid carcinoma (4;0.0178)	L-Carnitine(DB00583)	AGGGGAGACCGCACAAGCTCG	0.607																																						ENST00000318080.2																			0				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(4)|skin(1)|urinary_tract(2)	13						c.(1105-1107)Cgg>Tgg		carnitine O-acetyltransferase	L-Carnitine(DB00583)						118.0	104.0	109.0					9																	131860910		2203	4300	6503	SO:0001583	missense	1384				energy derivation by oxidation of organic compounds|fatty acid beta-oxidation using acyl-CoA oxidase|transport	endoplasmic reticulum|mitochondrial inner membrane|peroxisomal matrix	carnitine O-acetyltransferase activity	g.chr9:131860910G>A	X78706	CCDS6919.1	9q34.1	2010-04-27	2010-04-27		ENSG00000095321	ENSG00000095321	2.3.1.7		2342	protein-coding gene	gene with protein product		600184	"""carnitine acetyltransferase"""			7829107	Standard	NM_000755		Approved	CAT1	uc004bxh.3	P43155	OTTHUMG00000147343	ENST00000318080.2:c.1105C>T	9.37:g.131860910G>A	ENSP00000315013:p.Arg369Trp					RP11-247A12.1_ENST00000434250.1_RNA	p.R369W	NM_000755.3|NM_001257363.1	NP_000746.2|NP_001244292.1	P43155	CACP_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (4;0.0178)	9	1399	-			369					Q5T952|Q9BW16	Missense_Mutation	SNP	ENST00000318080.2	37	c.1105C>T	CCDS6919.1	.	.	.	.	.	.	.	.	.	.	G	17.77	3.470057	0.63625	.	.	ENSG00000095321	ENST00000351352;ENST00000318080	T	0.44482	0.92	5.13	3.1	0.35709	.	0.056122	0.64402	D	0.000002	T	0.54111	0.1838	M	0.74881	2.28	0.37868	D	0.929969	D	0.71674	0.998	P	0.54346	0.749	T	0.59542	-0.7435	10	0.27082	T	0.32	-40.4196	14.3146	0.66440	0.0:0.0:0.7749:0.2251	.	369	P43155	CACP_HUMAN	W	288;369	ENSP00000315013:R369W	ENSP00000315013:R369W	R	-	1	2	CRAT	130900731	0.019000	0.18553	0.765000	0.31456	0.694000	0.40290	1.150000	0.31639	0.670000	0.31165	0.561000	0.74099	CGG		0.607	CRAT-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253700.1			4	83	0	0	0	1	0	4	83				
AMOT	154796	broad.mit.edu	37	X	112058796	112058796	+	Silent	SNP	C	C	T			TCGA-P7-A5NY-05A-11D-A35D-08	TCGA-P7-A5NY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d	87bae02a-0994-4ce5-a27b-72494a4a1b5f	g.chrX:112058796C>T	ENST00000524145.1	-	3	1256	c.1182G>A	c.(1180-1182)caG>caA	p.Q394Q	AMOT_ENST00000371959.3_Silent_p.Q394Q|AMOT_ENST00000371962.1_Silent_p.Q162Q|AMOT_ENST00000371958.1_Silent_p.Q162Q|AMOT_ENST00000304758.1_5'UTR			Q4VCS5	AMOT_HUMAN	angiomotin	394					actin cytoskeleton organization (GO:0030036)|blood vessel endothelial cell migration (GO:0043534)|cell migration involved in gastrulation (GO:0042074)|cell-cell junction assembly (GO:0007043)|cellular protein localization (GO:0034613)|chemotaxis (GO:0006935)|establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|gastrulation with mouth forming second (GO:0001702)|hippo signaling (GO:0035329)|in utero embryonic development (GO:0001701)|negative regulation of angiogenesis (GO:0016525)|negative regulation of GTPase activity (GO:0034260)|negative regulation of vascular permeability (GO:0043116)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell size (GO:0045793)|positive regulation of embryonic development (GO:0040019)|positive regulation of stress fiber assembly (GO:0051496)|regulation of cell migration (GO:0030334)|regulation of small GTPase mediated signal transduction (GO:0051056)|vasculogenesis (GO:0001570)	actin filament (GO:0005884)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|ruffle (GO:0001726)|stress fiber (GO:0001725)|tight junction (GO:0005923)	angiostatin binding (GO:0043532)|receptor activity (GO:0004872)	p.Q394Q(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	43						gctgctgctgctgttgttggt	0.582																																						ENST00000371959.3																			1	Substitution - coding silent(1)	p.Q394Q(1)	lung(1)	breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	43						c.