#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
TMEM261	90871	broad.mit.edu	37	9	7799665	7799665	+	Missense_Mutation	SNP	C	C	T			TCGA-RW-A68D-01A-11D-A35D-08	TCGA-RW-A68D-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f81b6d24-ffdc-4d48-bce5-bca9de8c1939	8ee15795-2e6c-4e56-a9e5-5e280ac8c57c	g.chr9:7799665C>T	ENST00000358227.4	-	1	402	c.70G>A	c.(70-72)Gcc>Acc	p.A24T	TMEM261_ENST00000484082.1_Intron	NM_033428.1	NP_219500.1	Q96GE9	TM261_HUMAN	transmembrane protein 261	24						integral component of membrane (GO:0016021)											GCAGGTTTGGCGGGCGCGGCG	0.657																																						ENST00000358227.4																			0				lung(1)	1						c.(70-72)Gcc>Acc									20.0	25.0	23.0					9																	7799665		2201	4299	6500	SO:0001583	missense	90871					integral to membrane		g.chr9:7799665C>T	BC009510	CCDS34989.1	9p24.1	2014-02-21	2013-09-11	2013-09-11	ENSG00000137038	ENSG00000137038			30536	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 123"""	C9orf123		21666724	Standard	NM_033428		Approved	MGC4730	uc003zkj.3	Q96GE9	OTTHUMG00000019539	ENST00000358227.4:c.70G>A	9.37:g.7799665C>T	ENSP00000350961:p.Ala24Thr					C9orf123_ENST00000484082.1_Intron	p.A24T	NM_033428.1	NP_219500.1	Q96GE9	CI123_HUMAN		GBM - Glioblastoma multiforme(50;0.0561)	1	402	-		all_cancers(3;0.0539)|Lung NSC(3;3.36e-05)|all_lung(3;0.000156)|all_epithelial(3;0.0356)	24					A8K9B7|Q5T6Y9|Q9NT74	Missense_Mutation	SNP	ENST00000358227.4	37	c.70G>A	CCDS34989.1	.	.	.	.	.	.	.	.	.	.	c	16.10	3.027107	0.54683	.	.	ENSG00000137038	ENST00000358227	T	0.53857	0.6	4.78	0.707	0.18139	.	0.445007	0.19150	N	0.121477	T	0.38983	0.1061	L	0.36672	1.1	0.09310	N	1	D;D	0.56968	0.978;0.978	B;P	0.46718	0.395;0.525	T	0.20306	-1.0279	10	0.32370	T	0.25	-4.3416	3.4046	0.07336	0.167:0.4171:0.3243:0.0916	.	24;24	Q96GE9-2;Q96GE9	.;CI123_HUMAN	T	24	ENSP00000350961:A24T	ENSP00000350961:A24T	A	-	1	0	C9orf123	7789665	0.114000	0.22134	0.058000	0.19502	0.012000	0.07955	0.091000	0.15046	0.284000	0.22305	0.454000	0.30748	GCC		0.657	TMEM261-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051705.1	NM_033428		3	28	0	0	0	1	0	3	28				
EML5	161436	broad.mit.edu	37	14	89206879	89206879	+	Missense_Mutation	SNP	C	C	T			TCGA-RW-A68D-01A-11D-A35D-08	TCGA-RW-A68D-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f81b6d24-ffdc-4d48-bce5-bca9de8c1939	8ee15795-2e6c-4e56-a9e5-5e280ac8c57c	g.chr14:89206879C>T	ENST00000380664.5	-	5	562	c.563G>A	c.(562-564)cGa>cAa	p.R188Q	EML5_ENST00000352093.5_Missense_Mutation_p.R188Q|EML5_ENST00000554922.1_Missense_Mutation_p.R188Q			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	188						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	catalytic activity (GO:0003824)			breast(1)|endometrium(3)|kidney(4)|large_intestine(17)|lung(14)|ovary(3)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						AAAGACACCTCGTTTTGGGGT	0.368																																						ENST00000554922.1																			0				breast(1)|endometrium(3)|kidney(4)|large_intestine(17)|lung(14)|ovary(3)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						c.(562-564)cGa>cAa		echinoderm microtubule associated protein like 5							143.0	135.0	138.0					14																	89206879		1860	4102	5962	SO:0001583	missense	161436					cytoplasm|microtubule		g.chr14:89206879C>T	AY357725	CCDS45148.1	14q31.3	2013-01-10				ENSG00000165521		"""WD repeat domain containing"""	18197	protein-coding gene	gene with protein product							Standard	NM_183387		Approved	HuEMAP-2, EMAP-2	uc021ryf.1	Q05BV3		ENST00000380664.5:c.563G>A	14.37:g.89206879C>T	ENSP00000370039:p.Arg188Gln					EML5_ENST00000352093.5_Missense_Mutation_p.R188Q|EML5_ENST00000380664.5_Missense_Mutation_p.R188Q	p.R188Q	NM_183387.2	NP_899243.1	Q05BV3	EMAL5_HUMAN			5	811	-			188					B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Missense_Mutation	SNP	ENST00000380664.5	37	c.563G>A	CCDS45148.1	.	.	.	.	.	.	.	.	.	.	C	34	5.331765	0.95733	.	.	ENSG00000165521	ENST00000554922;ENST00000352093;ENST00000380664	T;T;T	0.21734	1.99;1.99;1.99	5.21	5.21	0.72293	WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.64402	D	0.000001	T	0.35278	0.0926	L	0.52364	1.645	0.53005	D	0.999962	D	0.71674	0.998	P	0.59703	0.862	T	0.04268	-1.0964	10	0.11485	T	0.65	-7.7252	18.7549	0.91828	0.0:1.0:0.0:0.0	.	188	Q05BV3	EMAL5_HUMAN	Q	188	ENSP00000451998:R188Q;ENSP00000298315:R188Q;ENSP00000370039:R188Q	ENSP00000298315:R188Q	R	-	2	0	EML5	88276632	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.412000	0.80091	2.417000	0.82017	0.591000	0.81541	CGA		0.368	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1			5	87	0	0	0	1	0	5	87				
ALMS1	7840	broad.mit.edu	37	2	73677777	73677777	+	Missense_Mutation	SNP	A	A	G			TCGA-RW-A68D-01A-11D-A35D-08	TCGA-RW-A68D-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f81b6d24-ffdc-4d48-bce5-bca9de8c1939	8ee15795-2e6c-4e56-a9e5-5e280ac8c57c	g.chr2:73677777A>G	ENST00000264448.6	+	8	4231	c.4120A>G	c.(4120-4122)Act>Gct	p.T1374A	ALMS1_ENST00000377715.1_Missense_Mutation_p.T1374A|ALMS1_ENST00000409009.1_Missense_Mutation_p.T1332A	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	1374	34 X 47 AA approximate tandem repeat.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.T1374A(1)		breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						TGGCACACCAACTGTAACCTC	0.443																																						ENST00000264448.6																			1	Substitution - Missense(1)	p.T1374A(1)	lung(1)	breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						c.(4120-4122)Act>Gct		Alstrom syndrome 1							83.0	85.0	85.0					2																	73677777		1864	4096	5960	SO:0001583	missense	7840				G2/M transition of mitotic cell cycle	centrosome|cilium|cytosol|microtubule basal body|spindle pole		g.chr2:73677777A>G	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.4120A>G	2.37:g.73677777A>G	ENSP00000264448:p.Thr1374Ala					ALMS1_ENST00000377715.1_Missense_Mutation_p.T1374A|ALMS1_ENST00000409009.1_Missense_Mutation_p.T1332A	p.T1374A	NM_015120.4	NP_055935.4	Q8TCU4	ALMS1_HUMAN			8	4231	+			1374			34 X 47 AA approximate tandem repeat.		Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	c.4120A>G	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	A	11.93	1.784251	0.31593	.	.	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.14391	3.41;3.41;2.51	3.23	-0.789	0.10935	.	.	.	.	.	T	0.07683	0.0193	L	0.28192	0.835	0.09310	N	1	B;P;P	0.37955	0.008;0.612;0.612	B;B;B	0.34590	0.01;0.186;0.186	T	0.28138	-1.0053	9	0.42905	T	0.14	.	4.312	0.10976	0.4675:0.4132:0.1194:0.0	.	1374;1332;1374	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	A	1332;1374;1374	ENSP00000386627:T1332A;ENSP00000264448:T1374A;ENSP00000366944:T1374A	ENSP00000264448:T1374A	T	+	1	0	ALMS1	73531285	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.389000	0.02530	-0.146000	0.11274	0.459000	0.35465	ACT		0.443	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		4	144	0	0	0	1	0	4	144				
LOC645752	645752	broad.mit.edu	37	15	78211548	78211548	+	lincRNA	SNP	T	T	C			TCGA-RW-A68D-01A-11D-A35D-08	TCGA-RW-A68D-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f81b6d24-ffdc-4d48-bce5-bca9de8c1939	8ee15795-2e6c-4e56-a9e5-5e280ac8c57c	g.chr15:78211548T>C	ENST00000565869.1	+	0	111				RP11-114H24.2_ENST00000567226.1_RNA|RN7SL214P_ENST00000487317.2_RNA																							CCACCTGGGATTGGAGCTTTC	0.562																																						ENST00000565869.1																			0																																																			645752							g.chr15:78211548T>C																													15.37:g.78211548T>C						RP11-114H24.2_ENST00000567226.1_RNA								0	111	+									RNA	SNP	ENST00000565869.1	37																																																																																						0.562	RP11-114H24.7-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000421587.1			5	94	0	0	0	1	0	5	94				
SLC35A4	113829	broad.mit.edu	37	5	139947373	139947373	+	Nonsense_Mutation	SNP	G	G	T			TCGA-RW-A68D-01A-11D-A35D-08	TCGA-RW-A68D-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f81b6d24-ffdc-4d48-bce5-bca9de8c1939	8ee15795-2e6c-4e56-a9e5-5e280ac8c57c	g.chr5:139947373G>T	ENST00000514199.1	+	2	2305	c.619G>T	c.(619-621)Gag>Tag	p.E207*	APBB3_ENST00000507279.1_Intron|SLC35A4_ENST00000323146.3_Nonsense_Mutation_p.E207*			Q96G79	S35A4_HUMAN	solute carrier family 35, member A4	207	Leu-rich.					Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	sugar:proton symporter activity (GO:0005351)			endometrium(4)|kidney(2)|large_intestine(3)|lung(4)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGTGTACACAGAGCTGCTCAT	0.577																																						ENST00000514199.1																			0				endometrium(4)|kidney(2)|large_intestine(3)|lung(4)	13						c.(619-621)Gag>Tag		solute carrier family 35, member A4							93.0	92.0	92.0					5																	139947373		2203	4300	6503	SO:0001587	stop_gained	113829					Golgi membrane|integral to membrane	sugar:hydrogen symporter activity	g.chr5:139947373G>T	AJ420598	CCDS4231.1	5q31.3	2013-05-22			ENSG00000176087	ENSG00000176087		"""Solute carriers"""	20753	protein-coding gene	gene with protein product							Standard	NM_080670		Approved		uc003lgg.1	Q96G79	OTTHUMG00000129495	ENST00000514199.1:c.619G>T	5.37:g.139947373G>T	ENSP00000424566:p.Glu207*					SLC35A4_ENST00000323146.3_Nonsense_Mutation_p.E207*|APBB3_ENST00000507279.1_Intron	p.E207*			Q96G79	S35A4_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		2	2305	+			207			Leu-rich.		A8K013	Nonsense_Mutation	SNP	ENST00000514199.1	37	c.619G>T	CCDS4231.1	.	.	.	.	.	.	.	.	.	.	G	45	11.730368	0.99596	.	.	ENSG00000176087	ENST00000323146;ENST00000514199	.	.	.	4.68	4.68	0.58851	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-12.2268	17.3673	0.87367	0.0:0.0:1.0:0.0	.	.	.	.	X	207	.	.	E	+	1	0	SLC35A4	139927557	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	9.259000	0.95561	2.423000	0.82170	0.462000	0.41574	GAG		0.577	SLC35A4-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372815.1	NM_080670		39	54	1	0	6.2361e-21	1	6.50724e-21	39	54				
RP11-423O2.5	0	broad.mit.edu	37	1	142803543	142803543	+	lincRNA	SNP	C	C	T			TCGA-RW-A68D-01A-11D-A35D-08	TCGA-RW-A68D-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f81b6d24-ffdc-4d48-bce5-bca9de8c1939	8ee15795-2e6c-4e56-a9e5-5e280ac8c57c	g.chr1:142803543C>T	ENST00000423385.1	-	0	1422																											TGTTGGAATTCCTGATGAATC	0.269																																						ENST00000423385.1																			0																																																			0							g.chr1:142803543C>T																													1.37:g.142803543C>T														0	1422	-									RNA	SNP	ENST00000423385.1	37																																																																																						0.269	RP11-423O2.5-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000193203.1			5	158	0	0	0	1	0	5	158				
DEPDC7	91614	broad.mit.edu	37	11	33047366	33047366	+	Missense_Mutation	SNP	C	C	G			TCGA-RW-A68D-01A-11D-A35D-08	TCGA-RW-A68D-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f81b6d24-ffdc-4d48-bce5-bca9de8c1939	8ee15795-2e6c-4e56-a9e5-5e280ac8c57c	g.chr11:33047366C>G	ENST00000241051.3	+	2	327	c.235C>G	c.(235-237)Cta>Gta	p.L79V	DEPDC7_ENST00000311388.3_Missense_Mutation_p.L70V	NM_001077242.1	NP_001070710.1	Q96QD5	DEPD7_HUMAN	DEP domain containing 7	79	DEP. {ECO:0000255|PROSITE- ProRule:PRU00066}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)				endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|skin(2)	17						TTTTTCTCACCTAATTCAGAA	0.393																																						ENST00000311388.3																			0				endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|skin(2)	17						c.