#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
RABL6	55684	broad.mit.edu	37	9	139734309	139734309	+	Missense_Mutation	SNP	G	G	C			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr9:139734309G>C	ENST00000311502.7	+	13	2158	c.1922G>C	c.(1921-1923)aGt>aCt	p.S641T	RABL6_ENST00000371675.3_Missense_Mutation_p.S526T|RABL6_ENST00000357466.2_Intron|RABL6_ENST00000432842.2_3'UTR|RABL6_ENST00000371663.4_Missense_Mutation_p.S642T			Q3YEC7	RABL6_HUMAN	RAB, member RAS oncogene family-like 6	641					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)										AAGGAGAGCAGTGAGGAAGGT	0.682																																						ENST00000371675.3											0										c.(1576-1578)aGt>aCt	RAB, member RAS oncogene family-like 6						18.0	23.0	22.0					9																	139734309		1961	4127	6088	SO:0001583	missense	55684						g.chr9:139734309G>C	AK094382	AK094382	CCDS48058.1, CCDS55352.1, CCDS55353.1	CCDS48058.1, CCDS55352.1, CCDS55353.1	9q34.3	2012-06-28	2012-06-28	2012-06-28	2012-06-28	2012-06-28	2012-06-28	ENSG00000196642	ENSG00000196642	ENSG00000196642	ENSG00000196642				24703	24703	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product	"""Rab-like protein 1"", ""partner of ARF"""	"""Rab-like protein 1"", ""partner of ARF"""	610615	610615	"""chromosome 9 open reading frame 86"""	C9orf86	"""chromosome 9 open reading frame 86"""	C9orf86		14702039, 16582619, 17962191, 19433581	14702039, 16582619, 17962191, 19433581	Standard	Standard	NM_024718	NM_024718		Approved	FLJ10101, FLJ13045, pp8875, bA216L13.9, Parf, RBEL1	uc004cjj.1	uc004cjj.1	Q3YEC7	Q3YEC7	OTTHUMG00000020947	OTTHUMG00000020947	ENST00000311502.7:c.1922G>C	9.37:g.139734309G>C	ENSP00000311134:p.Ser641Thr		RABL6_ENST00000357466.2_Intron|RABL6_ENST00000371663.4_Missense_Mutation_p.S642T|RABL6_ENST00000311502.7_Missense_Mutation_p.S641T|RABL6_ENST00000432842.2_3'UTR	p.S526T							13	2462	+					A8QVZ7|A8QVZ8|C6K8I4|C6K8I5|Q4F968|Q5T5R7|Q8IWK1|Q8TCL4|Q8WU94|Q96SR8|Q9BU21|Q9H935	Missense_Mutation	SNP	ENST00000311502.7	37	c.1577G>C	CCDS48058.1	.	.	.	.	.	.	.	.	.	.	.	11.74	1.728562	0.30593	.	.	ENSG00000196642	ENST00000371663;ENST00000311502;ENST00000371675;ENST00000435930	T;T;T;T	0.73152	-0.61;-0.63;-0.62;-0.72	4.72	4.72	0.59763	4.72	4.72	0.59763	.	0.338891	0.33127	N	0.005251	T	0.78635	0.4314	M	0.71581	2.175	0.46298	D	0.998971	D;D;P	0.71674	0.998;0.965;0.941	D;P;P	0.63703	0.917;0.655;0.453	T	0.77135	-0.2699	10	0.33940	T	0.23	-14.0842	8.9208	0.35610	0.1028:0.0:0.8972:0.0	.	435;642;641	B1AMX5;Q3YEC7-2;Q3YEC7	.;.;PARF_HUMAN	T	642;641;526;435	ENSP00000360727:S642T;ENSP00000311134:S641T;ENSP00000360740:S526T;ENSP00000408442:S435T	ENSP00000311134:S641T	S	+	2	0	0	C9orf86	138854130	138854130	1.000000	0.71417	0.169000	0.22859	0.034000	0.12701	6.146000	0.71777	2.162000	0.67917	0.561000	0.74099	AGT		0.682	RABL6-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055141.4		33.755183	0	0	17	17	NM_024718		10	34.331778	34.331778	4	0.714286	0	0	0	1	0	10	4	0.714286
RAB3GAP2	25782	broad.mit.edu	37	1	220364491	220364491	+	Missense_Mutation	SNP	G	G	A	rs151225064	byFrequency	TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr1:220364491G>A	ENST00000358951.2	-	14	1522	c.1406C>T	c.(1405-1407)gCg>gTg	p.A469V		NM_012414.3	NP_036546.2	Q9H2M9	RBGPR_HUMAN	RAB3 GTPase activating protein subunit 2 (non-catalytic)	469					establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|intracellular protein transport (GO:0006886)|positive regulation of catalytic activity (GO:0043085)|positive regulation of endoplasmic reticulum tubular network organization (GO:1903373)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of GTPase activity (GO:0043087)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	enzyme activator activity (GO:0008047)|enzyme regulator activity (GO:0030234)|GTPase activator activity (GO:0005096)|protein heterodimerization activity (GO:0046982)|Rab GTPase binding (GO:0017137)	p.A469V(1)		breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(1)	39				GBM - Glioblastoma multiforme(131;0.0443)		CCTTCTTGGCGCATAGATCAC	0.493																																						ENST00000358951.2											1	Substitution - Missense(1)	prostate(1)	breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(1)	39						c.