(1180-1182)caG>caA		angiomotin							38.0	34.0	36.0					X																	112058796		2203	4300	6503	SO:0001819	synonymous_variant	154796				actin cytoskeleton organization|cell-cell junction assembly|negative regulation of angiogenesis|negative regulation of vascular permeability|positive regulation of blood vessel endothelial cell migration|positive regulation of cell size|positive regulation of stress fiber assembly|regulation of cell migration	actin filament|cell surface|cytoplasm|endocytic vesicle|external side of plasma membrane|integral to membrane|lamellipodium|ruffle|stress fiber|tight junction	angiostatin binding|protein binding|receptor activity	g.chrX:112058796C>T	AB028994	CCDS14563.1, CCDS48154.1	Xq23	2006-02-08			ENSG00000126016	ENSG00000126016			17810	protein-coding gene	gene with protein product		300410				11257124, 16043488, 12406577	Standard	NM_001113490		Approved	KIAA1071	uc004epr.3	Q4VCS5	OTTHUMG00000022216	ENST00000524145.1:c.1182G>A	X.37:g.112058796C>T						AMOT_ENST00000371958.1_Silent_p.Q162Q|AMOT_ENST00000371962.1_Silent_p.Q162Q|AMOT_ENST00000304758.1_5'UTR|AMOT_ENST00000524145.1_Silent_p.Q394Q	p.Q394Q	NM_001113490.1	NP_001106962.1	Q4VCS5	AMOT_HUMAN			2	1181	-			394					Q504X5|Q9HD27|Q9UPT1	Silent	SNP	ENST00000524145.1	37	c.1182G>A	CCDS48154.1																																																																																				0.582	AMOT-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378570.1	NM_133265		3	43	0	0	0	1	0	3	43				
UBBP4	23666	broad.mit.edu	37	17	21730916	21730916	+	Missense_Mutation	SNP	G	G	T	rs111245273	byFrequency	TCGA-P7-A5NY-05A-11D-A35D-08	TCGA-P7-A5NY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d	87bae02a-0994-4ce5-a27b-72494a4a1b5f	g.chr17:21730916G>T	ENST00000578713.1	+	1	222	c.218G>T	c.(217-219)cGg>cTg	p.R73L	UBBP4_ENST00000583708.1_Intron|UBBP4_ENST00000584398.1_Intron|UBBP4_ENST00000584755.1_Missense_Mutation_p.R73L					ubiquitin B pseudogene 4									p.R73L(24)		endometrium(9)|kidney(4)|lung(4)|prostate(3)|urinary_tract(4)	24						GTCCTGCGTCGGAGAGGTGGT	0.552													.|||	27	0.00539137	0.0182	0.0029	5008	,	,		20752	0.0		0.0	False		,,,				2504	0.001					ENST00000584755.1																			24	Substitution - Missense(24)	p.R73L(24)	kidney(9)|urinary_tract(6)|endometrium(6)|prostate(3)	endometrium(9)|kidney(4)|lung(4)|prostate(3)|urinary_tract(4)	24						c.(217-219)cGg>cTg																																						SO:0001583	missense	23666							g.chr17:21730916G>T	X07499		17p11.2	2011-08-10				ENSG00000263563			12467	pseudogene	pseudogene						2834222	Standard	NG_002285		Approved		uc002gyy.3			ENST00000578713.1:c.218G>T	17.37:g.21730916G>T	ENSP00000464265:p.Arg73Leu					UBBP4_ENST00000578713.1_Missense_Mutation_p.R73L|UBBP4_ENST00000584398.1_Intron|UBBP4_ENST00000583708.1_Intron	p.R73L							2	615	+									Missense_Mutation	SNP	ENST00000578713.1	37	c.218G>T																																																																																					0.552	UBBP4-004	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444589.2			5	65	1	0	1.23904e-05	1	1.44555e-05	5	65				
LTBP2	4053	broad.mit.edu	37	14	75022242	75022242	+	Nonsense_Mutation	SNP	G	G	A			TCGA-P7-A5NY-05A-11D-A35D-08	TCGA-P7-A5NY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d	87bae02a-0994-4ce5-a27b-72494a4a1b5f	g.chr14:75022242G>A	ENST00000261978.4	-	4	1371	c.985C>T	c.(985-987)Cag>Tag	p.Q329*	LTBP2_ENST00000557425.1_Intron|LTBP2_ENST00000556690.1_Nonsense_Mutation_p.Q329*|CTD-2207P18.1_ENST00000554552.1_lincRNA	NM_000428.2	NP_000419.1	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding protein 2	329					protein secretion (GO:0009306)|protein targeting (GO:0006605)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|liver(1)|lung(29)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)		GGTACCGCCTGTTGGGTGCCA	0.627																																						ENST00000261978.4																			0				breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|liver(1)|lung(29)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						c.