#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_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	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_Description	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_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_AccessionNumbers	i_HGNC_CCDS IDs	i_HGNC_CCDSIDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_DateModified	i_HGNC_DateNameChanged	i_HGNC_DateSymbolChanged	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_EnsemblGeneID	i_HGNC_EnsemblIDsuppliedbyEnsembl	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_Genefamilydescription	i_HGNC_HGNC ID	i_HGNC_HGNCID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_LocusGroup	i_HGNC_LocusType	i_HGNC_Name Synonyms	i_HGNC_NameSynonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_OMIMIDsuppliedbyNCBI	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_PreviousNames	i_HGNC_PreviousSymbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_PubmedIDs	i_HGNC_Record Type	i_HGNC_RecordType	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_RefSeqsuppliedbyNCBI	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UCSCIDsuppliedbyUCSC	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_UniProtIDsuppliedbyUniProt	i_HGNC_VEGA IDs	i_HGNC_VEGAIDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	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_Region	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_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_folddegenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_hg18_pos1coor	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_init_n_lod	i_init_t_lod	i_n_alt_count	i_n_alt_count_full	i_n_ref_count	i_n_ref_count_full	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_lod_fstar	i_t_lod_fstar_full	i_t_ref_count_full	i_tumor_f_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	tumor_f
BTNL3	10917	broad.mit.edu	37	5	180432727	180432727	+	Missense_Mutation	SNP	C	C	T			TCGA-V4-A9EQ-01A-11D-A39W-08	TCGA-V4-A9EQ-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	da7b9dab-d5d2-42f1-b156-c627cf9f987c	a505db24-f411-4532-9291-41073c0938da	g.chr5:180432727C>T	ENST00000342868.6	+	8	1440	c.1256C>T	c.(1255-1257)tCc>tTc	p.S419F	RNU6-1036P_ENST00000383959.1_RNA	NM_197975.2	NP_932079.1	Q6UXE8	BTNL3_HUMAN	butyrophilin-like 3	419	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(1)|lung(10)|prostate(2)|skin(1)	25	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.00336)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)|all_lung(500;0.248)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000272)			GGGACCATCTCCTTCTTCAAT	0.478																																						ENST00000342868.6											0			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(1)|lung(10)|prostate(2)|skin(1)	25						c.(1255-1257)tCc>tTc	butyrophilin-like 3						114.0	110.0	111.0					5																	180432727		1908	4119	6027	SO:0001583	missense	10917			lipid metabolic process	integral to membrane		g.chr5:180432727C>T	AB020625	AB020625	CCDS47358.1	CCDS47358.1	5q35	2014-01-14			2014-01-14			ENSG00000168903	ENSG00000168903	ENSG00000168903	ENSG00000168903		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	1143	1143	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product	"""butyrophilin-like receptor"""	"""butyrophilin-like receptor"""	606192	606192						10429365	10429365	Standard	Standard	NM_197975	NM_197975		Approved	BTNLR, BTN9.1	uc003mmr.3	uc003mmr.3	Q6UXE8	Q6UXE8	OTTHUMG00000162091	OTTHUMG00000162091	ENST00000342868.6:c.1256C>T	5.37:g.180432727C>T	ENSP00000341787:p.Ser419Phe			p.S419F	NM_197975.2	NP_932079.1	Q6UXE8	BTNL3_HUMAN	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000272)		8	1440	+	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.00336)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)|all_lung(500;0.248)	419	B30.2/SPRY.	Q496L7|Q9Y2C7	Missense_Mutation	SNP	ENST00000342868.6	37	c.1256C>T	CCDS47358.1	.	.	.	.	.	.	.	.	.	.	C	16.91	3.251992	0.59212	.	.	ENSG00000168903	ENST00000342868;ENST00000376852	T	0.68765	-0.35	2.74	2.74	0.32292	2.74	2.74	0.32292	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	.	.	.	.	D	0.85392	0.5686	H	0.95294	3.65	0.34179	D	0.670675	D;D	0.89917	1.0;0.997	D;D	0.91635	0.999;0.995	D	0.90559	0.4514	9	0.87932	D	0	.	11.2087	0.48784	0.0:1.0:0.0:0.0	.	385;419	C9JDC2;Q6UXE8	.;BTNL3_HUMAN	F	419;385	ENSP00000341787:S419F	ENSP00000341787:S419F	S	+	2	0	0	BTNL3	180365333	180365333	0.993000	0.37304	0.094000	0.20943	0.130000	0.20726	2.307000	0.43682	1.253000	0.44018	0.174000	0.16983	TCC		0.478	BTNL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367176.2		69.448570	16	16	89	89	NM_197975		22	69.467396	69.467396	24	0.478261	0	0	0	1	0	22	24	0.478261
VWA5A	4013	broad.mit.edu	37	11	123988499	123988499	+	Missense_Mutation	SNP	A	A	G			TCGA-V4-A9EQ-01A-11D-A39W-08	TCGA-V4-A9EQ-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	da7b9dab-d5d2-42f1-b156-c627cf9f987c	a505db24-f411-4532-9291-41073c0938da	g.chr11:123988499A>G	ENST00000456829.2	+	4	414	c.163A>G	c.(163-165)Atg>Gtg	p.M55V	VWA5A_ENST00000361352.5_Missense_Mutation_p.M55V|VWA5A_ENST00000392744.4_Missense_Mutation_p.M71V|VWA5A_ENST00000360334.4_Missense_Mutation_p.M55V|VWA5A_ENST00000392748.1_Missense_Mutation_p.M55V|VWA5A_ENST00000449321.1_Missense_Mutation_p.M55V	NM_001130142.1	NP_001123614.1	O00534	VMA5A_HUMAN	von Willebrand factor A domain containing 5A	55	VIT. {ECO:0000255|PROSITE- ProRule:PRU00801}.									autonomic_ganglia(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	47						TGTGTTCCCCATGGATGAAGA	0.443																																						ENST00000456829.2											0			autonomic_ganglia(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	47						c.