(208-210)Cta>Gta		DEP domain containing 7							177.0	166.0	169.0					11																	33047366		1879	4124	6003	SO:0001583	missense	91614				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity	g.chr11:33047366C>G		CCDS41632.1, CCDS41633.1	11p13	2006-03-24			ENSG00000121690	ENSG00000121690			29899	protein-coding gene	gene with protein product		612294				10568747	Standard	NM_001077242		Approved		uc001mub.3	Q96QD5	OTTHUMG00000166242	ENST00000241051.3:c.235C>G	11.37:g.33047366C>G	ENSP00000241051:p.Leu79Val					DEPDC7_ENST00000241051.3_Missense_Mutation_p.L79V	p.L70V	NM_139160.2	NP_631899.2	Q96QD5	DEPD7_HUMAN			2	584	+			79			DEP.		G5E941|Q8N602|Q8NCU9|Q9UGK5	Missense_Mutation	SNP	ENST00000241051.3	37	c.208C>G	CCDS41632.1	.	.	.	.	.	.	.	.	.	.	C	17.85	3.490770	0.64074	.	.	ENSG00000121690	ENST00000241051;ENST00000311388	T;T	0.13538	2.58;2.58	6.04	2.13	0.27403	DEP domain (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.070787	0.56097	D	0.000024	T	0.32071	0.0817	M	0.73372	2.23	0.43408	D	0.995541	D;D;D;D	0.71674	0.998;0.985;0.996;0.992	D;P;P;P	0.74023	0.982;0.824;0.861;0.871	T	0.01488	-1.1342	10	0.72032	D	0.01	-5.2161	10.2438	0.43328	0.0:0.7332:0.0:0.2668	.	79;79;70;79	B4DJ78;B4DH51;G5E941;Q96QD5	.;.;.;DEPD7_HUMAN	V	79;70	ENSP00000241051:L79V;ENSP00000308971:L70V	ENSP00000241051:L79V	L	+	1	2	DEPDC7	33003942	0.670000	0.27512	0.821000	0.32701	0.984000	0.73092	1.250000	0.32850	0.147000	0.19030	-0.258000	0.10820	CTA		0.393	DEPDC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388655.1	NM_139160		7	185	0	0	0	1	0	7	185				
CD300LG	146894	broad.mit.edu	37	17	41926251	41926251	+	Silent	SNP	C	C	T			TCGA-RW-A68D-01A-11D-A35D-08	TCGA-RW-A68D-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f81b6d24-ffdc-4d48-bce5-bca9de8c1939	8ee15795-2e6c-4e56-a9e5-5e280ac8c57c	g.chr17:41926251C>T	ENST00000317310.4	+	2	410	c.369C>T	c.(367-369)ttC>ttT	p.F123F	CD300LG_ENST00000586233.1_Silent_p.F123F|CD300LG_ENST00000377203.4_Silent_p.F123F|CD300LG_ENST00000293396.8_Silent_p.F123F|CD300LG_ENST00000539718.1_Silent_p.F123F|CD300LG_ENST00000588884.1_Silent_p.F123F	NM_145273.3	NP_660316.2	Q6UXG3	CLM9_HUMAN	CD300 molecule-like family member g	123					immune system process (GO:0002376)|immunoglobulin transcytosis in epithelial cells (GO:0002414)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(2)|lung(5)|skin(4)	19		Breast(137;0.0199)		BRCA - Breast invasive adenocarcinoma(366;0.115)		TCTCTCTGTTCGTCTTTCCAG	0.557																																						ENST00000317310.4																			0				central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(2)|lung(5)|skin(4)	19						c.(367-369)ttC>ttT		CD300 molecule-like family member g							84.0	75.0	78.0					17																	41926251		2203	4300	6503	SO:0001819	synonymous_variant	146894					apical plasma membrane|basolateral plasma membrane|integral to membrane|multivesicular body membrane	receptor activity	g.chr17:41926251C>T	BC025395	CCDS11470.1, CCDS54131.1, CCDS54132.1, CCDS54133.1	17q21.31	2013-01-11	2006-03-29					"""Immunoglobulin superfamily / V-set domain containing"""	30455	protein-coding gene	gene with protein product	"""nepmucin"""	610520	"""CD300 antigen like family member G"""			16876123, 16754720	Standard	NM_001168322		Approved	Trem4, CLM9	uc002iem.3	Q6UXG3		ENST00000317310.4:c.369C>T	17.37:g.41926251C>T						CD300LG_ENST00000293396.8_Silent_p.F123F|CD300LG_ENST00000377203.4_Silent_p.F123F|CD300LG_ENST00000588884.1_Silent_p.F123F|CD300LG_ENST00000586233.1_Silent_p.F123F|CD300LG_ENST00000539718.1_Silent_p.F123F	p.F123F	NM_145273.3	NP_660316.2	Q6UXG3	CLM9_HUMAN		BRCA - Breast invasive adenocarcinoma(366;0.115)	2	410	+		Breast(137;0.0199)	123					B4DNY5|F5H7P9|F8W9M3|Q8IX38|Q8IX39|Q8TA95	Silent	SNP	ENST00000317310.4	37	c.369C>T	CCDS11470.1																																																																																				0.557	CD300LG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457646.1	NM_145273		20	28	0	0	0	1	0	20	28				
TIMELESS	8914	broad.mit.edu	37	12	56811930	56811930	+	Missense_Mutation	SNP	C	C	T			TCGA-RW-A68D-01A-11D-A35D-08	TCGA-RW-A68D-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f81b6d24-ffdc-4d48-bce5-bca9de8c1939	8ee15795-2e6c-4e56-a9e5-5e280ac8c57c	g.chr12:56811930C>T	ENST00000553532.1	-	27	3592	c.3442G>A	c.(3442-3444)Gca>Aca	p.A1148T	TIMELESS_ENST00000229201.4_Missense_Mutation_p.A1147T|TIMELESS_ENST00000554616.1_Missense_Mutation_p.A645T					timeless circadian clock											NS(1)|breast(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(8)|lung(14)|ovary(7)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	49						TCTGGGGATGCCAGGCCCGCT	0.542																																						ENST00000229201.4																			0				NS(1)|breast(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(8)|lung(14)|ovary(7)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	49						c.(3439-3441)Gca>Aca		timeless circadian clock							165.0	173.0	170.0					12																	56811930		2203	4300	6503	SO:0001583	missense	8914				cell division|circadian rhythm|detection of abiotic stimulus|mitosis|morphogenesis of an epithelium|negative regulation of transcription, DNA-dependent|regulation of S phase|response to DNA damage stimulus|transcription, DNA-dependent	nuclear chromatin		g.chr12:56811930C>T	AF098162	CCDS8918.1	12q13.3	2012-12-14	2012-12-14		ENSG00000111602	ENSG00000111602			11813	protein-coding gene	gene with protein product	"""Tof1 homolog (S. cerevisiae)"", ""timeless circadian clock 1"""	603887	"""timeless (Drosophila) homolog"", ""timeless homolog (Drosophila)"""			9856465	Standard	NM_003920		Approved	hTIM, TIM, TIM1	uc001slf.2	Q9UNS1	OTTHUMG00000170600	ENST00000553532.1:c.3442G>A	12.37:g.56811930C>T	ENSP00000450607:p.Ala1148Thr					TIMELESS_ENST00000554616.1_Missense_Mutation_p.A645T|TIMELESS_ENST00000553532.1_Missense_Mutation_p.A1148T	p.A1147T	NM_003920.3	NP_003911.2	Q9UNS1	TIM_HUMAN			27	3593	-			1148						Missense_Mutation	SNP	ENST00000553532.1	37	c.3439G>A	CCDS8918.1	.	.	.	.	.	.	.	.	.	.	C	11.49	1.653977	0.29425	.	.	ENSG00000111602	ENST00000229201;ENST00000553532;ENST00000554616	T;T;T	0.13657	2.57;2.57;2.57	5.05	3.14	0.36123	Timeless C-terminal (1);	1.502310	0.03919	N	0.283148	T	0.08582	0.0213	N	0.14661	0.345	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.35919	-0.9769	10	0.09590	T	0.72	2.8102	6.8016	0.23754	0.0:0.725:0.1738:0.1012	.	1148	Q9UNS1	TIM_HUMAN	T	1147;1148;645	ENSP00000229201:A1147T;ENSP00000450607:A1148T;ENSP00000450848:A645T	ENSP00000229201:A1148T	A	-	1	0	TIMELESS	55098197	0.000000	0.05858	0.003000	0.11579	0.047000	0.14425	-0.540000	0.06106	0.590000	0.29694	0.655000	0.94253	GCA		0.542	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409771.1	NM_003920		5	435	0	0	0	1	0	5	435				