(1405-1407)gCg>gTg	RAB3 GTPase activating protein subunit 2 (non-catalytic)	G	VAL/ALA	0,4406		0,0,2203	137.0	134.0	135.0		1406	5.7	0.9	1	dbSNP_134	135	2,8598	2.2+/-6.3	0,2,4298	no	missense	RAB3GAP2	NM_012414.3	64	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	469/1394	220364491	2,13004	2203	4300	6503	SO:0001583	missense	25782			intracellular protein transport	cytoplasm|soluble fraction	GTPase activator activity|protein heterodimerization activity	g.chr1:220364491G>A	AB020646	AB020646	CCDS31028.1	CCDS31028.1	1q41	2014-03-03			2014-03-03			ENSG00000118873	ENSG00000118873	ENSG00000118873	ENSG00000118873				17168	17168	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			609275	609275						15696165, 16532399, 24482476	15696165, 16532399, 24482476	Standard	Standard	NM_012414	NM_012414		Approved	RAB3-GAP150, KIAA0839, DKFZP434D245, SPG69	uc010puk.1	uc010puk.1	Q9H2M9	Q9H2M9	OTTHUMG00000037139	OTTHUMG00000037139	ENST00000358951.2:c.1406C>T	1.37:g.220364491G>A	ENSP00000351832:p.Ala469Val			p.A469V	NM_012414.3	NP_036546.2	Q9H2M9	RBGPR_HUMAN		GBM - Glioblastoma multiforme(131;0.0443)	14	1522	-			469		A6H8V0|O75872|Q9HAB0|Q9UFJ7|Q9UQ15	Missense_Mutation	SNP	ENST00000358951.2	37	c.1406C>T	CCDS31028.1	.	.	.	.	.	.	.	.	.	.	G	35	5.508939	0.96386	0.0	2.33E-4	ENSG00000118873	ENST00000358951	D	0.90444	-2.67	5.65	5.65	0.86999	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	D	0.94925	0.8359	M	0.65975	2.015	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.94568	0.7768	10	0.56958	D	0.05	.	19.7176	0.96129	0.0:0.0:1.0:0.0	.	469	Q9H2M9	RBGPR_HUMAN	V	469	ENSP00000351832:A469V	ENSP00000351832:A469V	A	-	2	0	0	RAB3GAP2	218431114	218431114	1.000000	0.71417	0.907000	0.35723	0.936000	0.57629	9.090000	0.94144	2.670000	0.90874	0.563000	0.77884	GCG		0.493	RAB3GAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090205.2		-21.343212	13	13	125	125	NM_012414		5	9.723141	9.723141	129	0.037313	0	0	0	1	0	5	129	0.037313
LRRTM3	347731	broad.mit.edu	37	10	68687631	68687631	+	Missense_Mutation	SNP	T	T	A			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr10:68687631T>A	ENST00000361320.4	+	2	1535	c.957T>A	c.(955-957)aaT>aaA	p.N319K	CTNNA3_ENST00000433211.2_Intron|CTNNA3_ENST00000373744.4_Intron	NM_178011.3	NP_821079.3	Q86VH5	LRRT3_HUMAN	leucine rich repeat transmembrane neuronal 3	319	LRRCT.				positive regulation of beta-amyloid formation (GO:1902004)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				breast(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	41						GCAGCAGAAATATTTGCTCCC	0.398																																						ENST00000361320.4											0			breast(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	41						c.(955-957)aaT>aaA	leucine rich repeat transmembrane neuronal 3						77.0	84.0	82.0					10																	68687631		2203	4300	6503	SO:0001583	missense	347731				integral to membrane		g.chr10:68687631T>A	BX640611	BX640611	CCDS7270.1	CCDS7270.1	10q22.1	2007-01-22			2007-01-22				ENSG00000198739		ENSG00000198739				19410	19410	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			610869	610869						12676565	12676565	Standard	Standard	XR_247527	XR_247527		Approved		uc001jmz.1	uc001jmz.1	Q86VH5	Q86VH5			ENST00000361320.4:c.957T>A	10.37:g.68687631T>A	ENSP00000355187:p.Asn319Lys		CTNNA3_ENST00000373744.4_Intron|CTNNA3_ENST00000433211.2_Intron	p.N319K	NM_178011.3	NP_821079.3	Q86VH5	LRRT3_HUMAN			2	1535	+			319	LRRCT.	