(163-165)Atg>Gtg	von Willebrand factor A domain containing 5A						151.0	153.0	152.0					11																	123988499		2201	4299	6500	SO:0001583	missense	4013						g.chr11:123988499A>G	AF002672	AF002672	CCDS8444.1, CCDS8445.1	CCDS8444.1, CCDS8445.1	11q24.1	2008-07-25	2008-07-25	2008-07-25	2008-07-25	2008-07-25	2008-07-25	ENSG00000110002	ENSG00000110002	ENSG00000110002	ENSG00000110002				6658	6658	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			602929	602929	"""loss of heterozygosity, 11, chromosomal region 2, gene A"""	LOH11CR2A	"""loss of heterozygosity, 11, chromosomal region 2, gene A"""	LOH11CR2A		9417908, 14504409	9417908, 14504409	Standard	Standard	NM_001130142	NM_001130142		Approved	BCSC-1	uc001pzt.3	uc001pzt.3	O00534	O00534	OTTHUMG00000165971	OTTHUMG00000165971	ENST00000456829.2:c.163A>G	11.37:g.123988499A>G	ENSP00000407726:p.Met55Val		VWA5A_ENST00000392744.4_Missense_Mutation_p.M71V|VWA5A_ENST00000361352.5_Missense_Mutation_p.M55V|VWA5A_ENST00000392748.1_Missense_Mutation_p.M55V|VWA5A_ENST00000449321.1_Missense_Mutation_p.M55V|VWA5A_ENST00000360334.4_Missense_Mutation_p.M55V	p.M55V	NM_001130142.1	NP_001123614.1	O00534	VMA5A_HUMAN			4	414	+			55	VIT.	Q6UN19|Q6UN20|Q9BVF8	Missense_Mutation	SNP	ENST00000456829.2	37	c.163A>G	CCDS8444.1	.	.	.	.	.	.	.	.	.	.	A	13.87	2.365114	0.41902	.	.	ENSG00000110002	ENST00000456829;ENST00000360334;ENST00000392748;ENST00000524524;ENST00000530025;ENST00000361352;ENST00000449321;ENST00000392744	T;T;T;T;T;T	0.19250	2.16;2.16;2.16;2.16;2.16;2.16	5.6	4.48	0.54585	5.6	4.48	0.54585	Vault protein inter-alpha-trypsin (2);Vault protein inter-alpha-trypsin, metazoa (1);	0.103318	0.64402	D	0.000001	T	0.11707	0.0285	N	0.12853	0.265	0.35310	D	0.783829	B;B	0.16166	0.005;0.016	B;B	0.28305	0.015;0.088	T	0.09796	-1.0658	10	0.49607	T	0.09	-46.0508	5.2844	0.15692	0.7296:0.181:0.0894:0.0	.	71;55	B4DHS6;O00534	.;VMA5A_HUMAN	V	55;55;55;55;55;55;55;71	ENSP00000407726:M55V;ENSP00000353485:M55V;ENSP00000376504:M55V;ENSP00000355070:M55V;ENSP00000404683:M55V;ENSP00000376501:M71V	ENSP00000353485:M55V	M	+	1	0	0	VWA5A	123493709	123493709	0.982000	0.34865	1.000000	0.80357	0.969000	0.65631	1.223000	0.32527	2.140000	0.66376	0.533000	0.62120	ATG		0.443	VWA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387273.1		98.592821	25	25	130	130	NM_014622		32	98.742877	98.742877	39	0.450704	0	0	0	1	0	32	39	0.450704
SH3RF2	153769	broad.mit.edu	37	5	145427382	145427382	+	Silent	SNP	C	C	T			TCGA-V4-A9EQ-01A-11D-A39W-08	TCGA-V4-A9EQ-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	da7b9dab-d5d2-42f1-b156-c627cf9f987c	a505db24-f411-4532-9291-41073c0938da	g.chr5:145427382C>T	ENST00000511217.1	+	5	1159	c.1107C>T	c.(1105-1107)gcC>gcT	p.A369A	SH3RF2_ENST00000359120.4_Silent_p.A369A			Q8TEC5	SH3R2_HUMAN	SH3 domain containing ring finger 2	369					negative regulation of phosphatase activity (GO:0010923)|protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|phosphatase binding (GO:0019902)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase inhibitor activity (GO:0004864)|zinc ion binding (GO:0008270)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(9)|ovary(1)|prostate(1)|skin(2)|stomach(1)	22			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ATTCCACAGCCGTGGTCAGTC	0.542																																						ENST00000511217.1											0			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(9)|ovary(1)|prostate(1)|skin(2)|stomach(1)	22						c.(1105-1107)gcC>gcT	SH3 domain containing ring finger 2						154.0	128.0	137.0					5																	145427382		2203	4300	6503	SO:0001819	synonymous_variant	153769					ligase activity|protein phosphatase 1 binding|zinc ion binding	g.chr5:145427382C>T	AL833297	AL833297	CCDS4280.1	CCDS4280.1	5q32	2013-01-09	2011-11-04	2011-11-04	2013-01-09	2011-11-04	2011-11-04	ENSG00000156463	ENSG00000156463	ENSG00000156463	ENSG00000156463		"""RING-type (C3HC4) zinc fingers"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	"""RING-type (C3HC4) zinc fingers"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	26299	26299	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product	"""heart protein phosphatase 1-binding protein"", ""POSH-eliminating RING protein"""	"""heart protein phosphatase 1-binding protein"", ""POSH-eliminating RING protein"""	613377	613377	"""protein phosphatase 1, regulatory subunit 39"""	PPP1R39	"""protein phosphatase 1, regulatory subunit 39"""	PPP1R39		22128169	22128169	Standard	Standard	NM_152550	NM_152550		Approved	FLJ23654, RNF158, Hepp1, POSHER	uc003lnt.3	uc003lnt.3	Q8TEC5	Q8TEC5	OTTHUMG00000129685	OTTHUMG00000129685	ENST00000511217.1:c.1107C>T	5.37:g.145427382C>T			SH3RF2_ENST00000359120.4_Silent_p.A369A	p.A369A			Q8TEC5	SH3R2_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		5	1159	+			369		A8K961|Q08AM9|Q6GMR9|Q8N5S8|Q96LP8	Silent	SNP	ENST00000511217.1	37	c.1107C>T	CCDS4280.1																																																																																									0.542	SH3RF2-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372804.1		73.353313	-16	-16	51	51	NM_152550		22	73.401091	73.401091	19	0.536585	0	0	0	1	0	22	19	0.536585
MC2R	4158	broad.mit.edu	37	18	13885067	13885067	+	Missense_Mutation	SNP	G	G	A			TCGA-V4-A9EQ-01A-11D-A39W-08	TCGA-V4-A9EQ-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	da7b9dab-d5d2-42f1-b156-c627cf9f987c	a505db24-f411-4532-9291-41073c0938da	g.chr18:13885067G>A	ENST00000327606.3	-	2	631	c.451C>T	c.(451-453)Ctt>Ttt	p.L151F		NM_000529.2	NP_000520.1	Q01718	ACTHR_HUMAN	melanocortin 2 receptor (adrenocorticotropic hormone)	151					G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|neuropeptide signaling pathway (GO:0007218)|placenta development (GO:0001890)|positive regulation of cAMP biosynthetic process (GO:0030819)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	corticotropin receptor activity (GO:0004978)|melanocortin receptor activity (GO:0004977)			breast(1)|endometrium(1)|kidney(2)|large_intestine(10)|lung(8)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30					Corticotropin(DB01285)|Cosyntropin(DB01284)	ATGACCGTAAGCACCACCACA	0.577																																					Colon(141;1584 1782 35999 48227 48692)	ENST00000327606.3											0			breast(1)|endometrium(1)|kidney(2)|large_intestine(10)|lung(8)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						c.