(985-987)Cag>Tag		latent transforming growth factor beta binding protein 2							98.0	88.0	91.0					14																	75022242		2203	4300	6503	SO:0001587	stop_gained	4053				protein secretion|protein targeting|transforming growth factor beta receptor signaling pathway	extracellular space|proteinaceous extracellular matrix	calcium ion binding|growth factor binding	g.chr14:75022242G>A		CCDS9831.1	14q24.3	2011-10-20	2001-12-04			ENSG00000119681		"""Latent transforming growth factor, beta binding proteins"""	6715	protein-coding gene	gene with protein product		602091	"""chromosome 14 open reading frame 141"""	LTBP3, C14orf141		7798248	Standard	NM_000428		Approved		uc001xqa.3	Q14767		ENST00000261978.4:c.985C>T	14.37:g.75022242G>A	ENSP00000261978:p.Gln329*					LTBP2_ENST00000556690.1_Nonsense_Mutation_p.Q329*|CTD-2207P18.1_ENST00000554552.1_lincRNA|LTBP2_ENST00000557425.1_Intron	p.Q329*	NM_000428.2	NP_000419.1	Q14767	LTBP2_HUMAN		BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)	4	1371	-			329					Q99907|Q9NS51	Nonsense_Mutation	SNP	ENST00000261978.4	37	c.985C>T	CCDS9831.1	.	.	.	.	.	.	.	.	.	.	G	37	6.408900	0.97542	.	.	ENSG00000119681	ENST00000261978;ENST00000556690	.	.	.	5.12	5.12	0.69794	.	0.214284	0.23622	U	0.046228	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	.	13.5661	0.61819	0.0:0.0:0.8454:0.1546	.	.	.	.	X	329	.	ENSP00000261978:Q329X	Q	-	1	0	LTBP2	74091995	0.765000	0.28485	0.925000	0.36789	0.250000	0.25880	4.106000	0.57804	2.655000	0.90218	0.556000	0.70494	CAG		0.627	LTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413595.1	NM_000428		9	38	0	0	0	1	0	9	38				
SIRPB1	10326	broad.mit.edu	37	20	1585397	1585397	+	Intron	SNP	T	T	C	rs148754551	byFrequency	TCGA-P7-A5NY-05A-11D-A35D-08	TCGA-P7-A5NY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d	87bae02a-0994-4ce5-a27b-72494a4a1b5f	g.chr20:1585397T>C	ENST00000381605.4	-	1	141				RP4-576H24.4_ENST00000564763.1_Intron|SIRPB1_ENST00000381596.1_5'Flank|SIRPB1_ENST00000381603.3_Intron|SIRPB1_ENST00000279477.7_Missense_Mutation_p.T248A|SIRPB1_ENST00000568365.1_Missense_Mutation_p.T248A	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1						cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)		p.T248A(5)		central_nervous_system(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	31						CCTCGGATGGTCTCAGACAAG	0.627													t|||	2569	0.512979	0.6967	0.33	5008	,	,		3683	0.4435		0.4473	False		,,,				2504	0.5337					ENST00000279477.7																			5	Substitution - Missense(5)	p.T248A(5)	kidney(3)|prostate(2)	central_nervous_system(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	31						c.(742-744)Acc>Gcc		signal-regulatory protein beta 1							20.0	30.0	27.0					20																	1585397		375	895	1270	SO:0001627	intron_variant	10326				cell junction assembly|cell surface receptor linked signaling pathway	integral to plasma membrane	protein binding	g.chr20:1585397T>C	Y10376	CCDS13019.1, CCDS42850.1, CCDS46571.1	20p13	2013-01-11			ENSG00000101307	ENSG00000101307		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	15928	protein-coding gene	gene with protein product		603889				9062191, 16339511	Standard	NM_001083910		Approved	SIRP-BETA-1, CD172b	uc010gai.3	O00241	OTTHUMG00000031676	ENST00000381605.4:c.76+15117A>G	20.37:g.1585397T>C						SIRPB1_ENST00000381605.4_Intron|RP4-576H24.4_ENST00000564763.1_Intron|SIRPB1_ENST00000568365.1_Missense_Mutation_p.T248A|SIRPB1_ENST00000381603.3_Intron	p.T248A	NM_001135844.2	NP_001129316.1	O00241	SIRB1_HUMAN			3	806	-			248					A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Missense_Mutation	SNP	ENST00000381605.4	37	c.742A>G	CCDS13019.1	757	0.3466117216117216	239	0.48577235772357724	97	0.26795580110497236	219	0.38286713286713286	202	0.26649076517150394	.	