A8K2A3|Q2NKX7|Q6N0A3	Missense_Mutation	SNP	ENST00000361320.4	37	c.957T>A	CCDS7270.1	.	.	.	.	.	.	.	.	.	.	T	2.049	-0.418154	0.04766	.	.	ENSG00000198739	ENST00000361320;ENST00000373722	T	0.04317	3.65	5.8	0.496	0.16896	5.8	0.496	0.16896	.	0.000000	0.85682	D	0.000000	T	0.02610	0.0079	N	0.13043	0.29	0.42989	D	0.994482	B;B	0.20459	0.007;0.045	B;B	0.21360	0.009;0.034	T	0.50048	-0.8873	10	0.10636	T	0.68	.	9.5846	0.39508	0.0:0.3875:0.0:0.6125	.	319;319	Q86VH5;Q86VH5-2	LRRT3_HUMAN;.	K	319	ENSP00000355187:N319K	ENSP00000355187:N319K	N	+	3	2	2	LRRTM3	68357637	68357637	1.000000	0.71417	0.999000	0.59377	0.983000	0.72400	1.623000	0.37008	0.058000	0.16222	-0.280000	0.10049	AAT		0.398	LRRTM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048277.2		32.011942	16	16	89	89	NM_178011		14	38.279393	38.279393	58	0.194444	0	0	0	1	0	14	58	0.194444
GNA11	2767	broad.mit.edu	37	19	3118942	3118942	+	Missense_Mutation	SNP	A	A	T			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr19:3118942A>T	ENST00000078429.4	+	5	868	c.626A>T	c.(625-627)cAg>cTg	p.Q209L	GNA11_ENST00000586180.1_3'UTR|AC005262.3_ENST00000587701.1_RNA|AC005262.2_ENST00000585980.1_RNA	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		76.588246	-11	-11	70	70	NM_002067		25	76.823517	76.823517	33	0.431034	0	0	0	1	0	25	33	0.431034
CSMD3	114788	broad.mit.edu	37	8	113694820	113694820	+	Missense_Mutation	SNP	G	G	A			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr8:113694820G>A	ENST00000297405.5	-	16	2772	c.2528C>T	c.(2527-2529)gCa>gTa	p.A843V	CSMD3_ENST00000455883.2_Missense_Mutation_p.A739V|CSMD3_ENST00000352409.3_Missense_Mutation_p.A843V|CSMD3_ENST00000343508.3_Missense_Mutation_p.A803V	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	843	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						AAACCGCCGTGCATTGATTGG	0.348										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																												ENST00000297405.5											0			breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						c.(2527-2529)gCa>gTa	CUB and Sushi multiple domains 3						99.0	99.0	99.0					8																	113694820		2203	4300	6503	SO:0001583	missense	114788				integral to membrane|plasma membrane		g.chr8:113694820G>A	AY210419	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			2007-01-06			ENSG00000164796	ENSG00000164796	ENSG00000164796	ENSG00000164796				19291	19291	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			608399	608399								Standard	Standard	NM_052900	NM_052900		Approved		uc003ynu.3	uc003ynu.3	Q7Z407	Q7Z407	OTTHUMG00000157027	OTTHUMG00000157027	ENST00000297405.5:c.2528C>T	8.37:g.113694820G>A	ENSP00000297405:p.Ala843Val		CSMD3_ENST00000455883.2_Missense_Mutation_p.A739V|CSMD3_ENST00000343508.3_Missense_Mutation_p.A803V|CSMD3_ENST00000352409.3_Missense_Mutation_p.A843V	p.A843V	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN			16	2772	-			843	Sushi 4.	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	c.2528C>T	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.769141	0.90020	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.25912	1.77;1.77;1.77;1.77;1.77	5.58	5.58	0.84498	5.58	5.58	0.84498	Complement control module (2);Sushi/SCR/CCP (3);	0.075478	0.52532	D	0.000071	T	0.50446	0.1616	L	0.60904	1.88	0.40393	D	0.979562	D;D;D	0.76494	0.999;0.999;0.989	D;D;D	0.91635	0.998;0.999;0.921	T	0.48387	-0.9040	10	0.59425	D	0.04	.	19.557	0.95354	0.0:0.0:1.0:0.0	.	739;843;803	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	V	803;843;183;739;843	ENSP00000345799:A803V;ENSP00000297405:A843V;ENSP00000341558:A183V;ENSP00000412263:A739V;ENSP00000343124:A843V	ENSP00000297405:A843V	A	-	2	0	0	CSMD3	113763996	113763996	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	4.687000	0.61708	2.623000	0.88846	0.650000	0.86243	GCA		0.348	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1		59.911682	27	27	130	130	NM_052900		28	72.871382	72.871382	118	0.191781	0	0	0	1	0	28	118	0.191781