EPAS1	2034	broad.mit.edu	37	2	46607406	46607406	+	Missense_Mutation	SNP	A	A	G			TCGA-RW-A68D-01A-11D-A35D-08	TCGA-RW-A68D-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f81b6d24-ffdc-4d48-bce5-bca9de8c1939	8ee15795-2e6c-4e56-a9e5-5e280ac8c57c	g.chr2:46607406A>G	ENST00000263734.3	+	12	2105	c.1595A>G	c.(1594-1596)tAt>tGt	p.Y532C		NM_001430.4	NP_001421.2	Q99814	EPAS1_HUMAN	endothelial PAS domain protein 1	532	NTAD.				angiogenesis (GO:0001525)|blood vessel remodeling (GO:0001974)|cell maturation (GO:0048469)|cellular response to hypoxia (GO:0071456)|embryonic placenta development (GO:0001892)|erythrocyte differentiation (GO:0030218)|lung development (GO:0030324)|mitochondrion organization (GO:0007005)|myoblast fate commitment (GO:0048625)|norepinephrine metabolic process (GO:0042415)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of heart rate (GO:0002027)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|surfactant homeostasis (GO:0043129)|transcription from RNA polymerase II promoter (GO:0006366)|visual perception (GO:0007601)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|histone acetyltransferase binding (GO:0035035)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	LUSC - Lung squamous cell carcinoma(58;0.151)			CTGGCACCCTATATCCCCATG	0.587																																						ENST00000263734.3																			0				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						c.(1594-1596)tAt>tGt		endothelial PAS domain protein 1							84.0	92.0	89.0					2																	46607406		2203	4300	6503	SO:0001583	missense	2034				angiogenesis|myoblast cell fate commitment|positive regulation of transcription from RNA polymerase II promoter|response to hypoxia	transcription factor complex	histone acetyltransferase binding|protein heterodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|signal transducer activity|transcription coactivator activity|transcription factor binding	g.chr2:46607406A>G	U81984	CCDS1825.1	2p21-p16	2013-05-21			ENSG00000116016	ENSG00000116016		"""Basic helix-loop-helix proteins"""	3374	protein-coding gene	gene with protein product	"""HIF-1 alpha-like factor"""	603349				9000051, 9079689, 18378852	Standard	NM_001430		Approved	MOP2, PASD2, HIF2A, HLF, bHLHe73	uc002ruv.3	Q99814	OTTHUMG00000128818	ENST00000263734.3:c.1595A>G	2.37:g.46607406A>G	ENSP00000263734:p.Tyr532Cys						p.Y532C	NM_001430.4	NP_001421.2	Q99814	EPAS1_HUMAN	LUSC - Lung squamous cell carcinoma(58;0.151)		12	2105	+		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	532			NTAD.		Q86VA2|Q99630	Missense_Mutation	SNP	ENST00000263734.3	37	c.1595A>G	CCDS1825.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.246852	0.80024	.	.	ENSG00000116016	ENST00000263734	D	0.98400	-4.91	5.06	5.06	0.68205	.	0.000000	0.85682	D	0.000000	D	0.98673	0.9555	M	0.70595	2.14	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99861	1.1083	10	0.87932	D	0	.	14.8316	0.70153	1.0:0.0:0.0:0.0	.	532	Q99814	EPAS1_HUMAN	C	532	ENSP00000263734:Y532C	ENSP00000263734:Y532C	Y	+	2	0	EPAS1	46460910	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	9.335000	0.96500	1.915000	0.55452	0.402000	0.26972	TAT		0.587	EPAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250752.2	NM_001430		68	65	0	0	0	1	0	68	65				
IL16	3603	broad.mit.edu	37	15	81591746	81591746	+	Silent	SNP	C	C	T	rs528190343		TCGA-RW-A68D-01A-11D-A35D-08	TCGA-RW-A68D-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f81b6d24-ffdc-4d48-bce5-bca9de8c1939	8ee15795-2e6c-4e56-a9e5-5e280ac8c57c	g.chr15:81591746C>T	ENST00000302987.4	+	13	2079	c.2079C>T	c.(2077-2079)caC>caT	p.H693H	IL16_ENST00000560230.1_Intron|IL16_ENST00000394660.2_Silent_p.H693H|IL16_ENST00000394652.2_5'UTR			Q14005	IL16_HUMAN	interleukin 16	693					immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|leukocyte chemotaxis (GO:0030595)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						CGATAAAACACCCACTGCTTA	0.438																																						ENST00000394660.2																			0				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						c.(2077-2079)caC>caT		interleukin 16							233.0	247.0	242.0					15																	81591746		2203	4300	6503	SO:0001819	synonymous_variant	3603				immune response|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|extracellular space|nucleus|plasma membrane	cytokine activity	g.chr15:81591746C>T	U82972	CCDS10317.1, CCDS42069.1, CCDS53966.1	15q26.3	2011-07-14	2011-07-14		ENSG00000172349	ENSG00000172349		"""Interleukins and interleukin receptors"""	5980	protein-coding gene	gene with protein product	"""prointerleukin 16"", ""lymphocyte chemoattractant factor"""	603035	"""interleukin 16 (lymphocyte chemoattractant factor)"""			9144227	Standard	NM_004513		Approved	LCF, IL-16, prIL-16, HsT19289, FLJ42735, FLJ16806	uc021ssh.1	Q14005	OTTHUMG00000144186	ENST00000302987.4:c.2079C>T	15.37:g.81591746C>T						IL16_ENST00000302987.4_Silent_p.H693H|IL16_ENST00000560230.1_Intron|IL16_ENST00000394652.2_5'UTR	p.H693H	NM_001172128.1|NM_172217.3	NP_001165599.1|NP_757366.2	Q14005	IL16_HUMAN			14	2439	+			693					A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Silent	SNP	ENST00000302987.4	37	c.2079C>T	CCDS42069.1																																																																																				0.438	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217		100	165	0	0	0	1	0	100	165				