(451-453)Ctt>Ttt	melanocortin 2 receptor (adrenocorticotropic hormone)						130.0	107.0	115.0					18																	13885067		2203	4300	6503	SO:0001583	missense	0			G-protein signaling, coupled to cyclic nucleotide second messenger|positive regulation of cAMP biosynthetic process	integral to plasma membrane	corticotropin receptor activity|protein binding	g.chr18:13885067G>A			CCDS11869.1	CCDS11869.1	18p11.2	2012-08-10			2012-08-10			ENSG00000185231	ENSG00000185231	ENSG00000185231	ENSG00000185231		"""GPCR / Class A : Melanocortin receptors"""	"""GPCR / Class A : Melanocortin receptors"""	6930	6930	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			607397	607397						8390157	8390157	Standard	Standard	NM_001291911	NM_001291911		Approved	ACTHR	uc002ksp.1	uc002ksp.1	Q01718	Q01718	OTTHUMG00000131721	OTTHUMG00000131721	ENST00000327606.3:c.451C>T	18.37:g.13885067G>A	ENSP00000333821:p.Leu151Phe			p.L151F	NM_000529.2	NP_000520.1	Q01718	ACTHR_HUMAN			2	631	-			151		A8K016|Q3MI45|Q504X6	Missense_Mutation	SNP	ENST00000327606.3	37	c.451C>T	CCDS11869.1	.	.	.	.	.	.	.	.	.	.	G	11.33	1.606582	0.28623	.	.	ENSG00000185231	ENST00000327606;ENST00000399821	T	0.73047	-0.71	5.28	5.28	0.74379	5.28	5.28	0.74379	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000001	D	0.83008	0.5161	M	0.80422	2.495	0.29368	N	0.864217	D	0.89917	1.0	D	0.85130	0.997	T	0.80211	-0.1476	10	0.87932	D	0	.	10.5734	0.45212	0.1498:0.0:0.8502:0.0	.	151	Q01718	ACTHR_HUMAN	F	151	ENSP00000333821:L151F	ENSP00000333821:L151F	L	-	1	0	0	MC2R	13875067	13875067	0.519000	0.26242	0.045000	0.18777	0.001000	0.01503	0.914000	0.28624	2.469000	0.83416	0.655000	0.94253	CTT		0.577	MC2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254639.2		50.197173	0	0	53	53			16	50.253043	50.253043	19	0.457143	0	0	0	1	0	16	19	0.457143
ABCA6	23460	broad.mit.edu	37	17	67119475	67119475	+	Silent	SNP	A	A	G			TCGA-V4-A9EQ-01A-11D-A39W-08	TCGA-V4-A9EQ-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	da7b9dab-d5d2-42f1-b156-c627cf9f987c	a505db24-f411-4532-9291-41073c0938da	g.chr17:67119475A>G	ENST00000284425.2	-	10	1515	c.1341T>C	c.(1339-1341)aaT>aaC	p.N447N		NM_080284.2	NP_525023.2	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 6	447					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(6)|endometrium(5)|kidney(17)|large_intestine(18)|lung(20)|ovary(3)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	82	Breast(10;5.65e-12)					TAACCTTAGCATTAGTCCTTT	0.368																																						ENST00000284425.2											0			breast(6)|endometrium(5)|kidney(17)|large_intestine(18)|lung(20)|ovary(3)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	82						c.(1339-1341)aaT>aaC	ATP-binding cassette, sub-family A (ABC1), member 6						112.0	108.0	109.0					17																	67119475		2203	4300	6503	SO:0001819	synonymous_variant	23460			transport	integral to membrane	ATP binding|ATPase activity	g.chr17:67119475A>G	U66680	U66680	CCDS11683.1	CCDS11683.1	17q21	2012-03-14			2012-03-14			ENSG00000154262	ENSG00000154262	ENSG00000154262	ENSG00000154262		"""ATP binding cassette transporters / subfamily A"""	"""ATP binding cassette transporters / subfamily A"""	36	36	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			612504	612504						8894702	8894702	Standard	Standard	NM_080284	NM_080284		Approved	EST155051	uc002jhw.1	uc002jhw.1	Q8N139	Q8N139			ENST00000284425.2:c.1341T>C	17.37:g.67119475A>G				p.N447N	NM_080284.2	NP_525023.2	Q8N139	ABCA6_HUMAN			10	1515	-	Breast(10;5.65e-12)		447		Q6NSH9|Q8N856|Q8WWZ6	Silent	SNP	ENST00000284425.2	37	c.1341T>C	CCDS11683.1																																																																																									0.368	ABCA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450463.1		43.210090	14	14	55	55	NM_080284		15	44.317073	44.317073	30	0.333333	0	0	0	1	0	15	30	0.333333
DOCK3	1795	broad.mit.edu	37	3	51417579	51417579	+	Missense_Mutation	SNP	G	G	A			TCGA-V4-A9EQ-01A-11D-A39W-08	TCGA-V4-A9EQ-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	da7b9dab-d5d2-42f1-b156-c627cf9f987c	a505db24-f411-4532-9291-41073c0938da	g.chr3:51417579G>A	ENST00000266037.9	+	52	5547	c.5524G>A	c.(5524-5526)Gcc>Acc	p.A1842T		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	1842					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		ACACTTTGACGCCTTCCACCA	0.607																																						ENST00000266037.9											0			breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45						c.(5524-5526)Gcc>Acc	dedicator of cytokinesis 3						108.0	108.0	108.0					3																	51417579		1936	4129	6065	SO:0001583	missense	1795				cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding	g.chr3:51417579G>A	AB002297	AB002297	CCDS46835.1	CCDS46835.1	3p21	2008-02-01			2008-02-01			ENSG00000088538	ENSG00000088538	ENSG00000088538	ENSG00000088538				2989	2989	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			603123	603123	"""dedicator of cyto-kinesis 3"""		"""dedicator of cyto-kinesis 3"""			9205841	9205841	Standard	Standard	NM_004947	NM_004947		Approved	KIAA0299, MOCA, PBP	uc011bds.2	uc011bds.2	Q8IZD9	Q8IZD9	OTTHUMG00000156892	OTTHUMG00000156892	ENST00000266037.9:c.5524G>A	3.37:g.51417579G>A	ENSP00000266037:p.Ala1842Thr			p.A1842T	NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN		BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)	52	5547	+			1842		O15017	Missense_Mutation	SNP	ENST00000266037.9	37	c.5524G>A	CCDS46835.1	.	.	.	.	.	.	.	.	.	.	G	18.94	3.730367	0.69074	.	.	ENSG00000088538	ENST00000266037	T	0.05199	3.48	5.8	4.93	0.64822	5.8	4.93	0.64822	.	0.052912	0.85682	N	0.000000	T	0.07234	0.0183	L	0.47716	1.5	0.58432	D	0.999998	B	0.31837	0.342	B	0.24541	0.054	T	0.27673	-1.0067	10	0.30078	T	0.28	.	14.8663	0.70419	0.0686:0.0:0.9314:0.0	.	1842	Q8IZD9	DOCK3_HUMAN	T	1842	ENSP00000266037:A1842T	ENSP00000266037:A1842T	A	+	1	0	0	DOCK3	51392619	51392619	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.790000	0.69038	1.470000	0.48102	0.561000	0.74099	GCC		0.607	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5		25.216820	-6	-6	30	30	NM_004947		8	26.431323	26.431323	1	0.888889	0	0	0	1	0	8	1	0.888889