0.464	-0.887787	0.02511	.	.	ENSG00000101307	ENST00000279477	T	0.11930	2.73	2.24	-0.597	0.11653	.	.	.	.	.	T	0.00012	0.0000	N	0.20530	0.585	0.47778	P	4.809999999999537E-4	B	0.02656	0.0	B	0.06405	0.002	T	0.45483	-0.9258	8	0.13470	T	0.59	.	3.263	0.06855	0.2055:0.1485:0.0:0.646	.	248	Q5TFQ8	SIRBL_HUMAN	A	248	ENSP00000279477:T248A	ENSP00000279477:T248A	T	-	1	0	SIRPB1	1533397	0.001000	0.12720	0.631000	0.29282	0.161000	0.22273	-0.285000	0.08410	-0.814000	0.04352	-1.120000	0.02017	ACC		0.627	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065		4	22	0	0	0	1	0	4	22				
OCA2	4948	broad.mit.edu	37	15	28231750	28231750	+	Missense_Mutation	SNP	C	C	T			TCGA-P7-A5NY-05A-11D-A35D-08	TCGA-P7-A5NY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d	87bae02a-0994-4ce5-a27b-72494a4a1b5f	g.chr15:28231750C>T	ENST00000354638.3	-	12	1377	c.1222G>A	c.(1222-1224)Gat>Aat	p.D408N	OCA2_ENST00000353809.5_Missense_Mutation_p.D384N|OCA2_ENST00000382996.2_Missense_Mutation_p.D408N	NM_000275.2	NP_000266.2	Q04671	P_HUMAN	oculocutaneous albinism II	408					cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|spermatid development (GO:0007286)|tyrosine transport (GO:0015828)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|melanosome membrane (GO:0033162)	L-tyrosine transmembrane transporter activity (GO:0005302)|transporter activity (GO:0005215)	p.D408N(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(48)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)		GCACAATAATCGAAAAATCCC	0.294									Oculocutaneous Albinism																													ENST00000354638.3																			1	Substitution - Missense(1)	p.D408N(1)	pancreas(1)	NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(48)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	85						c.(1222-1224)Gat>Aat		oculocutaneous albinism II							96.0	102.0	100.0					15																	28231750		2203	4300	6503	SO:0001583	missense	4948	Oculocutaneous Albinism	Familial Cancer Database		eye pigment biosynthetic process	endoplasmic reticulum membrane|endosome membrane|integral to membrane|lysosomal membrane|melanosome membrane	arsenite transmembrane transporter activity|citrate transmembrane transporter activity|L-tyrosine transmembrane transporter activity|protein binding	g.chr15:28231750C>T		CCDS10020.1, CCDS73701.1	15q12	2013-01-08	2008-01-30		ENSG00000104044	ENSG00000104044			8101	protein-coding gene	gene with protein product	"""melanocyte-specific transporter protein"""	611409	"""oculocutaneous albinism II (pink-eye dilution (murine) homolog)"", ""eye color 3 (brown)"", ""eye color 2 (central brown)"", ""oculocutaneous albinism II (pink-eye dilution homolog, mouse)"""	D15S12, P, EYCL3, EYCL2			Standard	NM_000275		Approved	BEY2, EYCL, BEY, BEY1	uc001zbh.4	Q04671	OTTHUMG00000128871	ENST00000354638.3:c.1222G>A	15.37:g.28231750C>T	ENSP00000346659:p.Asp408Asn					OCA2_ENST00000353809.5_Missense_Mutation_p.D384N|OCA2_ENST00000382996.2_Missense_Mutation_p.D408N	p.D408N	NM_000275.2	NP_000266.2	Q04671	P_HUMAN		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)	12	1377	-		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)	408					Q15211|Q15212|Q96EN1|Q9UMI5	Missense_Mutation	SNP	ENST00000354638.3	37	c.1222G>A	CCDS10020.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.728546	0.89390	.	.	ENSG00000104044	ENST00000354638;ENST00000353809;ENST00000382996	D;D;D	0.93019	-3.15;-3.15;-3.15	5.57	5.57	0.84162	Divalent ion symporter (1);	0.000000	0.85682	D	0.000000	D	0.94879	0.8345	L	0.35487	1.065	0.49687	D	0.999811	D;D	0.89917	0.995;1.0	P;D	0.85130	0.84;0.997	D	0.95523	0.8596	10	0.87932	D	0	-22.9196	18.5465	0.91048	0.0:1.0:0.0:0.0	.	384;408	Q04671-2;Q04671	.;P_HUMAN	N	408;384;408	ENSP00000346659:D408N;ENSP00000261276:D384N;ENSP00000372457:D408N	ENSP00000261276:D384N	D	-	1	0	OCA2	25905345	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	6.677000	0.74503	2.616000	0.88540	0.557000	0.71058	GAT		0.294	OCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250823.1	NM_000275		28	46	0	0	0	1	0	28	46				