APEH	327	broad.mit.edu	37	3	49716365	49716365	+	Missense_Mutation	SNP	G	G	A			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr3:49716365G>A	ENST00000296456.5	+	12	1541	c.1141G>A	c.(1141-1143)Gct>Act	p.A381T	APEH_ENST00000438011.1_Missense_Mutation_p.A381T	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase	381					beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		CTTTGACTCGGCTCAGCGCAG	0.607																																						ENST00000296456.5											0			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15						c.(1141-1143)Gct>Act	acylaminoacyl-peptide hydrolase						77.0	72.0	74.0					3																	49716365		2203	4300	6503	SO:0001583	missense	327			proteolysis	cytoplasm|nuclear membrane	serine-type endopeptidase activity	g.chr3:49716365G>A	D38441	D38441	CCDS2801.1	CCDS2801.1	3p21	2013-05-29	2013-05-29		2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	ENSG00000164062	ENSG00000164062	3.4.19.1			586	586	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product	"""acylaminoacyl-peptidase"""	"""acylaminoacyl-peptidase"""	102645	102645	"""N-acylaminoacyl-peptide hydrolase"""	D3F15S2, DNF15S2, D3S48E	"""N-acylaminoacyl-peptide hydrolase"""	D3F15S2, DNF15S2, D3S48E		2392324	2392324	Standard	Standard	NM_001640	NM_001640		Approved		uc003cxf.3	uc003cxf.3	P13798	P13798	OTTHUMG00000156882	OTTHUMG00000156882	ENST00000296456.5:c.1141G>A	3.37:g.49716365G>A	ENSP00000296456:p.Ala381Thr		APEH_ENST00000438011.1_Missense_Mutation_p.A381T	p.A381T	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN		BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)	12	1541	+			381		Q9BQ33|Q9P0Y2	Missense_Mutation	SNP	ENST00000296456.5	37	c.1141G>A	CCDS2801.1	.	.	.	.	.	.	.	.	.	.	G	15.57	2.871281	0.51695	.	.	ENSG00000164062	ENST00000296456;ENST00000442186;ENST00000438011	T;T	0.43294	0.95;0.95	5.62	4.72	0.59763	5.62	4.72	0.59763	Six-bladed beta-propeller, TolB-like (1);Peptidase S9A/B/C, oligopeptidase, N-terminal beta-propeller (1);	0.405904	0.28322	N	0.015780	T	0.38427	0.1040	L	0.56280	1.765	0.31060	N	0.714217	B;B	0.18968	0.032;0.014	B;B	0.19946	0.027;0.017	T	0.38650	-0.9651	10	0.12766	T	0.61	-24.1998	15.3547	0.74418	0.0:0.2638:0.7362:0.0	.	381;381	C9JIF9;P13798	.;ACPH_HUMAN	T	381;306;381	ENSP00000296456:A381T;ENSP00000415862:A381T	ENSP00000296456:A381T	A	+	1	0	0	APEH	49691369	49691369	0.220000	0.23631	0.766000	0.31476	0.910000	0.53928	1.111000	0.31159	1.306000	0.44926	0.561000	0.74099	GCT		0.607	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2		-6.438822	0	0	124	124			4	7.957368	7.957368	66	0.057143	0	0	0	1	0	4	66	0.057143
BLOC1S6	26258	broad.mit.edu	37	15	45884472	45884472	+	Silent	SNP	C	C	T			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr15:45884472C>T	ENST00000220531.3	+	2	543	c.222C>T	c.(220-222)ctC>ctT	p.L74L	BLOC1S6_ENST00000562384.1_Intron|BLOC1S6_ENST00000567740.1_Intron|RP11-96O20.4_ENST00000564080.1_Intron|BLOC1S6_ENST00000564765.1_5'UTR|BLOC1S6_ENST00000568816.1_5'UTR|BLOC1S6_ENST00000565323.1_Silent_p.L79L|BLOC1S6_ENST00000565409.1_5'UTR|Y_RNA_ENST00000363549.1_RNA|BLOC1S6_ENST00000565216.1_Intron|BLOC1S6_ENST00000566753.1_Silent_p.L74L|BLOC1S6_ENST00000567461.1_Intron	NM_012388.2	NP_036520.1	Q9UL45	BL1S6_HUMAN	biogenesis of lysosomal organelles complex-1, subunit 6, pallidin	74					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|blood coagulation (GO:0007596)|endosome to melanosome transport (GO:0035646)|melanocyte differentiation (GO:0030318)|melanosome organization (GO:0032438)|melanosome transport (GO:0032402)|membrane fusion (GO:0061025)|membrane organization (GO:0061024)|neuron projection development (GO:0031175)|positive regulation of natural killer cell activation (GO:0032816)|positive regulation of pigment cell differentiation (GO:0050942)|post-Golgi vesicle-mediated transport (GO:0006892)|secretion of lysosomal enzymes (GO:0033299)|synaptic vesicle docking involved in exocytosis (GO:0016081)	BLOC-1 complex (GO:0031083)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extrinsic component of membrane (GO:0019898)|transport vesicle (GO:0030133)	actin filament binding (GO:0051015)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|syntaxin binding (GO:0019905)										TCCAGGAACTCACGTAAGCTA	0.363																																						ENST00000220531.3											0										c.(220-222)ctC>ctT	biogenesis of lysosomal organelles complex-1, subunit 6, pallidin						80.0	81.0	80.0					15																	45884472		2198	4298	6496	SO:0001819	synonymous_variant	26258						g.chr15:45884472C>T	AF080470	AF080470	CCDS10126.1	CCDS10126.1	15q21.1	2013-09-27	2012-08-07	2012-08-01	2013-09-27	2012-08-07	2012-08-01	ENSG00000104164	ENSG00000104164	ENSG00000104164	ENSG00000104164		"""Biogenesis of lysosomal organelles complex-1 subunits"""	"""Biogenesis of lysosomal organelles complex-1 subunits"""	8549	8549	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			604310	604310	"""pallid (mouse) homolog, pallidin"", ""pallidin homolog (mouse)"""	PA, PLDN	"""pallid (mouse) homolog, pallidin"", ""pallidin homolog (mouse)"""	PA, PLDN		10610180	10610180	Standard	Standard	NM_012388	NM_012388		Approved	HPS9	uc001zvq.3	uc001zvq.3	Q9UL45	Q9UL45	OTTHUMG00000131477	OTTHUMG00000131477	ENST00000220531.3:c.222C>T	15.37:g.45884472C>T			BLOC1S6_ENST00000568816.1_5'UTR|BLOC1S6_ENST00000565323.1_Silent_p.L79L|BLOC1S6_ENST00000562384.1_Intron|RP11-96O20.4_ENST00000564080.1_Intron|BLOC1S6_ENST00000566753.1_Silent_p.L74L|BLOC1S6_ENST00000567461.1_Intron|BLOC1S6_ENST00000565216.1_Intron|BLOC1S6_ENST00000567740.1_Intron|BLOC1S6_ENST00000565409.1_5'UTR|BLOC1S6_ENST00000564765.1_5'UTR	p.L74L	NM_012388.2	NP_036520.1					2	543	+						Silent	SNP	ENST00000220531.3	37	c.222C>T	CCDS10126.1																																																																																									0.363	BLOC1S6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254320.2		64.470688	-2	-2	60	60	NM_012388		21	64.546318	64.546318	25	0.456522	0	0	0	1	0	21	25	0.456522
SLC23A3	151295	broad.mit.edu	37	2	220033409	220033409	+	Silent	SNP	G	G	C			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr2:220033409G>C	ENST00000409878.3	-	5	671	c.639C>G	c.(637-639)gcC>gcG	p.A213A	SLC23A3_ENST00000455516.2_Silent_p.A221A|SLC23A3_ENST00000295738.7_Silent_p.A213A|SLC23A3_ENST00000396775.3_Intron	NM_001144889.1	NP_001138361.1	Q6PIS1	S23A3_HUMAN	solute carrier family 23, member 3	213					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	11		Renal(207;0.0474)		Epithelial(149;9.27e-07)|all cancers(144;0.000156)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGCAGAACTGGGCTACCTCCC	0.672																																						ENST00000455516.2											0			endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	11						c.(661-663)gcC>gcG	solute carrier family 23, member 3						29.0	34.0	32.0					2																	220033409		1993	4161	6154	SO:0001819	synonymous_variant	151295			transmembrane transport	integral to membrane	protein binding|transporter activity	g.chr2:220033409G>C	BC030243	BC030243	CCDS42819.1, CCDS46517.1, CCDS46518.1	CCDS42819.1, CCDS46517.1, CCDS46518.1	2q35	2013-07-18	2013-07-18		2013-07-18	2013-07-18		ENSG00000213901	ENSG00000213901	ENSG00000213901	ENSG00000213901		"""Solute carriers"""	"""Solute carriers"""	20601	20601	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product												