NEDD9	4739	broad.mit.edu	37	6	11213718	11213718	+	Silent	SNP	G	G	A			TCGA-V4-A9EQ-01A-11D-A39W-08	TCGA-V4-A9EQ-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	da7b9dab-d5d2-42f1-b156-c627cf9f987c	a505db24-f411-4532-9291-41073c0938da	g.chr6:11213718G>A	ENST00000379446.5	-	2	421	c.255C>T	c.(253-255)acC>acT	p.T85T	NEDD9_ENST00000379433.5_Silent_p.T85T|RP3-510L9.1_ENST00000500636.2_RNA|NEDD9_ENST00000504387.1_Silent_p.T85T	NM_001271033.1|NM_006403.3	NP_001257962.1|NP_006394.1	Q14511	CASL_HUMAN	neural precursor cell expressed, developmentally down-regulated 9	85					actin filament bundle assembly (GO:0051017)|cell adhesion (GO:0007155)|cytoskeleton organization (GO:0007010)|integrin-mediated signaling pathway (GO:0007229)|mitotic nuclear division (GO:0007067)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle pole (GO:0000922)				endometrium(3)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	Breast(50;0.0768)|Ovarian(93;0.152)	all_hematologic(90;0.135)	Epithelial(50;0.0647)|all cancers(50;0.179)			GTTGGCCAAAGGTCTGCTGCA	0.552																																						ENST00000379446.5											0			endometrium(3)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						c.(253-255)acC>acT	neural precursor cell expressed, developmentally down-regulated 9						154.0	148.0	150.0					6																	11213718		2203	4300	6503	SO:0001819	synonymous_variant	4739			actin filament bundle assembly|cell adhesion|cell division|integrin-mediated signaling pathway|mitosis|regulation of growth	cell cortex|focal adhesion|Golgi apparatus|lamellipodium|nucleus	protein binding	g.chr6:11213718G>A	L43821	L43821	CCDS4520.1, CCDS34340.1, CCDS47373.1, CCDS75400.1	CCDS4520.1, CCDS34340.1, CCDS47373.1, CCDS75400.1	6p25-p24	2011-04-13			2011-04-13			ENSG00000111859	ENSG00000111859	ENSG00000111859	ENSG00000111859		"""Cas scaffolding proteins"""	"""Cas scaffolding proteins"""	7733	7733	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product	"""Cas scaffolding protein family member 2"", ""Cas-like"""	"""Cas scaffolding protein family member 2"", ""Cas-like"""	602265	602265								Standard	Standard	NM_182966	NM_182966		Approved	HEF1, CAS-L, CASS2	uc003mzv.2	uc003mzv.2	Q14511	Q14511	OTTHUMG00000014255	OTTHUMG00000014255	ENST00000379446.5:c.255C>T	6.37:g.11213718G>A			NEDD9_ENST00000504387.1_Silent_p.T85T|RP3-510L9.1_ENST00000500636.2_RNA|NEDD9_ENST00000379433.5_Silent_p.T85T	p.T85T	NM_001271033.1|NM_006403.3	NP_001257962.1|NP_006394.1	Q14511	CASL_HUMAN	Epithelial(50;0.0647)|all cancers(50;0.179)		2	421	-	Breast(50;0.0768)|Ovarian(93;0.152)	all_hematologic(90;0.135)	85		A8K9G7|A8MSJ9|G5E9Y9|Q5T9R4|Q5XKI0	Silent	SNP	ENST00000379446.5	37	c.255C>T	CCDS4520.1																																																																																									0.552	NEDD9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039853.2		57.415766	16	16	98	98	NM_006403		19	58.141951	58.141951	32	0.372549	0	0	0	1	0	19	32	0.372549
SLC4A1	6521	broad.mit.edu	37	17	42335930	42335930	+	Missense_Mutation	SNP	C	C	A			TCGA-V4-A9EQ-01A-11D-A39W-08	TCGA-V4-A9EQ-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	da7b9dab-d5d2-42f1-b156-c627cf9f987c	a505db24-f411-4532-9291-41073c0938da	g.chr17:42335930C>A	ENST00000262418.6	-	10	1093	c.938G>T	c.(937-939)gGc>gTc	p.G313V	AC003043.1_ENST00000597382.1_Intron|SLC4A1_ENST00000471005.1_5'Flank	NM_000342.3	NP_000333.1	P02730	B3AT_HUMAN	solute carrier family 4 (anion exchanger), member 1 (Diego blood group)	313	Dimerization arm.				anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|cellular ion homeostasis (GO:0006873)|chloride transport (GO:0006821)|ion transport (GO:0006811)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|cortical cytoskeleton (GO:0030863)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	anion transmembrane transporter activity (GO:0008509)|anion:anion antiporter activity (GO:0015301)|ankyrin binding (GO:0030506)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	40		Breast(137;0.014)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.115)		GTCCAGGAAGCCCTCTAGGGA	0.647																																						ENST00000262418.6											0			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	40						c.(937-939)gGc>gTc	solute carrier family 4 (anion exchanger), member 1						40.0	41.0	41.0					17																	42335930		2202	4299	6501	SO:0001583	missense	6521			bicarbonate transport|cellular ion homeostasis	basolateral plasma membrane|cortical cytoskeleton|integral to plasma membrane|Z disc	ankyrin binding|chloride transmembrane transporter activity|inorganic anion exchanger activity|protein anchor|protein homodimerization activity	g.chr17:42335930C>A			CCDS11481.1	CCDS11481.1	17q21.31	2014-07-19	2014-01-02		2014-07-19	2014-01-02		ENSG00000004939	ENSG00000004939	ENSG00000004939	ENSG00000004939		"""CD molecules"", ""Blood group antigens"", ""Solute carriers"""	"""CD molecules"", ""Blood group antigens"", ""Solute carriers"""	11027	11027	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product	"""Froese blood group"", ""Swann blood group"", ""Wright blood group"""	"""Froese blood group"", ""Swann blood group"", ""Wright blood group"""	109270	109270	"""Waldner blood group"", ""erythrocyte membrane protein band 3"", ""Diego blood group"", ""solute carrier family 4, anion exchanger, member 1 (erythrocyte membrane protein band 3, Diego blood group)"", ""solute carrier family 4 (anion exchanger), member 1"""	EPB3, AE1, DI, WD	"""Waldner blood group"", ""erythrocyte membrane protein band 3"", ""Diego blood group"", ""solute carrier family 4, anion exchanger, member 1 (erythrocyte membrane protein band 3, Diego blood group)"", ""solute carrier family 4 (anion exchanger), member 1"""	EPB3, AE1, DI, WD		8434259	8434259	Standard	Standard	NM_000342	NM_000342		Approved	RTA1A, CD233, FR, SW, WR	uc002igf.4	uc002igf.4	P02730	P02730	OTTHUMG00000156843	OTTHUMG00000156843	ENST00000262418.6:c.938G>T	17.37:g.42335930C>A	ENSP00000262418:p.Gly313Val		AC003043.1_ENST00000597382.1_Intron	p.G313V	NM_000342.3	NP_000333.1	P02730	B3AT_HUMAN		BRCA - Breast invasive adenocarcinoma(366;0.115)	10	1093	-		Breast(137;0.014)|Prostate(33;0.0181)	313		G4V2I6|P78487|Q1ZZ45|Q4KKW9|Q4VB84|Q9UCY7|Q9UDJ1	Missense_Mutation	SNP	ENST00000262418.6	37	c.938G>T	CCDS11481.1	.	.	.	.	.	.	.	.	.	.	N	12.17	1.858642	0.32791	.	.	ENSG00000004939	ENST00000262418	T	0.67865	-0.29	4.5	2.51	0.30379	4.5	2.51	0.30379	Bicarbonate transporter, cytoplasmic (2);Phosphotransferase/anion transporter (1);	0.320832	0.32416	N	0.006133	T	0.66954	0.2842	L	0.52364	1.645	0.44635	D	0.997611	D;B	0.56968	0.978;0.284	P;B	0.57204	0.815;0.188	T	0.65438	-0.6168	10	0.72032	D	0.01	.	4.0537	0.09806	0.0:0.4817:0.168:0.3502	.	313;313	E2RVJ0;P02730	.;B3AT_HUMAN	V	313	ENSP00000262418:G313V	ENSP00000262418:G313V	G	-	2	0	0	SLC4A1	39691456	39691456	0.965000	0.33210	0.341000	0.25589	0.227000	0.25037	2.095000	0.41729	0.535000	0.28714	0.306000	0.20318	GGC		0.647	SLC4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346194.1		37.469495	0	0	22	22	NM_000342		13	37.500811	37.500811	15	0.464286	1	0	5.50884e-06	1	5.50884e-06	13	15	0.464286