FANCC	2176	broad.mit.edu	37	9	97864024	97864024	+	Nonsense_Mutation	SNP	G	G	A	rs104886457		TCGA-RW-A68D-01A-11D-A35D-08	TCGA-RW-A68D-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f81b6d24-ffdc-4d48-bce5-bca9de8c1939	8ee15795-2e6c-4e56-a9e5-5e280ac8c57c	g.chr9:97864024G>A	ENST00000289081.3	-	15	1896	c.1642C>T	c.(1642-1644)Cga>Tga	p.R548*	FANCC_ENST00000375305.1_Nonsense_Mutation_p.R548*	NM_000136.2	NP_000127.2	Q00597	FANCC_HUMAN	Fanconi anemia, complementation group C	548					DNA repair (GO:0006281)|germ cell development (GO:0007281)|myeloid cell homeostasis (GO:0002262)|nucleotide-excision repair (GO:0006289)|protein complex assembly (GO:0006461)|removal of superoxide radicals (GO:0019430)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				kidney(1)|skin(1)|upper_aerodigestive_tract(1)	3		Acute lymphoblastic leukemia(62;0.138)				AGGAGCTCTCGGGCCAGTTTT	0.547			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																													ENST00000289081.3			yes	Rec		Fanconi anaemia C	9	9q22.3	2176	"""D, Mis, N, F, S"""	"""Fanconi anemia, complementation group C"""			L		"""AML, leukemia"""			0				kidney(1)|skin(1)|upper_aerodigestive_tract(1)	3	GRCh37	CM930241	FANCC	M	rs104886457	c.(1642-1644)Cga>Tga	Involved in tolerance or repair of DNA crosslinks	Fanconi anemia, complementation group C		G	stop/ARG	0,4406		0,0,2203	70.0	66.0	67.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1642	2.4	1.0	9	dbSNP_132	67	1,8599	1.2+/-3.3	0,1,4299	yes	stop-gained	FANCC	NM_000136.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		548/559	97864024	1,13005	2203	4300	6503	SO:0001587	stop_gained	2176	Fanconi Anemia	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	protein complex assembly	cytosol|nucleoplasm	protein binding	g.chr9:97864024G>A	BC006303	CCDS35071.1, CCDS75861.1	9q22.3	2014-09-17			ENSG00000158169	ENSG00000158169		"""Fanconi anemia, complementation groups"""	3584	protein-coding gene	gene with protein product		613899		FACC		1303234	Standard	NM_001243743		Approved	FAC, FA3	uc004avh.3	Q00597	OTTHUMG00000020279	ENST00000289081.3:c.1642C>T	9.37:g.97864024G>A	ENSP00000289081:p.Arg548*					FANCC_ENST00000375305.1_Nonsense_Mutation_p.R548*	p.R548*	NM_000136.2	NP_000127.2	Q00597	FANCC_HUMAN			15	1896	-		Acute lymphoblastic leukemia(62;0.138)	548					B1ALR8	Nonsense_Mutation	SNP	ENST00000289081.3	37	c.1642C>T	CCDS35071.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.454280	0.84209	0.0	1.16E-4	ENSG00000158169	ENST00000289081;ENST00000375305	.	.	.	4.76	2.43	0.29744	.	0.508870	0.21219	N	0.078170	.	.	.	.	.	.	0.49687	A	0.999815	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.1258	9.8369	0.40975	0.0:0.0:0.3843:0.6157	.	.	.	.	X	548	.	ENSP00000289081:R548X	R	-	1	2	FANCC	96903845	0.921000	0.31238	0.999000	0.59377	0.152000	0.21847	0.367000	0.20382	0.335000	0.23614	-0.397000	0.06425	CGA		0.547	FANCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053219.1	NM_000136		12	17	0	0	0	1	0	12	17				
ETV1	2115	broad.mit.edu	37	7	13975516	13975516	+	Missense_Mutation	SNP	T	T	C			TCGA-RW-A68D-01A-11D-A35D-08	TCGA-RW-A68D-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f81b6d24-ffdc-4d48-bce5-bca9de8c1939	8ee15795-2e6c-4e56-a9e5-5e280ac8c57c	g.chr7:13975516T>C	ENST00000430479.1	-	8	1038	c.371A>G	c.(370-372)tAt>tGt	p.Y124C	ETV1_ENST00000420159.2_Missense_Mutation_p.Y66C|ETV1_ENST00000343495.5_Missense_Mutation_p.Y106C|ETV1_ENST00000242066.5_Missense_Mutation_p.Y106C|ETV1_ENST00000399357.3_Intron|ETV1_ENST00000403527.1_Missense_Mutation_p.Y84C|ETV1_ENST00000403685.1_Missense_Mutation_p.Y106C|ETV1_ENST00000476720.2_5'UTR|ETV1_ENST00000405358.4_Missense_Mutation_p.Y138C|ETV1_ENST00000405218.2_Missense_Mutation_p.Y124C|ETV1_ENST00000405192.2_Missense_Mutation_p.Y124C	NM_004956.4	NP_004947.2	P50549	ETV1_HUMAN	ets variant 1	124					axon guidance (GO:0007411)|cell differentiation (GO:0030154)|mechanosensory behavior (GO:0007638)|muscle organ development (GO:0007517)|peripheral nervous system neuron development (GO:0048935)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	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 positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)		TMPRSS2/ETV1(34)|ACSL3_ENST00000357430/ETV1(2)|EWSR1/ETV1(7)|KLK2/ETV1(3)|SLC45A3/ETV1(3)|HNRNPA2B1/ETV1(8)	breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	31						CTTCTGATCATAGGCACTACC	0.443			T	"""EWSR1, TMPRSS2, SLC45A3, C15orf21, HNRNPA2B1. ACSL3"""	"""Ewing sarcoma, prostate"""																																	ENST00000343495.5				Dom	yes		7	7p22	2115	T	ets variant gene 1			"""M, E"""	"""EWSR1, TMPRSS2, SLC45A3, C15orf21, HNRNPA2B1. ACSL3"""		"""Ewing sarcoma, prostate"""	TMPRSS2/ETV1(34)|ACSL3_ENST00000357430/ETV1(2)|EWSR1/ETV1(7)|KLK2/ETV1(3)|SLC45A3/ETV1(3)|HNRNPA2B1/ETV1(8)	0				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	31						c.(316-318)tAt>tGt		ets variant 1							80.0	79.0	80.0					7																	13975516		1962	4155	6117	SO:0001583	missense	2115				transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chr7:13975516T>C		CCDS55083.1, CCDS55084.1, CCDS55085.1, CCDS55086.1, CCDS55087.1, CCDS55088.1	7p22	2008-09-12	2008-09-12		ENSG00000006468	ENSG00000006468			3490	protein-coding gene	gene with protein product		600541	"""ets variant gene 1"""			1340465	Standard	NM_004956		Approved	ER81	uc003ssw.4	P50549	OTTHUMG00000152403	ENST00000430479.1:c.371A>G	7.37:g.13975516T>C	ENSP00000405327:p.Tyr124Cys					ETV1_ENST00000399357.3_Intron|ETV1_ENST00000405192.2_Missense_Mutation_p.Y124C|ETV1_ENST00000242066.5_Missense_Mutation_p.Y106C|ETV1_ENST00000405218.2_Missense_Mutation_p.Y124C|ETV1_ENST00000405358.4_Missense_Mutation_p.Y138C|ETV1_ENST00000403685.1_Missense_Mutation_p.Y106C|ETV1_ENST00000430479.1_Missense_Mutation_p.Y124C|ETV1_ENST00000420159.2_Missense_Mutation_p.Y66C|ETV1_ENST00000403527.1_Missense_Mutation_p.Y84C|ETV1_ENST00000476720.2_5'UTR	p.Y106C			P50549	ETV1_HUMAN			7	1055	-			124					A4D118|B2R768|B7Z2I4|B7Z618|B7Z9P2|C9JT37|E9PHB1|F5GXR2|O75849|Q4KMQ6|Q59GA7|Q6AI30|Q9UQ71|Q9Y636	Missense_Mutation	SNP	ENST00000430479.1	37	c.317A>G	CCDS55088.1	.	