Standard	Standard	NM_144712	NM_144712		Approved	SVCT3, FLJ31168, Yspl1	uc010zkr.2	uc010zkr.2	Q6PIS1	Q6PIS1	OTTHUMG00000154616	OTTHUMG00000154616	ENST00000409878.3:c.639C>G	2.37:g.220033409G>C			SLC23A3_ENST00000396775.3_Intron|SLC23A3_ENST00000295738.7_Silent_p.A213A|SLC23A3_ENST00000409878.3_Silent_p.A213A	p.A221A	NM_001144890.1	NP_001138362.1	Q6PIS1	S23A3_HUMAN		Epithelial(149;9.27e-07)|all cancers(144;0.000156)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	5	710	-		Renal(207;0.0474)	213		B7Z512|Q2PYN6|Q96NA6	Silent	SNP	ENST00000409878.3	37	c.663C>G	CCDS46518.1																																																																																									0.672	SLC23A3-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336331.2		22.392425	5	5	30	30	NM_144712		8	22.862795	22.862795	15	0.347826	0	0	0	1	0	8	15	0.347826
NDUFA5	4698	broad.mit.edu	37	7	123190629	123190629	+	Silent	SNP	T	T	A	rs371230838		TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr7:123190629T>A	ENST00000355749.2	-	3	537	c.78A>T	c.(76-78)atA>atT	p.I26I	NDUFA5_ENST00000467117.1_5'UTR|NDUFA5_ENST00000471770.1_Silent_p.I26I	NM_001282419.1|NM_005000.2	NP_001269348.1|NP_004991.1	Q16718	NDUA5_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 5	26					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			large_intestine(1)|urinary_tract(1)	2						TTGTGTACAATATTCTTAGCC	0.318																																						ENST00000471770.1											0			large_intestine(1)|urinary_tract(1)	2						c.(76-78)atA>atT	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 5						76.0	83.0	81.0					7																	123190629		2202	4299	6501	SO:0001819	synonymous_variant	4698			mitochondrial electron transport, NADH to ubiquinone|transport	mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity	g.chr7:123190629T>A			CCDS5788.1, CCDS64760.1, CCDS75655.1, CCDS75656.1	CCDS5788.1, CCDS64760.1, CCDS75655.1, CCDS75656.1	7q31.33	2013-06-19	2013-06-19		2013-06-19	2013-06-19		ENSG00000128609	ENSG00000128609	ENSG00000128609	ENSG00000128609		"""Mitochondrial respiratory chain complex / Complex I"""	"""Mitochondrial respiratory chain complex / Complex I"""	7688	7688	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product	"""complex I 13kDa subunit B"", ""ubiquinone reductase"", ""type I dehydrogenase"", ""NADH-ubiquinone oxidoreductase 13 kDa-B subunit"""	"""complex I 13kDa subunit B"", ""ubiquinone reductase"", ""type I dehydrogenase"", ""NADH-ubiquinone oxidoreductase 13 kDa-B subunit"""	601677	601677	"""NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 5 (13kD, B13)"", ""NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 5, 13kDa"""		"""NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 5 (13kD, B13)"", ""NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 5, 13kDa"""			9763677, 9021153	9763677, 9021153	Standard	Standard	XM_005250371	XM_005250371		Approved	B13, NUFM, CI-13KD-B, UQOR13, CI-13kB	uc003vks.3	uc003vks.3	Q16718	Q16718	OTTHUMG00000157348	OTTHUMG00000157348	ENST00000355749.2:c.78A>T	7.37:g.123190629T>A			NDUFA5_ENST00000355749.2_Silent_p.I26I|NDUFA5_ENST00000467117.1_5'UTR	p.I26I	NM_001282419.1|NM_001282420.1|NM_001282421.1	NP_001269348.1|NP_001269349.1|NP_001269350.1	Q16718	NDUA5_HUMAN			3	212	-			26		B2RD98|Q5H9R2|Q6IRX7	Silent	SNP	ENST00000355749.2	37	c.78A>T	CCDS5788.1	.	.	.	.	.	.	.	.	.	.	T	7.828	0.719297	0.15372	.	.	ENSG00000128609	ENST00000378795	.	.	.	5.54	4.35	0.52113	5.54	4.35	0.52113	.	.	.	.	.	T	0.64724	0.2624	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63812	-0.6552	5	0.46703	T	0.11	.	11.0704	0.47999	0.1393:0.0:0.0:0.8607	.	.	.	.	F	22	.	ENSP00000368072:I22F	I	-	1	0	0	NDUFA5	122977865	122977865	1.000000	0.71417	0.262000	0.24481	0.710000	0.40934	1.396000	0.34531	0.972000	0.38314	0.533000	0.62120	ATT		0.318	NDUFA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348533.1		5.005542	13	13	101	101	NM_005000		6	14.84921	14.849210	55	0.098361	0	0	0	1	0	6	55	0.098361