TSHZ3	57616	broad.mit.edu	37	19	31768209	31768209	+	Silent	SNP	G	G	A			TCGA-P7-A5NY-05A-11D-A35D-08	TCGA-P7-A5NY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d	87bae02a-0994-4ce5-a27b-72494a4a1b5f	g.chr19:31768209G>A	ENST00000240587.4	-	2	2817	c.2490C>T	c.(2488-2490)gtC>gtT	p.V830V		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	830					in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					TGAATGATACGACGGCAGATG	0.527																																						ENST00000240587.4																			0				breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123						c.(2488-2490)gtC>gtT		teashirt zinc finger homeobox 3							141.0	128.0	133.0					19																	31768209		2203	4300	6503	SO:0001819	synonymous_variant	57616				negative regulation of transcription, DNA-dependent|regulation of respiratory gaseous exchange by neurological system process	growth cone|nucleus	chromatin binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr19:31768209G>A	AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	30700	protein-coding gene	gene with protein product	"""teashirt 3"""	614119	"""zinc finger protein 537"", ""teashirt family zinc finger 3"""	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.2490C>T	19.37:g.31768209G>A							p.V830V	NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN			2	2817	-	Esophageal squamous(110;0.226)		830					Q9H0G6|Q9P254	Silent	SNP	ENST00000240587.4	37	c.2490C>T	CCDS12421.2																																																																																				0.527	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856		20	108	0	0	0	1	0	20	108				
PMS2P3	5387	broad.mit.edu	37	7	75142142	75142142	+	RNA	DEL	A	A	-	rs35519730	byFrequency	TCGA-P7-A5NY-05A-11D-A35D-08	TCGA-P7-A5NY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d	87bae02a-0994-4ce5-a27b-72494a4a1b5f	g.chr7:75142142delA	ENST00000418756.1	-	0	991				Y_RNA_ENST00000364004.1_RNA	NR_028059.1		Q13401	PM2P3_HUMAN	postmeiotic segregation increased 2 pseudogene 3						mismatch repair (GO:0006298)|regulation of transcription, DNA-templated (GO:0006355)	mismatch repair complex (GO:0032300)	nucleic acid binding (GO:0003676)			lung(1)	1						tctcaaaaagaaaaaaaaaaa	0.418													|||unknown(NO_COVERAGE)	2287	0.456669	0.1619	0.6037	5008	,	,		12703	0.6558		0.4861	False		,,,				2504	0.5153				NSCLC(70;602 1339 5301 18528 38453)	ENST00000418756.1																			0				lung(1)	1																																														5387							g.chr7:75142142delA	D38437		7q11.23	2010-10-26	2010-10-26	2010-10-26	ENSG00000127957	ENSG00000127957			9128	pseudogene	pseudogene			"""postmeiotic segregation increased 2-like 3"", ""postmeiotic segregation increased 2-like 3, pseudogene"""	PMS2L9, PMS2L3		8586419	Standard	NR_028059		Approved	PMS5, PMSR3	uc022agi.1	Q13401	OTTHUMG00000156049		7.37:g.75142142delA								NR_028059.1						0	991	-								A6NG70|Q3MJ29	RNA	DEL	ENST00000418756.1	37																																																																																						0.418	PMS2P3-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000342862.2	NR_028059		2	4						2	4	---	---	---	---