GNA11	2767	broad.mit.edu	37	19	3118942	3118942	+	Missense_Mutation	SNP	A	A	T			TCGA-V4-A9EQ-01A-11D-A39W-08	TCGA-V4-A9EQ-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	da7b9dab-d5d2-42f1-b156-c627cf9f987c	a505db24-f411-4532-9291-41073c0938da	g.chr19:3118942A>T	ENST00000078429.4	+	5	868	c.626A>T	c.(625-627)cAg>cTg	p.Q209L	AC005262.2_ENST00000585980.1_RNA|AC005262.3_ENST00000587701.1_RNA|GNA11_ENST00000586180.1_3'UTR	NM_002067.2	NP_002058.2	P29992	GNA11_HUMAN	guanine nucleotide binding protein (G protein), alpha 11 (Gq class)	209					action potential (GO:0001508)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|cellular response to pH (GO:0071467)|developmental pigmentation (GO:0048066)|heart development (GO:0007507)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|regulation of melanocyte differentiation (GO:0045634)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)|type 2A serotonin receptor binding (GO:0031826)	p.Q209L(80)|p.Q209P(2)		endometrium(2)|eye(132)|kidney(1)|large_intestine(2)|lung(1)|meninges(5)|ovary(1)|prostate(1)|skin(16)	161		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.79e-05)|OV - Ovarian serous cystadenocarcinoma(105;2.68e-113)|Epithelial(107;1.22e-111)|all cancers(105;5.78e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00141)|STAD - Stomach adenocarcinoma(1328;0.181)		GTGGGGGGCCAGCGGTCGGAG	0.612			Mis		uveal melanoma																																	ENST00000078429.4		Dom	yes		19	19p13.3	2767	"""guanine nucleotide binding protein (G protein), alpha 11 (Gq class)"""		E	82	Substitution - Missense(82)	eye(69)|skin(8)|meninges(5)	endometrium(2)|eye(132)|kidney(1)|large_intestine(2)|lung(1)|meninges(5)|ovary(1)|prostate(1)|skin(16)	161						c.(625-627)cAg>cTg	guanine nucleotide binding protein (G protein), alpha 11 (Gq class)						104.0	89.0	94.0					19																	3118942		2203	4300	6503	SO:0001583	missense	2767			activation of phospholipase C activity by dopamine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|platelet activation|protein ADP-ribosylation|regulation of action potential	cytoplasm|heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity	g.chr19:3118942A>T	AF493900	AF493900	CCDS12103.1	CCDS12103.1	19p13.3	2014-02-04			2014-02-04			ENSG00000088256	ENSG00000088256	ENSG00000088256	ENSG00000088256				4379	4379	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			139313	139313	"""hypocalciuric hypercalcemia 2"""	HHC2	"""hypocalciuric hypercalcemia 2"""	HHC2		1302014, 23802516	1302014, 23802516	Standard	Standard	NM_002067	NM_002067		Approved	FBH, FBH2, FHH2	uc002lxd.3	uc002lxd.3	P29992	P29992	OTTHUMG00000180631	OTTHUMG00000180631	ENST00000078429.4:c.626A>T	19.37:g.3118942A>T	ENSP00000078429:p.Gln209Leu		AC005262.3_ENST00000587701.1_RNA|GNA11_ENST00000586180.1_3'UTR	p.Q209L	NM_002067.2	NP_002058.2	P29992	GNA11_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (162;6.79e-05)|OV - Ovarian serous cystadenocarcinoma(105;2.68e-113)|Epithelial(107;1.22e-111)|all cancers(105;5.78e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00141)|STAD - Stomach adenocarcinoma(1328;0.181)	5	868	+		Hepatocellular(1079;0.137)	209		O15109|Q14350|Q6IB00	Missense_Mutation	SNP	ENST00000078429.4	37	c.626A>T	CCDS12103.1	.	.	.	.	.	.	.	.	.	.	.	15.05	2.718086	0.48622	.	.	ENSG00000088256	ENST00000078429	D	0.91237	-2.81	3.26	3.26	0.37387	3.26	3.26	0.37387	.	0.000000	0.64402	U	0.000006	D	0.96950	0.9004	H	0.99357	4.53	0.80722	D	1	D	0.59767	0.986	D	0.68483	0.958	D	0.96823	0.9605	10	0.87932	D	0	.	10.7338	0.46113	1.0:0.0:0.0:0.0	.	209	P29992	GNA11_HUMAN	L	209	ENSP00000078429:Q209L	ENSP00000078429:Q209L	Q	+	2	0	0	GNA11	3069942	3069942	1.000000	0.71417	0.438000	0.26821	0.027000	0.11550	9.104000	0.94239	1.256000	0.44068	0.379000	0.24179	CAG		0.612	GNA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452261.2		62.262923	12	12	93	93	NM_002067		21	63.129194	63.129194	36	0.368421	0	0	0	1	0	21	36	0.368421
GSTA4	2941	broad.mit.edu	37	6	52849353	52849353	+	Missense_Mutation	SNP	A	A	T			TCGA-V4-A9EQ-01A-11D-A39W-08	TCGA-V4-A9EQ-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	da7b9dab-d5d2-42f1-b156-c627cf9f987c	a505db24-f411-4532-9291-41073c0938da	g.chr6:52849353A>T	ENST00000370959.1	-	5	440	c.323T>A	c.(322-324)aTg>aAg	p.M108K	GSTA4_ENST00000541324.1_Missense_Mutation_p.M15K|GSTA4_ENST00000486559.1_5'UTR|GSTA4_ENST00000370960.1_Missense_Mutation_p.M15K			O15217	GSTA4_HUMAN	glutathione S-transferase alpha 4	108	GST C-terminal.				glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	glutathione transferase activity (GO:0004364)|protein homodimerization activity (GO:0042803)			endometrium(1)|lung(3)|skin(2)|urinary_tract(1)	7	Lung NSC(77;0.103)				Glutathione(DB00143)	GAAAGGATGCATGATAAGCAG	0.423																																						ENST00000541324.1											0			endometrium(1)|lung(3)|skin(2)|urinary_tract(1)	7						c.(43-45)aTg>aAg	glutathione S-transferase alpha 4						135.0	116.0	122.0					6																	52849353		2203	4300	6503	SO:0001583	missense	2941			glutathione metabolic process|xenobiotic metabolic process	cytosol	glutathione transferase activity|protein homodimerization activity	g.chr6:52849353A>T	AF020918	AF020918	CCDS4948.1	CCDS4948.1	6p12.2	2012-06-21	2008-11-26		2012-06-21	2008-11-26		ENSG00000170899	ENSG00000170899	ENSG00000170899	ENSG00000170899	2.5.1.18	"""Glutathione S-transferases / Soluble"""	"""Glutathione S-transferases / Soluble"""	4629	4629	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			605450	605450	"""glutathione S-transferase A4"""		"""glutathione S-transferase A4"""			9480897	9480897	Standard	Standard	NM_001512	NM_001512		Approved		uc003pbf.3	uc003pbf.3	O15217	O15217	OTTHUMG00000014868	OTTHUMG00000014868	ENST00000370959.1:c.323T>A	6.37:g.52849353A>T	ENSP00000359998:p.Met108Lys		GSTA4_ENST00000370960.1_Missense_Mutation_p.M15K|GSTA4_ENST00000486559.1_5'UTR|GSTA4_ENST00000370959.1_Missense_Mutation_p.M108K	p.M15K			O15217	GSTA4_HUMAN			3	309	-	Lung NSC(77;0.103)		108	GST N-terminal.	B2RD15|Q5T7Q8|Q6P4G1|Q9BX18|Q9H414	Missense_Mutation	SNP	ENST00000370959.1	37	c.44T>A	CCDS4948.1	.	.	.	.	.	.	.	.	.	.	A	13.16	2.154369	0.38021	.	