OTUD4	54726	broad.mit.edu	37	4	146059006	146059006	+	Missense_Mutation	SNP	G	G	A	rs558808115		TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr4:146059006G>A	ENST00000447906.2	-	21	3108	c.2921C>T	c.(2920-2922)aCt>aTt	p.T974I	OTUD4_ENST00000454497.2_Missense_Mutation_p.T909I|OTUD4_ENST00000455611.2_Intron			Q01804	OTUD4_HUMAN	OTU deubiquitinase 4	974					protein K48-linked deubiquitination (GO:0071108)		poly(A) RNA binding (GO:0044822)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(180;0.151)					AACAGGCACAGTTTCTCTCTC	0.463																																						ENST00000454497.2											0			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33						c.(2725-2727)aCt>aTt	OTU domain containing 4						128.0	133.0	131.0					4																	146059006		2203	4300	6503	SO:0001583	missense	54726					protein binding	g.chr4:146059006G>A			CCDS3764.1, CCDS47139.1	CCDS3764.1, CCDS47139.1	4q31.21	2014-02-24	2014-02-24		2014-02-24	2014-02-24		ENSG00000164164	ENSG00000164164	ENSG00000164164	ENSG00000164164		"""OTU domain containing"""	"""OTU domain containing"""	24949	24949	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			611744	611744	"""OTU domain containing 4"""		"""OTU domain containing 4"""			1475186, 12727813, 19996094	1475186, 12727813, 19996094	Standard	Standard	NM_001102653	NM_001102653		Approved	HSHIN1, KIAA1046, DUBA6	uc003ika.4	uc003ika.4	Q01804	Q01804	OTTHUMG00000161480	OTTHUMG00000161480	ENST00000447906.2:c.2921C>T	4.37:g.146059006G>A	ENSP00000395487:p.Thr974Ile		OTUD4_ENST00000455611.2_Intron|OTUD4_ENST00000447906.2_Missense_Mutation_p.T974I	p.T909I	NM_001102653.1	NP_001096123.1	Q01804	OTUD4_HUMAN			21	2863	-	all_hematologic(180;0.151)		973		B4DYS4|Q147U2|Q1ZYK1|Q6PG39|Q96MQ5|Q9NT94|Q9UPV6	Missense_Mutation	SNP	ENST00000447906.2	37	c.2726C>T		.	.	.	.	.	.	.	.	.	.	G	13.28	2.191504	0.38707	.	.	ENSG00000164164	ENST00000454497;ENST00000447906	T;T	0.34275	1.37;1.37	6.17	5.33	0.75918	6.17	5.33	0.75918	.	1.059000	0.07258	N	0.867023	T	0.32793	0.0841	N	0.24115	0.695	0.80722	D	1	B;B	0.13145	0.007;0.004	B;B	0.14023	0.01;0.004	T	0.02275	-1.1184	10	0.59425	D	0.04	-0.3286	15.5098	0.75772	0.0658:0.0:0.9342:0.0	.	974;973	G3V0I6;Q01804	.;OTUD4_HUMAN	I	909;974	ENSP00000409279:T909I;ENSP00000395487:T974I	ENSP00000395487:T974I	T	-	2	0	0	OTUD4	146278456	146278456	0.027000	0.19231	0.108000	0.21378	0.880000	0.50808	2.210000	0.42816	1.621000	0.50320	0.655000	0.94253	ACT		0.463	OTUD4-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000365117.2		-22.105384	45	45	191	191	NM_017493		4	7.258989	7.258989	119	0.032520	0	0	0	1	0	4	119	0.03252
PCDHB7	56129	broad.mit.edu	37	5	140554267	140554267	+	Silent	SNP	G	G	A			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr5:140554267G>A	ENST00000231137.3	+	1	2025	c.1851G>A	c.(1849-1851)gtG>gtA	p.V617V		NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	617	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(20)|lung(54)|ovary(5)|prostate(7)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	119			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TATTCGGCGTGTGGGCGCACA	0.677																																						ENST00000231137.3											0			NS(2)|breast(2)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(20)|lung(54)|ovary(5)|prostate(7)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	119						c.