FAM66B	100128890	broad.mit.edu	37	8	7196263	7196264	+	lincRNA	DEL	AC	AC	-			TCGA-P7-A5NY-05A-11D-A35D-08	TCGA-P7-A5NY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d	87bae02a-0994-4ce5-a27b-72494a4a1b5f	g.chr8:7196263_7196264delAC	ENST00000606573.1	-	0	703									family with sequence similarity 66, member B																		ACTGAGGGGTacacacacacac	0.5																																						ENST00000606573.1																			0																																																			100128890							g.chr8:7196263_7196264delAC			8p23.1	2013-07-05			ENSG00000215374	ENSG00000215374		"""Long non-coding RNAs"""	28890	non-coding RNA	RNA, long non-coding							Standard	NR_027423		Approved				OTTHUMG00000165383		8.37:g.7196273_7196274delAC														0	703	-									RNA	DEL	ENST00000606573.1	37																																																																																						0.500	FAM66B-002	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000470344.1	NR_027423		3	4						3	4	---	---	---	---
MYRF	745	broad.mit.edu	37	11	61547022	61547022	+	Frame_Shift_Del	DEL	C	C	-			TCGA-P7-A5NY-05A-11D-A35D-08	TCGA-P7-A5NY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d	87bae02a-0994-4ce5-a27b-72494a4a1b5f	g.chr11:61547022delC	ENST00000278836.5	+	16	2323	c.2227delC	c.(2227-2229)cccfs	p.P744fs	TMEM258_ENST00000535042.1_Intron|MYRF_ENST00000265460.5_Frame_Shift_Del_p.P735fs|MYRF_ENST00000327797.1_Frame_Shift_Del_p.P388fs|MYRF_ENST00000389602.4_Frame_Shift_Del_p.P135fs	NM_001127392.1	NP_001120864.1	Q9Y2G1	MRF_HUMAN	myelin regulatory factor	744					central nervous system myelin maintenance (GO:0032286)|central nervous system myelination (GO:0022010)|oligodendrocyte development (GO:0014003)|oligodendrocyte differentiation (GO:0048709)|positive regulation of myelination (GO:0031643)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)										CAAGAAGAGGCCCCCCAAGGT	0.652																																						ENST00000278836.5																			0											c.(2227-2229)ccfs		myelin regulatory factor							18.0	25.0	23.0					11																	61547022		2183	4284	6467	SO:0001589	frameshift_variant	745							g.chr11:61547022delC		CCDS31579.1, CCDS44622.1	11q12-q13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000124920	ENSG00000124920			1181	protein-coding gene	gene with protein product	"""myelin gene regulatory factor"""	608329	"""chromosome 11 open reading frame 9"""	C11orf9		10828591, 12384578	Standard	NM_001127392		Approved	Ndt80, pqn-47, MRF	uc001nsc.1	Q9Y2G1	OTTHUMG00000168161	ENST00000278836.5:c.2227delC	11.37:g.61547022delC	ENSP00000278836:p.Pro744fs					MYRF_ENST00000327797.1_Frame_Shift_Del_p.P388fs|TMEM258_ENST00000535042.1_Intron|MYRF_ENST00000389602.4_Frame_Shift_Del_p.P135fs|MYRF_ENST00000265460.5_Frame_Shift_Del_p.P735fs	p.P744fs	NM_001127392.1	NP_001120864.1					16	2323	+								O43582|Q9P1Q6	Frame_Shift_Del	DEL	ENST00000278836.5	37	c.2227delC	CCDS44622.1																																																																																				0.652	MYRF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398519.2	NM_013279		2	4						2	4	---	---	---	---
HERC2P2	400322	broad.mit.edu	37	15	23312380	23312380	+	RNA	DEL	T	T	-			TCGA-P7-A5NY-05A-11D-A35D-08	TCGA-P7-A5NY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d	87bae02a-0994-4ce5-a27b-72494a4a1b5f	g.chr15:23312380delT	ENST00000560464.1	-	0	3118									hect domain and RLD 2 pseudogene 2																		TGTTAttttcttttttttttt	0.398																																						ENST00000560464.1																			0																																																			400322							g.chr15:23312380delT	AF041080		15q11.2	2014-03-18			ENSG00000140181				4870	pseudogene	pseudogene						9730612	Standard	NR_002824		Approved	D15F37S3	uc001yvq.2		OTTHUMG00000171926		15.37:g.23312380delT														0	3118	-									RNA	DEL	ENST00000560464.1	37																																																																																						0.398	HERC2P2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000415936.1			3	5						3	5	---	---	---	---