.	ENSG00000170899	ENST00000370963;ENST00000541324;ENST00000370960;ENST00000370959;ENST00000457564	T;T;T;T;T	0.01998	4.51;4.51;4.51;4.51;4.51	5.0	3.83	0.44106	5.0	3.83	0.44106	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);Glutathione S-transferase, C-terminal (1);	0.558985	0.21306	N	0.076723	T	0.00784	0.0026	L	0.35542	1.07	0.41028	D	0.985137	B	0.06786	0.001	B	0.09377	0.004	T	0.50659	-0.8802	10	0.30078	T	0.28	-12.824	8.2267	0.31572	0.8407:0.0:0.1593:0.0	.	108	O15217	GSTA4_HUMAN	K	108;15;15;108;15	ENSP00000360002:M108K;ENSP00000439439:M15K;ENSP00000359999:M15K;ENSP00000359998:M108K;ENSP00000394228:M15K	ENSP00000359998:M108K	M	-	2	0	0	GSTA4	52957312	52957312	0.033000	0.19621	0.997000	0.53966	0.984000	0.73092	0.656000	0.24948	0.835000	0.34877	0.455000	0.32223	ATG		0.423	GSTA4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040946.1		117.129240	8	8	114	114	NM_001512		38	117.669803	117.669803	53	0.417582	0	0	0	1	0	38	53	0.417582
TRAV8-2	28684	broad.mit.edu	37	14	22314952	22314952	+	RNA	SNP	G	G	C			TCGA-V4-A9EQ-01A-11D-A39W-08	TCGA-V4-A9EQ-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	da7b9dab-d5d2-42f1-b156-c627cf9f987c	a505db24-f411-4532-9291-41073c0938da	g.chr14:22314952G>C	ENST00000390434.3	+	0	234									T cell receptor alpha variable 8-2																		CCATGCTCCTGCTGCTCGTCC	0.527											OREG0022570	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000390434.3											0																	113.0	112.0	112.0					14																	22314952		2031	4218	6249			0						g.chr14:22314952G>C	AE000659	AE000659			14q11.2	2012-02-07			2012-02-07			ENSG00000211786	ENSG00000211786	ENSG00000211786	ENSG00000211786		"""T cell receptors / TRA locus"""	"""T cell receptors / TRA locus"""	12147	12147	other	T cell receptor gene	other	T cell receptor gene										8188290	8188290	Standard	Standard	NG_001332	NG_001332		Approved						OTTHUMG00000168991	OTTHUMG00000168991		14.37:g.22314952G>C		755									0	234	+						RNA	SNP	ENST00000390434.3	37																																																																																											0.527	TRAV8-2-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	TR_V_gene	TR_V_gene	OTTHUMT00000401889.1		55.469113	-14	-14	74	74	NG_001332		17	55.665343	55.665343	23	0.425000	0	0	0	1	0	17	23	0.425
FAM161A	84140	broad.mit.edu	37	2	62066857	62066857	+	Missense_Mutation	SNP	T	T	C			TCGA-V4-A9EQ-01A-11D-A39W-08	TCGA-V4-A9EQ-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	da7b9dab-d5d2-42f1-b156-c627cf9f987c	a505db24-f411-4532-9291-41073c0938da	g.chr2:62066857T>C	ENST00000405894.3	-	3	1383	c.1282A>G	c.(1282-1284)Act>Gct	p.T428A	FAM161A_ENST00000404929.1_Missense_Mutation_p.T428A	NM_032180.2	NP_115556.2	Q3B820	F161A_HUMAN	family with sequence similarity 161, member A	428					cilium assembly (GO:0042384)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|photoreceptor connecting cilium (GO:0032391)				breast(1)|endometrium(5)|large_intestine(8)|lung(4)|ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						AAATCAGGAGTTGGGCACCTA	0.463																																						ENST00000404929.1											0			breast(1)|endometrium(5)|large_intestine(8)|lung(4)|ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						c.(1282-1284)Act>Gct	family with sequence similarity 161, member A						121.0	110.0	114.0					2																	62066857		1911	4121	6032	SO:0001583	missense	84140			response to stimulus|visual perception	centrosome		g.chr2:62066857T>C			CCDS42687.2, CCDS56120.1	CCDS42687.2, CCDS56120.1	2p15	2011-03-15			2011-03-15			ENSG00000170264	ENSG00000170264	ENSG00000170264	ENSG00000170264				25808	25808	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			613596	613596	"""retinitis pigmentosa 28 (autosomal recessive)"""	RP28	"""retinitis pigmentosa 28 (autosomal recessive)"""	RP28		10507729, 20705278, 20705279	10507729, 20705278, 20705279	Standard	Standard	NM_032180	NM_032180		Approved	FLJ13305	uc002sbm.4	uc002sbm.4	Q3B820	Q3B820	OTTHUMG00000152165	OTTHUMG00000152165	ENST00000405894.3:c.1282A>G	2.37:g.62066857T>C	ENSP00000385893:p.Thr428Ala		FAM161A_ENST00000405894.3_Missense_Mutation_p.T428A	p.T428A	NM_001201543.1	NP_001188472.1	Q3B820	F161A_HUMAN			3	1293	-			428		B4DJV7|Q9H8R2	Missense_Mutation	SNP	ENST00000405894.3	37	c.1282A>G	CCDS42687.2	.	.	.	.	.	.	.	.	.	.	T	12.46	1.944426	0.34283	.	.	ENSG00000170264	ENST00000404929;ENST00000405894	T;T	0.21734	1.99;1.99	5.67	0.161	0.14977	5.67	0.161	0.14977	.	0.829500	0.11062	N	0.603908	T	0.11623	0.0283	N	0.25144	0.715	0.09310	N	1	B;B	0.13145	0.007;0.005	B;B	0.16289	0.015;0.005	T	0.35748	-0.9776	10	0.23302	T	0.38	-3.2393	5.5361	0.17011	0.0:0.2378:0.283:0.4792	.	428;428	Q3B820;Q3B820-3	F161A_HUMAN;.	A	428	ENSP00000385158:T428A;ENSP00000385893:T428A	ENSP00000385158:T428A	T	-	1	0	0	FAM161A	61920361	61920361	0.007000	0.16637	0.001000	0.08648	0.279000	0.26890	0.101000	0.15251	0.040000	0.15660	0.528000	0.53228	ACT		0.463	FAM161A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325537.2		114.375297	26	26	131	131	NM_032180		36	115.994141	115.994141	63	0.363636	0	0	0	1	0	36	63	0.363636
ZNF845	91664	broad.mit.edu	37	19	53855032	53855032	+	Silent	SNP	A	A	G			TCGA-V4-A9EQ-01A-11D-A39W-08	TCGA-V4-A9EQ-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	da7b9dab-d5d2-42f1-b156-c627cf9f987c	a505db24-f411-4532-9291-41073c0938da	g.chr19:53855032A>G	ENST00000595091.1	+	5	1323	c.1104A>G	c.(1102-1104)tcA>tcG	p.S368S	ZNF845_ENST00000458035.1_Silent_p.S368S			Q96IR2	ZN845_HUMAN	zinc finger protein 845	368					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						GTTTCAAATCAAACCTTGAAA	0.403																																						ENST00000458035.1											0			endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						c.(1102-1104)tcA>tcG	zinc finger protein 845						31.0	30.0	30.0					19																	53855032		692	1591	2283	SO:0001819	synonymous_variant	91664			regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr19:53855032A>G	BC007307	BC007307	CCDS46170.1	CCDS46170.1	19q13.42	2013-01-08			2013-01-08			ENSG00000213799	ENSG00000213799	ENSG00000213799	ENSG00000213799		"""Zinc fingers, C2H2-type"", ""-"""	"""Zinc fingers, C2H2-type"", ""-"""	25112	25112	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product												Standard	Standard	NM_138374	NM_138374		Approved		uc010ydv.1	uc010ydv.1	Q96IR2	Q96IR2			ENST00000595091.1:c.1104A>G	19.37:g.53855032A>G			ZNF845_ENST00000595091.1_Silent_p.S368S	p.S368S	NM_138374.1	NP_612383.1	Q96IR2	ZN845_HUMAN			4	1221	+			368			Silent	SNP	ENST00000595091.1	37	c.1104A>G	CCDS46170.1																																																																																									0.403	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1		2.801436	-13	-13	58	58	XM_039908		3	6.360424	6.360424	22	0.120000	0	0	0	1	0	3	22	0.12