.	.	.	.	.	.	.	.	.	T	19.68	3.872094	0.72180	.	.	ENSG00000006468	ENST00000430479;ENST00000242066;ENST00000343495;ENST00000420159;ENST00000405192;ENST00000405358;ENST00000403527;ENST00000405218;ENST00000403685;ENST00000438956	T;T;T;T;T;T;T;T;T;T	0.23950	1.88;1.88;1.88;1.88;1.88;1.88;1.88;1.88;1.88;1.88	5.83	5.83	0.93111	PEA3-type ETS-domain transcription factor, N-terminal (1);	0.120390	0.64402	D	0.000018	T	0.46927	0.1418	L	0.52266	1.64	0.80722	D	1	D;B;D;D;D;B	0.89917	1.0;0.05;1.0;0.999;1.0;0.395	D;B;D;D;D;B	0.87578	0.992;0.061;0.992;0.995;0.998;0.366	T	0.40117	-0.9580	10	0.62326	D	0.03	.	16.2579	0.82526	0.0:0.0:0.0:1.0	.	135;106;138;66;84;124	Q59GA7;P50549-2;B5MCT2;F5GXR2;E9PHB1;P50549	.;.;.;.;.;ETV1_HUMAN	C	124;106;106;66;124;138;84;124;106;66	ENSP00000405327:Y124C;ENSP00000242066:Y106C;ENSP00000340853:Y106C;ENSP00000411626:Y66C;ENSP00000385381:Y124C;ENSP00000384085:Y138C;ENSP00000384138:Y84C;ENSP00000385551:Y124C;ENSP00000385686:Y106C;ENSP00000393078:Y66C	ENSP00000242066:Y106C	Y	-	2	0	ETV1	13942041	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	7.652000	0.83633	2.250000	0.74265	0.529000	0.55759	TAT		0.443	ETV1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326111.1	NM_004956		3	43	0	0	0	1	0	3	43				
SQRDL	58472	broad.mit.edu	37	15	45951173	45951173	+	Missense_Mutation	SNP	T	T	A			TCGA-RW-A68D-01A-11D-A35D-08	TCGA-RW-A68D-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f81b6d24-ffdc-4d48-bce5-bca9de8c1939	8ee15795-2e6c-4e56-a9e5-5e280ac8c57c	g.chr15:45951173T>A	ENST00000260324.7	+	2	438	c.52T>A	c.(52-54)Tgc>Agc	p.C18S	SQRDL_ENST00000568606.1_Missense_Mutation_p.C18S|RP11-96O20.4_ENST00000564080.1_Missense_Mutation_p.C18S	NM_021199.3	NP_067022.1	Q9Y6N5	SQRD_HUMAN	sulfide quinone reductase-like (yeast)	18					cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)	mitochondrial inner membrane (GO:0005743)	sulfide:quinone oxidoreductase activity (GO:0070224)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)	11		Lung NSC(122;0.000117)|all_lung(180;0.000737)|Melanoma(134;0.0417)		all cancers(107;5.89e-18)|GBM - Glioblastoma multiforme(94;1.21e-06)|COAD - Colon adenocarcinoma(120;0.17)|Colorectal(133;0.188)		GCTCTTTGCCTGCCTGCTCAG	0.647																																						ENST00000260324.7																			0				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)	11						c.(52-54)Tgc>Agc		sulfide quinone reductase-like (yeast)							14.0	16.0	15.0					15																	45951173		2197	4296	6493	SO:0001583	missense	58472						oxidoreductase activity	g.chr15:45951173T>A	AF042284	CCDS10127.1	15q21.1	2010-08-05			ENSG00000137767	ENSG00000137767			20390	protein-coding gene	gene with protein product						10810093, 10224084	Standard	NM_021199		Approved	CGI-44	uc001zvu.4	Q9Y6N5	OTTHUMG00000131476	ENST00000260324.7:c.52T>A	15.37:g.45951173T>A	ENSP00000260324:p.Cys18Ser					SQRDL_ENST00000568606.1_Missense_Mutation_p.C18S|RP11-96O20.4_ENST00000564080.1_Missense_Mutation_p.C18S	p.C18S	NM_021199.2	NP_067022.1	Q9Y6N5	SQRD_HUMAN		all cancers(107;5.89e-18)|GBM - Glioblastoma multiforme(94;1.21e-06)|COAD - Colon adenocarcinoma(120;0.17)|Colorectal(133;0.188)	2	438	+		Lung NSC(122;0.000117)|all_lung(180;0.000737)|Melanoma(134;0.0417)	18					Q9UQM8	Missense_Mutation	SNP	ENST00000260324.7	37	c.52T>A	CCDS10127.1	.	.	.	.	.	.	.	.	.	.	T	9.139	1.013276	0.19277	.	.	ENSG00000137767	ENST00000260324	T	0.39229	1.09	4.96	1.04	0.20106	.	0.858072	0.10812	N	0.631515	T	0.22666	0.0547	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.24905	-1.0147	10	0.18710	T	0.47	.	4.5527	0.12120	0.0:0.1724:0.323:0.5046	.	18	Q9Y6N5	SQRD_HUMAN	S	18	ENSP00000260324:C18S	ENSP00000260324:C18S	C	+	1	0	SQRDL	43738465	0.001000	0.12720	0.413000	0.26509	0.924000	0.55760	0.404000	0.20999	0.228000	0.21019	0.533000	0.62120	TGC		0.647	SQRDL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254319.2			6	4	0	0	0	1	0	6	4				
SLC30A5	64924	broad.mit.edu	37	5	68412389	68412389	+	Missense_Mutation	SNP	G	G	C			TCGA-RW-A68D-01A-11D-A35D-08	TCGA-RW-A68D-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f81b6d24-ffdc-4d48-bce5-bca9de8c1939	8ee15795-2e6c-4e56-a9e5-5e280ac8c57c	g.chr5:68412389G>C	ENST00000396591.3	+	10	1851	c.1241G>C	c.(1240-1242)aGt>aCt	p.S414T	CTC-498J12.3_ENST00000504129.1_RNA	NM_022902.4	NP_075053.2	Q8TAD4	ZNT5_HUMAN	solute carrier family 30 (zinc transporter), member 5	414					cellular protein metabolic process (GO:0044267)|cellular zinc ion homeostasis (GO:0006882)|cobalt ion transport (GO:0006824)|regulation of proton transport (GO:0010155)|response to zinc ion (GO:0010043)|transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)|zinc ion transport (GO:0006829)	apical plasma membrane (GO:0016324)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|secretory granule (GO:0030141)|secretory granule membrane (GO:0030667)	zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		Lung NSC(167;0.000986)|Prostate(74;0.00809)|Colorectal(97;0.0508)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;1.24e-56)|Epithelial(20;1.12e-52)|all cancers(19;2.63e-48)|Lung(70;0.0177)		CTTGAGGAGAGTGACTCTAGG	0.333																																						ENST00000396591.3																			0				breast(3)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						c.