DUOX2	50506	broad.mit.edu	37	15	45399034	45399034	+	Frame_Shift_Del	DEL	G	G	-			TCGA-P7-A5NY-05A-11D-A35D-08	TCGA-P7-A5NY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d	87bae02a-0994-4ce5-a27b-72494a4a1b5f	g.chr15:45399034delG	ENST00000603300.1	-	15	2029	c.1827delC	c.(1825-1827)cccfs	p.P609fs	DUOX2_ENST00000389039.6_Frame_Shift_Del_p.P609fs	NM_014080.4	NP_054799.4	Q9NRD8	DUOX2_HUMAN	dual oxidase 2	609					adenohypophysis morphogenesis (GO:0048855)|bone mineralization (GO:0030282)|cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|fertilization (GO:0009566)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|inner ear development (GO:0048839)|multicellular organism growth (GO:0035264)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|response to virus (GO:0009615)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|peroxidase activity (GO:0004601)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	63		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)		GCTCACCTAAGGGAAGGCAGC	0.587																																						ENST00000389039.6																			0				NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	63						c.(1825-1827)ccfs		dual oxidase 2							40.0	41.0	41.0					15																	45399034		2198	4293	6491	SO:0001589	frameshift_variant	50506				cuticle development|cytokine-mediated signaling pathway|hormone biosynthetic process|hydrogen peroxide catabolic process|response to cAMP|response to virus	apical plasma membrane|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|peroxidase activity	g.chr15:45399034delG	AF181972	CCDS10117.1	15q15.3-q21	2013-01-10			ENSG00000140279	ENSG00000140279		"""EF-hand domain containing"""	13273	protein-coding gene	gene with protein product	"""dual oxidase-like domains 2"", ""nicotinamide adenine dinucleotide phosphate oxidase"", ""flavoprotein NADPH oxidase"", ""NADPH thyroid oxidase 2"", ""NADH/NADPH thyroid oxidase p138-tox"", ""NADPH oxidase/peroxidase DUOX2"""	606759				10601291, 10806195	Standard	NM_014080		Approved	P138-TOX, P138(TOX), THOX2, LNOX2	uc010bea.3	Q9NRD8	OTTHUMG00000131355	ENST00000603300.1:c.1827delC	15.37:g.45399034delG	ENSP00000475084:p.Pro609fs					DUOX2_ENST00000603300.1_Frame_Shift_Del_p.P609fs	p.P609fs			Q9NRD8	DUOX2_HUMAN		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)	15	2212	-		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)	609					A8MQ13|D2XI64|Q9NR02|Q9UHF9	Frame_Shift_Del	DEL	ENST00000603300.1	37	c.1827delC	CCDS10117.1																																																																																				0.587	DUOX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_014080		2	4						2	4	---	---	---	---
UBE2Q2P1	388165	broad.mit.edu	37	15	85081721	85081721	+	RNA	DEL	C	C	-			TCGA-P7-A5NY-05A-11D-A35D-08	TCGA-P7-A5NY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d	87bae02a-0994-4ce5-a27b-72494a4a1b5f	g.chr15:85081721delC	ENST00000339094.1	-	0	1678					NR_003661.2				ubiquitin-conjugating enzyme E2Q family member 2 pseudogene 1																		caaatatatacccccattcat	0.323																																						ENST00000339094.1																			0																																																			388165							g.chr15:85081721delC			15q25.2	2013-11-05	2009-12-17	2009-12-17	ENSG00000189136	ENSG00000189136			37439	pseudogene	pseudogene			"""ubiquitin-conjugating enzyme E2Q family pseudogene 1"""	UBE2QP1			Standard	NR_003661		Approved	FLJ43276	uc002bkn.1		OTTHUMG00000148662		15.37:g.85081721delC								NR_003661.2						0	1678	-									RNA	DEL	ENST00000339094.1	37																																																																																						0.323	UBE2Q2P1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000308970.2	NR_003661		2	4						2	4	---	---	---	---