IL22RA1	58985	ucsc.edu	37	1	24463667	24463667	+	Silent	SNP	G	G	A			TCGA-V4-A9EQ-01A-11D-A39W-08	TCGA-V4-A9EQ-10A-01D-A39Z-08	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	da7b9dab-d5d2-42f1-b156-c627cf9f987c	a505db24-f411-4532-9291-41073c0938da	g.chr1:24463667G>A	ENST00000270800.1	-	3	347	c.309C>T	c.(307-309)ggC>ggT	p.G103G		NM_021258.3	NP_067081.2	Q8N6P7	I22R1_HUMAN	interleukin 22 receptor, alpha 1	103	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-negative bacterium (GO:0050829)	integral component of membrane (GO:0016021)	interferon receptor activity (GO:0004904)			breast(2)|endometrium(2)|large_intestine(4)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	19		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000992)|all_lung(284;0.00138)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;3.84e-24)|Colorectal(126;6.43e-08)|COAD - Colon adenocarcinoma(152;3.51e-06)|GBM - Glioblastoma multiforme(114;5.06e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00911)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.148)		TGGCTGACCGGCCTCCCGCAC	0.612																																																	0																	64.0	58.0	60.0					1																	24463667		2203	4300	6503	SO:0001819	synonymous_variant	58985							AF286095	AF286095	CCDS247.1	CCDS247.1	1p36.11	2009-10-06	2002-12-02	2002-12-06	2009-10-06	2002-12-02	2002-12-06	ENSG00000142677	ENSG00000142677	ENSG00000142677	ENSG00000142677		"""Interleukins and interleukin receptors"""	"""Interleukins and interleukin receptors"""	13700	13700	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			605457	605457	"""interleukin 22 receptor"""	IL22R	"""interleukin 22 receptor"""	IL22R		10875937	10875937	Standard	Standard	NM_021258	NM_021258		Approved	CRF2-9	uc001biq.2	uc001biq.2	Q8N6P7	Q8N6P7	OTTHUMG00000003041	OTTHUMG00000003041	ENST00000270800.1:c.309C>T	1.37:g.24463667G>A																		A8K839|B2R9Y9|Q9HB22	Silent	SNP	ENST00000270800.1	37		CCDS247.1																																																																																									0.612	IL22RA1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008412.1			-8	-8	51	51			4			30							4	30	
ZNF654	55279	ucsc.edu	37	3	88190009	88190009	+	Missense_Mutation	SNP	C	C	A			TCGA-V4-A9EQ-01A-11D-A39W-08	TCGA-V4-A9EQ-10A-01D-A39Z-08	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	da7b9dab-d5d2-42f1-b156-c627cf9f987c	a505db24-f411-4532-9291-41073c0938da	g.chr3:88190009C>A	ENST00000309495.5	+	1	1756	c.1549C>A	c.(1549-1551)Cca>Aca	p.P517T	CGGBP1_ENST00000462901.1_Intron	NM_018293.2	NP_060763.2	Q8IZM8	ZN654_HUMAN	zinc finger protein 654	517					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|large_intestine(2)|lung(1)|ovary(2)|pancreas(1)|prostate(3)	12		Lung NSC(201;0.0283)		UCEC - Uterine corpus endometrioid carcinoma (27;0.194)|LUSC - Lung squamous cell carcinoma(29;0.00353)|Lung(72;0.00661)		TCTTAGTATGCCAAAACGCAG	0.363																																																	0																	115.0	105.0	108.0					3																	88190009		1856	4104	5960	SO:0001583	missense	55279							AF543494	AF543494	CCDS46874.1	CCDS46874.1	3p11.1	2005-01-10			2005-01-10			ENSG00000175105	ENSG00000175105	ENSG00000175105	ENSG00000175105				25612	25612	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product												Standard	Standard	NM_018293	NM_018293		Approved	FLJ10997, FLJ21142	uc003dqv.3	uc003dqv.3	Q8IZM8	Q8IZM8	OTTHUMG00000159097	OTTHUMG00000159097	ENST00000309495.5:c.1549C>A	3.37:g.88190009C>A	ENSP00000312141:p.Pro517Thr																	Q9H791|Q9NV14	Missense_Mutation	SNP	ENST00000309495.5	37		CCDS46874.1	.	.	.	.	.	.	.	.	.	.	c	19.49	3.836653	0.71373	.	.	ENSG00000175105	ENST00000309495	T	0.18338	2.22	5.48	5.48	0.80851	5.48	5.48	0.80851	.	.	.	.	.	T	0.32526	0.0832	L	0.29908	0.895	0.50632	D	0.999882	D	0.89917	1.0	D	0.77004	0.989	T	0.04565	-1.0942	9	0.72032	D	0.01	.	18.3314	0.90270	0.0:1.0:0.0:0.0	.	517	Q8IZM8	ZN654_HUMAN	T	517	ENSP00000312141:P517T	ENSP00000312141:P517T	P	+	1	0	0	ZNF654	88272699	88272699	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.985000	0.76193	2.560000	0.86352	0.574000	0.79327	CCA		0.363	ZNF654-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353285.2			-9	-9	90	90	NM_018293		4			38							4	38	
NPHP3	27031	broad.mit.edu	37	3	132411619	132411619	+	Missense_Mutation	SNP	G	G	A			TCGA-V4-A9EQ-01A-11D-A39W-08	TCGA-V4-A9EQ-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	da7b9dab-d5d2-42f1-b156-c627cf9f987c	a505db24-f411-4532-9291-41073c0938da	g.chr3:132411619G>A	ENST00000337331.5	-	17	2440	c.2354C>T	c.(2353-2355)tCa>tTa	p.S785L	NPHP3_ENST00000326682.8_3'UTR	NM_153240.4	NP_694972.3	Q7Z494	NPHP3_HUMAN	nephronophthisis 3 (adolescent)	785					atrial septum development (GO:0003283)|cilium morphogenesis (GO:0060271)|convergent extension involved in gastrulation (GO:0060027)|determination of intestine left/right asymmetry (GO:0071908)|determination of left/right symmetry (GO:0007368)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|determination of stomach left/right asymmetry (GO:0071909)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|establishment or maintenance of cell polarity (GO:0007163)|extracellular matrix organization (GO:0030198)|heart looping (GO:0001947)|kidney development (GO:0001822)|kidney morphogenesis (GO:0060993)|lipid metabolic process (GO:0006629)|lung development (GO:0030324)|maintenance of organ identity (GO:0048496)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|photoreceptor cell maintenance (GO:0045494)|regulation of cAMP metabolic process (GO:0030814)|regulation of planar cell polarity pathway involved in neural tube closure (GO:2000167)|regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000095)|ureter development (GO:0072189)|Wnt signaling pathway (GO:0016055)	cilium (GO:0005929)|primary cilium (GO:0072372)				NS(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(15)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						CATCAGTTCTGATTCACTCAC	0.383																																						ENST00000337331.5											0			NS(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(15)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						c.