(1240-1242)aGt>aCt		solute carrier family 30 (zinc transporter), member 5							62.0	65.0	64.0					5																	68412389		2203	4300	6503	SO:0001583	missense	64924				cellular zinc ion homeostasis|cobalt ion transport|regulation of proton transport|response to zinc ion	apical plasma membrane|Golgi apparatus|integral to plasma membrane|membrane fraction|secretory granule membrane	zinc ion binding|zinc ion transmembrane transporter activity	g.chr5:68412389G>C	AF212235	CCDS3996.1, CCDS34173.1, CCDS58955.1	5q13.1	2013-05-22			ENSG00000145740	ENSG00000145740		"""Solute carriers"""	19089	protein-coding gene	gene with protein product		607819				11937503, 11904301	Standard	NM_022902		Approved	ZTL1, ZnT-5, FLJ12496, FLJ12756, ZNT5, MGC5499, ZNTL1	uc003jvh.3	Q8TAD4	OTTHUMG00000131253	ENST00000396591.3:c.1241G>C	5.37:g.68412389G>C	ENSP00000379836:p.Ser414Thr					CTC-498J12.3_ENST00000504129.1_RNA	p.S414T	NM_022902.4	NP_075053.2	Q8TAD4	ZNT5_HUMAN		OV - Ovarian serous cystadenocarcinoma(47;1.24e-56)|Epithelial(20;1.12e-52)|all cancers(19;2.63e-48)|Lung(70;0.0177)	10	1851	+		Lung NSC(167;0.000986)|Prostate(74;0.00809)|Colorectal(97;0.0508)|Ovarian(174;0.16)	414					B7ZM89|Q6UX54|Q7L4M4|Q8TDG3|Q9BVY8|Q9H9H1	Missense_Mutation	SNP	ENST00000396591.3	37	c.1241G>C	CCDS3996.1	.	.	.	.	.	.	.	.	.	.	G	11.09	1.536808	0.27475	.	.	ENSG00000145740	ENST00000396591;ENST00000438236	T	0.65364	-0.15	5.87	4.94	0.65067	.	0.132704	0.64402	D	0.000001	T	0.46014	0.1371	L	0.33189	0.99	0.80722	D	1	B;B;B	0.21520	0.024;0.057;0.024	B;B;B	0.28305	0.017;0.088;0.017	T	0.32188	-0.9916	10	0.14656	T	0.56	.	5.253	0.15532	0.4716:0.0:0.5284:0.0	.	243;243;414	Q9H9X0;Q8TAD4-2;Q8TAD4	.;.;ZNT5_HUMAN	T	414;27	ENSP00000379836:S414T	ENSP00000379836:S414T	S	+	2	0	SLC30A5	68448145	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.234000	0.65343	1.455000	0.47813	0.655000	0.94253	AGT		0.333	SLC30A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254017.2			14	45	0	0	0	1	0	14	45				
RARG	5916	broad.mit.edu	37	12	53609167	53609167	+	Missense_Mutation	SNP	C	C	T			TCGA-RW-A68D-01A-11D-A35D-08	TCGA-RW-A68D-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f81b6d24-ffdc-4d48-bce5-bca9de8c1939	8ee15795-2e6c-4e56-a9e5-5e280ac8c57c	g.chr12:53609167C>T	ENST00000425354.2	-	5	872	c.385G>A	c.(385-387)Gac>Aac	p.D129N	RARG_ENST00000338561.5_Missense_Mutation_p.D118N|RARG_ENST00000327550.3_Missense_Mutation_p.D57N|RARG_ENST00000543762.1_5'UTR|RARG_ENST00000543726.1_Missense_Mutation_p.D107N|RARG_ENST00000394426.1_Missense_Mutation_p.D129N	NM_000966.5	NP_000957.1	P13631	RARG_HUMAN	retinoic acid receptor, gamma	129					anterior/posterior pattern specification (GO:0009952)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|embryonic camera-type eye development (GO:0031076)|embryonic eye morphogenesis (GO:0048048)|embryonic hindlimb morphogenesis (GO:0035116)|face development (GO:0060324)|gene expression (GO:0010467)|glandular epithelial cell development (GO:0002068)|growth plate cartilage chondrocyte growth (GO:0003430)|Harderian gland development (GO:0070384)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of programmed cell death (GO:0043068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland epithelium morphogenesis (GO:0060740)|regulation of cell size (GO:0008361)|regulation of myelination (GO:0031641)|response to retinoic acid (GO:0032526)|retinal pigment epithelium development (GO:0003406)|retinoic acid receptor signaling pathway (GO:0048384)|trachea cartilage development (GO:0060534)|transcription initiation from RNA polymerase II promoter (GO:0006367)	integral component of membrane (GO:0016021)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|retinoic acid receptor activity (GO:0003708)|retinoid X receptor binding (GO:0046965)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Tazarotene(DB00799)|Tretinoin(DB00755)	CAGTTTTTGTCGCGGTGACAC	0.537																																						ENST00000425354.2																			0				breast(3)|endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20						c.(385-387)Gac>Aac		retinoic acid receptor, gamma	Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)|Tazarotene(DB00799)|Tretinoin(DB00755)						249.0	193.0	212.0					12																	53609167		2203	4300	6503	SO:0001583	missense	5916				canonical Wnt receptor signaling pathway|embryonic eye morphogenesis|embryonic hindlimb morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter|regulation of cell size|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to retinoic acid	integral to membrane|transcription factor complex	retinoic acid receptor activity|retinoid X receptor binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding	g.chr12:53609167C>T	M57707	CCDS8850.1, CCDS41790.1, CCDS58236.1, CCDS58237.1	12q13	2013-01-16			ENSG00000172819	ENSG00000172819		"""Nuclear hormone receptors"""	9866	protein-coding gene	gene with protein product		180190				1849262	Standard	NM_001042728		Approved	RARC, NR1B3	uc001scf.3	P13631	OTTHUMG00000048077	ENST00000425354.2:c.385G>A	12.37:g.53609167C>T	ENSP00000388510:p.Asp129Asn					RARG_ENST00000394426.1_Missense_Mutation_p.D129N|RARG_ENST00000338561.5_Missense_Mutation_p.D118N|RARG_ENST00000327550.3_Missense_Mutation_p.D57N|RARG_ENST00000543726.1_Missense_Mutation_p.D107N|RARG_ENST00000543762.1_5'UTR	p.D129N	NM_000966.5	NP_000957.1	P13631	RARG_HUMAN			5	872	-			129					B7Z492|B7Z4F1|B7ZAE4|J3KNP6|P22932|Q15281|Q52LZ8|Q9BYX8|Q9H1I3|Q9UJ38	Missense_Mutation	SNP	ENST00000425354.2	37	c.385G>A	CCDS8850.1	.	.	.	.	.	.	.	.	.	.	C	18.10	3.549352	0.65311	.	.	ENSG00000172819	ENST00000425354;ENST00000394426;ENST00000327550;ENST00000338561;ENST00000543726;ENST00000550265	D;D;D;D;D	0.97066	-4.23;-4.23;-4.23;-4.23;-4.23	4.45	4.45	0.53987	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (3);	0.055994	0.64402	D	0.000002	D	0.94670	0.8281	N	0.03016	-0.435	0.80722	D	1	P;D;D;P	0.89917	0.758;1.0;1.0;0.535	B;D;D;B	0.87578	0.163;0.995;0.998;0.229	D	0.92259	0.5815	10	0.12103	T	0.63	.	16.3946	0.83586	0.0:1.0:0.0:0.0	.	166;107;129;118	F8VR45;B7Z4F1;P13631;F1D8P1	.;.;RARG_HUMAN;.	N	129;129;57;118;107;166	ENSP00000388510:D129N;ENSP00000377947:D129N;ENSP00000332695:D57N;ENSP00000343698:D118N;ENSP00000444335:D107N	ENSP00000332695:D57N	D	-	1	0	RARG	51895434	1.000000	0.71417	0.980000	0.43619	0.779000	0.44077	7.590000	0.82653	2.471000	0.83476	0.591000	0.81541	GAC		0.537	RARG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109404.2	NM_000966		4	199	0	0	0	1	0	4	199				