C16orf74	404550	broad.mit.edu	37	16	85743879	85743881	+	In_Frame_Del	DEL	GCT	GCT	-	rs374238893		TCGA-P7-A5NY-05A-11D-A35D-08	TCGA-P7-A5NY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d	87bae02a-0994-4ce5-a27b-72494a4a1b5f	g.chr16:85743879_85743881delGCT	ENST00000284245.4	-	3	244_246	c.61_63delAGC	c.(61-63)agcdel	p.S21del	C16orf74_ENST00000602719.1_In_Frame_Del_p.S21del|C16orf74_ENST00000602766.1_5'UTR|C16orf74_ENST00000602675.1_5'UTR|C16orf74_ENST00000602914.1_Intron|C16orf74_ENST00000602758.1_Intron|C16orf74_ENST00000602583.1_In_Frame_Del_p.S9del	NM_206967.2	NP_996850.1	Q96GX8	CP074_HUMAN	chromosome 16 open reading frame 74	21																	CCTCGTCGTGGCTGCTGCTGCTG	0.635																																						ENST00000602583.1																			0											c.(25-27)del		chromosome 16 open reading frame 74																																				SO:0001651	inframe_deletion	404550							g.chr16:85743879_85743881delGCT	BC009078	CCDS45540.1	16q24.1	2014-05-28			ENSG00000154102	ENSG00000154102			23362	protein-coding gene	gene with protein product							Standard	NM_206967		Approved	MGC17624	uc002fjc.4	Q96GX8	OTTHUMG00000183875	ENST00000284245.4:c.61_63delAGC	16.37:g.85743888_85743890delGCT	ENSP00000284245:p.Ser21del					C16orf74_ENST00000284245.4_In_Frame_Del_p.S21del|C16orf74_ENST00000602675.1_5'UTR|C16orf74_ENST00000602914.1_Intron|C16orf74_ENST00000602719.1_In_Frame_Del_p.S21del|C16orf74_ENST00000602766.1_5'UTR|C16orf74_ENST00000602758.1_Intron	p.S9del			Q96GX8	CP074_HUMAN			1	575_577	-			21						In_Frame_Del	DEL	ENST00000284245.4	37	c.25_27delAGC	CCDS45540.1																																																																																				0.635	C16orf74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467253.1	NM_206967		3	6						3	6	---	---	---	---
TNPO2	30000	broad.mit.edu	37	19	12830109	12830110	+	Frame_Shift_Ins	INS	-	-	T			TCGA-P7-A5NY-05A-11D-A35D-08	TCGA-P7-A5NY-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d	87bae02a-0994-4ce5-a27b-72494a4a1b5f	g.chr19:12830109_12830110insT	ENST00000592287.1	-	3	248_249	c.140_141insA	c.(139-141)tacfs	p.Y47fs	TNPO2_ENST00000588216.1_Frame_Shift_Ins_p.Y47fs|TNPO2_ENST00000356861.5_Frame_Shift_Ins_p.Y47fs|TNPO2_ENST00000425528.1_Frame_Shift_Ins_p.Y47fs|TNPO2_ENST00000441499.1_Frame_Shift_Ins_p.Y47fs|TNPO2_ENST00000589956.1_5'UTR|TNPO2_ENST00000450764.2_Frame_Shift_Ins_p.Y47fs	NM_001136196.1	NP_001129668.1	O14787	TNPO2_HUMAN	transportin 2	47	Importin N-terminal.				intracellular protein transport (GO:0006886)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nuclear localization sequence binding (GO:0008139)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						CGAAAATCAGGTAGTTGTTGAA	0.545																																						ENST00000425528.1																			0				autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						c.(139-141)tctfs		transportin 2																																				SO:0001589	frameshift_variant	30000				intracellular protein transport	cytoplasm|nucleus	nuclear localization sequence binding|protein binding|protein transporter activity	g.chr19:12830109_12830110insT	AF019039	CCDS45991.1, CCDS45992.1	19p13.13	2009-01-12	2009-01-12			ENSG00000105576		"""Importins"""	19998	protein-coding gene	gene with protein product	"""importin 3"", ""karyopherin beta 2b"""	603002				9298975, 12384575	Standard	NM_013433		Approved	IPO3, KPNB2B, FLJ12155, TRN2	uc002muo.3	O14787		ENST00000592287.1:c.141dupA	19.37:g.12830110_12830110dupT	ENSP00000468434:p.Tyr47fs					TNPO2_ENST00000588216.1_Frame_Shift_Ins_p.S47fs|TNPO2_ENST00000592287.1_Frame_Shift_Ins_p.S47fs|TNPO2_ENST00000450764.2_Frame_Shift_Ins_p.S47fs|TNPO2_ENST00000589956.1_5'UTR|TNPO2_ENST00000356861.5_Frame_Shift_Ins_p.S47fs|TNPO2_ENST00000441499.1_Frame_Shift_Ins_p.S47fs	p.S47fs			O14787	TNPO2_HUMAN			4	497_498	-			47			Importin N-terminal.		O14655|Q6IN77	Frame_Shift_Ins	INS	ENST00000592287.1	37	c.140_141insA	CCDS45991.1																																																																																				0.545	TNPO2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450785.1	NM_013433		10	23						10	23	---	---	---	---