(2353-2355)tCa>tTa	nephronophthisis 3 (adolescent)						112.0	98.0	103.0					3																	132411619		2203	4300	6503	SO:0001583	missense	27031			maintenance of organ identity|negative regulation of canonical Wnt receptor signaling pathway|photoreceptor cell maintenance|regulation of Wnt receptor signaling pathway, planar cell polarity pathway|Wnt receptor signaling pathway	cilium	protein binding	g.chr3:132411619G>A	AB056657	AB056657	CCDS3078.1	CCDS3078.1	3q22	2014-07-18			2014-07-18			ENSG00000113971	ENSG00000113971	ENSG00000113971	ENSG00000113971		"""Tetratricopeptide (TTC) repeat domain containing"""	"""Tetratricopeptide (TTC) repeat domain containing"""	7907	7907	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product	"""nephrocystin-3"", ""Meckel syndrome, type 7"", ""cilia and flagella associated protein 31"""	"""nephrocystin-3"", ""Meckel syndrome, type 7"", ""cilia and flagella associated protein 31"""	608002	608002						12872122, 15381417	12872122, 15381417	Standard	Standard	NM_153240	NM_153240		Approved	NPH3, KIAA2000, FLJ30691, FLJ36696, MKS7, SLSN3, CFAP31	uc003epe.2	uc003epe.2	Q7Z494	Q7Z494	OTTHUMG00000159713	OTTHUMG00000159713	ENST00000337331.5:c.2354C>T	3.37:g.132411619G>A	ENSP00000338766:p.Ser785Leu		NPHP3_ENST00000326682.8_3'UTR	p.S785L	NM_153240.4	NP_694972.3	Q7Z494	NPHP3_HUMAN			17	2440	-			785		Q5JPE3|Q5JPE6|Q68D99|Q6NVH3|Q7Z492|Q7Z493|Q8N9R2|Q8NCM5|Q96N70|Q96NK2	Missense_Mutation	SNP	ENST00000337331.5	37	c.2354C>T	CCDS3078.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.022318	0.75275	.	.	ENSG00000113971	ENST00000393144;ENST00000337331	D	0.91792	-2.91	5.3	5.3	0.74995	5.3	5.3	0.74995	.	0.138123	0.50627	D	0.000116	D	0.90007	0.6880	L	0.59436	1.845	0.80722	D	1	P	0.35077	0.483	B	0.30943	0.122	D	0.89970	0.4093	10	0.52906	T	0.07	-15.7516	17.1141	0.86684	0.0:0.0:1.0:0.0	.	785	Q7Z494	NPHP3_HUMAN	L	65;785	ENSP00000338766:S785L	ENSP00000338766:S785L	S	-	2	0	0	NPHP3	133894309	133894309	1.000000	0.71417	0.703000	0.30354	0.971000	0.66376	7.619000	0.83057	2.470000	0.83445	0.585000	0.79938	TCA		0.383	NPHP3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357020.2		49.378007	7	7	46	46	NM_153240		14	51.581613	51.581613	1	0.933333	0	0	0	1	0	14	1	0.933333
NXF4	55999	broad.mit.edu	37	X	101805202	101805203	+	RNA	INS	-	-	C			TCGA-V4-A9EQ-01A-11D-A39W-08	TCGA-V4-A9EQ-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	da7b9dab-d5d2-42f1-b156-c627cf9f987c	a505db24-f411-4532-9291-41073c0938da	g.chrX:101805202_101805203insC	ENST00000360035.2	+	0	221					NR_002216.1				nuclear RNA export factor 4 pseudogene											endometrium(2)|lung(8)	10						AGCTTCCCTGACCCCTTTTGTT	0.485																																						ENST00000360035.2											0			endometrium(2)|lung(8)	10																																												0						g.chrX:101805202_101805203insC	AK124700	AK124700			Xq22	2005-01-24			2005-01-24			ENSG00000196970	ENSG00000196970	ENSG00000196970	ENSG00000196970				8074	8074	pseudogene	pseudogene	pseudogene	pseudogene			300318	300318	"""nuclear RNA export factor 4"""		"""nuclear RNA export factor 4"""			11566096	11566096	Standard	Standard	NR_002216	NR_002216		Approved		uc004ejf.1	uc004ejf.1			OTTHUMG00000039695	OTTHUMG00000039695		X.37:g.101805206_101805206dupC					NR_002216.1						0	221	+						RNA	INS	ENST00000360035.2	37																																																																																											0.485	NXF4-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000095720.1	.	.	-8	-8	8	8			2			4	0.33						2	4	0.33
RAP1GAP2	23108	broad.mit.edu	37	17	2699865	2699865	+	Splice_Site	DEL	G	G	-			TCGA-V4-A9EQ-01A-11D-A39W-08	TCGA-V4-A9EQ-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	da7b9dab-d5d2-42f1-b156-c627cf9f987c	a505db24-f411-4532-9291-41073c0938da	g.chr17:2699865delG	ENST00000254695.8	+	1	134	c.44delG	c.(43-45)tgg>tg	p.W15fs	RAP1GAP2_ENST00000542807.1_Splice_Site_p.W15fs|RAP1GAP2_ENST00000366401.4_Splice_Site_p.W15fs|RAP1GAP2_ENST00000540393.2_Intron	NM_015085.4	NP_055900.4	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2	15					negative regulation of neuron projection development (GO:0010977)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)|nuclear membrane (GO:0031965)	Rap GTPase activator activity (GO:0046582)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	11						GGCTTCGGATGGTGGGTGACA	0.622																																						ENST00000254695.8											0			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	11						c.(43-45)tgg>tg	RAP1 GTPase activating protein 2						16.0	19.0	18.0					17																	2699865		1912	4088	6000	SO:0001630	splice_region_variant	23108			regulation of small GTPase mediated signal transduction	centrosome|cytosol|perinuclear region of cytoplasm	GTPase activator activity	g.chr17:2699865delG	AB028962	AB028962	CCDS45573.1, CCDS45574.1	CCDS45573.1, CCDS45574.1	17p13.3	2009-09-14	2009-09-14	2009-09-14	2009-09-14	2009-09-14	2009-09-14		ENSG00000132359		ENSG00000132359				29176	29176	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product					"""GTPase activating RANGAP domain-like 4"", ""GTPase activating Rap/RanGAP domain-like 4"""	GARNL4	"""GTPase activating RANGAP domain-like 4"", ""GTPase activating Rap/RanGAP domain-like 4"""	GARNL4		15632203	15632203	Standard	Standard	NM_015085	NM_015085		Approved	KIAA1039	uc010ckd.3	uc010ckd.3	Q684P5	Q684P5			ENST00000254695.8:c.44+1G>-	17.37:g.2699865delG			RAP1GAP2_ENST00000540393.2_Intron|RAP1GAP2_ENST00000366401.4_Splice_Site_p.W15fs|RAP1GAP2_ENST00000542807.1_Splice_Site_p.W15fs	p.W15fs	NM_015085.4	NP_055900.4	Q684P5	RPGP2_HUMAN			1	134	+			15		B2RTY5|Q684P4|Q6AI00|Q6ZVF0|Q9UPW2	Splice_Site	DEL	ENST00000254695.8	37	c.44delG	CCDS45573.1																																																																																									0.622	RAP1GAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438208.2	.	.	6	6	10	10		Frame_Shift_Del	2			4	0.33						2	4	0.33