HERC2P2	400322	broad.mit.edu	37	15	23299146	23299147	+	RNA	INS	-	-	A	rs572079359	byFrequency	TCGA-RW-A68D-01A-11D-A35D-08	TCGA-RW-A68D-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f81b6d24-ffdc-4d48-bce5-bca9de8c1939	8ee15795-2e6c-4e56-a9e5-5e280ac8c57c	g.chr15:23299146_23299147insA	ENST00000560464.1	-	0	4510									hect domain and RLD 2 pseudogene 2																		TACATTCAAAGAAAAAAAAAAA	0.317																																						ENST00000560464.1																			0																																																			400322							g.chr15:23299146_23299147insA	AF041080		15q11.2	2014-03-18			ENSG00000140181				4870	pseudogene	pseudogene						9730612	Standard	NR_002824		Approved	D15F37S3	uc001yvq.2		OTTHUMG00000171926		15.37:g.23299157_23299157dupA														0	4510	-									RNA	INS	ENST00000560464.1	37																																																																																						0.317	HERC2P2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000415936.1			3	3						3	3	---	---	---	---
SLC43A2	124935	broad.mit.edu	37	17	1531078	1531078	+	Frame_Shift_Del	DEL	G	G	-			TCGA-RW-A68D-01A-11D-A35D-08	TCGA-RW-A68D-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f81b6d24-ffdc-4d48-bce5-bca9de8c1939	8ee15795-2e6c-4e56-a9e5-5e280ac8c57c	g.chr17:1531078delG	ENST00000301335.5	-	2	179	c.91delC	c.(91-93)ctgfs	p.L31fs	SLC43A2_ENST00000571650.1_Frame_Shift_Del_p.L31fs|SLC43A2_ENST00000382147.4_Frame_Shift_Del_p.L31fs	NM_001284498.1|NM_001284499.1	NP_001271427.1|NP_001271428.1	Q8N370	LAT4_HUMAN	solute carrier family 43 (amino acid system L transporter), member 2	31					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-amino acid transmembrane transporter activity (GO:0015179)			endometrium(4)|large_intestine(4)|liver(1)|lung(2)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (25;0.0883)		CCCCAGCCCAGGAGGACTGCC	0.672																																						ENST00000571650.1																			0				endometrium(4)|large_intestine(4)|liver(1)|lung(2)|upper_aerodigestive_tract(1)	12						c.(91-93)tgfs		solute carrier family 43 (amino acid system L transporter), member 2							27.0	22.0	24.0					17																	1531078		2203	4298	6501	SO:0001589	frameshift_variant	124935				cellular nitrogen compound metabolic process|ion transport	integral to membrane|plasma membrane		g.chr17:1531078delG	BC027923	CCDS11006.1, CCDS67107.1, CCDS67108.1	17p13.3	2013-07-17	2013-07-17		ENSG00000167703	ENSG00000167703		"""Solute carriers"""	23087	protein-coding gene	gene with protein product		610791				23268354	Standard	NM_001284498		Approved	MGC34680	uc002fsv.3	Q8N370	OTTHUMG00000090345	ENST00000301335.5:c.91delC	17.37:g.1531078delG	ENSP00000301335:p.Leu31fs					SLC43A2_ENST00000382147.4_Frame_Shift_Del_p.L31fs|SLC43A2_ENST00000301335.4_Frame_Shift_Del_p.L31fs	p.L31fs			Q8N370	LAT4_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (25;0.0883)	2	397	-			31					B7Z6X9|C9JNU8|D3DTH9|Q5CD75|Q6IPM1|Q8NBX1|Q8NC21|Q8WZ00	Frame_Shift_Del	DEL	ENST00000301335.5	37	c.91delC	CCDS11006.1																																																																																				0.672	SLC43A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206717.4	NM_152346		2	4						2	4	---	---	---	---
WDR81	124997	broad.mit.edu	37	17	1631341	1631343	+	In_Frame_Del	DEL	GAG	GAG	-	rs577690948|rs200758098|rs35048651	byFrequency	TCGA-RW-A68D-01A-11D-A35D-08	TCGA-RW-A68D-10A-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f81b6d24-ffdc-4d48-bce5-bca9de8c1939	8ee15795-2e6c-4e56-a9e5-5e280ac8c57c	g.chr17:1631341_1631343delGAG	ENST00000409644.1	+	1	3088_3090	c.3088_3090delGAG	c.(3088-3090)gagdel	p.E1033del	WDR81_ENST00000437219.2_Intron|WDR81_ENST00000419248.1_Intron|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000545662.1_5'Flank|WDR81_ENST00000309182.5_5'UTR|WDR81_ENST00000446363.1_Intron	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	1033				Missing (in Ref. 1; BAB84937). {ECO:0000305}.	negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		AGGGGCTGCTGAGGAGGAGGAGA	0.695														1061	0.211861	0.115	0.196	5008	,	,		16982	0.1835		0.1948	False		,,,				2504	0.4008					ENST00000409644.1																			0				cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16						c.(3088-3090)del		WD repeat domain 81			,,,	549,3367		98,353,1507					,,,	-11.3	0.0		dbSNP_130	17	1642,6232		262,1118,2557	no	utr-5,intron,coding,intron	WDR81	NM_152348.3,NM_001163811.1,NM_001163809.1,NM_001163673.1	,,,	360,1471,4064	A1A1,A1R,RR		20.8534,14.0194,18.5835	,,,	,,,		2191,9599				SO:0001651	inframe_deletion	124997							g.chr17:1631341_1631343delGAG	AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"""WD repeat domain containing"""	26600	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 166"""	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.3088_3090delGAG	17.37:g.1631350_1631352delGAG	ENSP00000386609:p.Glu1033del					WDR81_ENST00000419248.1_Intron|WDR81_ENST00000437219.2_Intron|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000309182.5_5'UTR|WDR81_ENST00000446363.1_Intron	p.E1033del	NM_001163809.1	NP_001157281.1	B3KXU1	B3KXU1_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)	1	3088_3090	+			305					B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	In_Frame_Del	DEL	ENST00000409644.1	37	c.3088_3090delGAG	CCDS54062.1																																																																																				0.695	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348		6	4						6	4	---	---	---	---