(1849-1851)gtG>gtA							33.0	50.0	44.0					5																	140554267		2163	4261	6424	SO:0001819	synonymous_variant	0			calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	g.chr5:140554267G>A	AF152500	AF152500	CCDS4249.1	CCDS4249.1	5q31	2010-01-26			2010-01-26			ENSG00000113212	ENSG00000113212	ENSG00000113212	ENSG00000113212		"""Cadherins / Protocadherins : Clustered"""	"""Cadherins / Protocadherins : Clustered"""	8692	8692	other	protocadherin	other	protocadherin			606333	606333						10380929	10380929	Standard	Standard	NM_018940	NM_018940		Approved	PCDH-BETA7	uc003lit.3	uc003lit.3	Q9Y5E2	Q9Y5E2	OTTHUMG00000129608	OTTHUMG00000129608	ENST00000231137.3:c.1851G>A	5.37:g.140554267G>A				p.V617V	NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)		1	2025	+			617	Cadherin 6.	A1L3Y8	Silent	SNP	ENST00000231137.3	37	c.1851G>A	CCDS4249.1																																																																																									0.677	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2		43.051129	-23	-23	137	137	NM_018940		23	55.405236	55.405236	105	0.179687	0	0	0	1	0	23	105	0.179687
OR52M1	119772	broad.mit.edu	37	11	4567078	4567078	+	Missense_Mutation	SNP	T	T	C			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr11:4567078T>C	ENST00000360213.1	+	1	658	c.658T>C	c.(658-660)Tcc>Ccc	p.S220P		NM_001004137.1	NP_001004137.1	Q8NGK5	O52M1_HUMAN	olfactory receptor, family 52, subfamily M, member 1	220						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(2)|lung(9)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;8.45e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		TATTGCTGCATCCTATGTGAT	0.522																																						ENST00000360213.1											0			endometrium(2)|large_intestine(2)|lung(9)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18						c.(658-660)Tcc>Ccc	olfactory receptor, family 52, subfamily M, member 1						263.0	247.0	252.0					11																	4567078		2201	4298	6499	SO:0001583	missense	119772			sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:4567078T>C	AB065789	AB065789	CCDS31353.1	CCDS31353.1	11p15.4	2012-08-09	2002-11-13	2002-11-15	2012-08-09	2002-11-13	2002-11-15	ENSG00000197790	ENSG00000197790	ENSG00000197790	ENSG00000197790		"""GPCR / Class A : Olfactory receptors"""	"""GPCR / Class A : Olfactory receptors"""	15225	15225	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product					"""olfactory receptor, family 52, subfamily M, member 1 pseudogene"""	OR52M1P	"""olfactory receptor, family 52, subfamily M, member 1 pseudogene"""	OR52M1P				Standard	Standard	NM_001004137	NM_001004137		Approved		uc010qyf.2	uc010qyf.2	Q8NGK5	Q8NGK5	OTTHUMG00000165706	OTTHUMG00000165706	ENST00000360213.1:c.658T>C	11.37:g.4567078T>C	ENSP00000353343:p.Ser220Pro			p.S220P	NM_001004137.1	NP_001004137.1	Q8NGK5	O52M1_HUMAN		Epithelial(150;8.45e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)	1	658	+		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)	220			Missense_Mutation	SNP	ENST00000360213.1	37	c.658T>C	CCDS31353.1	.	.	.	.	.	.	.	.	.	.	T	15.74	2.922553	0.52653	.	.	ENSG00000197790	ENST00000360213	T	0.46819	0.86	5.01	5.01	0.66863	5.01	5.01	0.66863	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47093	D	0.000258	T	0.78130	0.4235	H	0.97516	4.02	0.25075	N	0.990962	D	0.69078	0.997	D	0.67231	0.95	T	0.76713	-0.2858	10	0.87932	D	0	.	13.9773	0.64282	0.0:0.0:0.0:1.0	.	220	Q8NGK5	O52M1_HUMAN	P	220	ENSP00000353343:S220P	ENSP00000353343:S220P	S	+	1	0	0	OR52M1	4523654	4523654	0.957000	0.32711	0.969000	0.41365	0.789000	0.44602	3.065000	0.49994	2.233000	0.73108	0.528000	0.53228	TCC		0.522	OR52M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385847.1		-27.830942	19	19	230	230	NM_001004137		4	7.864828	7.864828	141	0.027586	0	0	0	1	0	4	141	0.027586
PYROXD2	84795	broad.mit.edu	37	10	100147057	100147057	+	Silent	SNP	A	A	G			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr10:100147057A>G	ENST00000370575.4	-	14	1503	c.1455T>C	c.(1453-1455)gaT>gaC	p.D485D	PYROXD2_ENST00000483923.1_5'UTR	NM_032709.2	NP_116098.2	Q8N2H3	PYRD2_HUMAN	pyridine nucleotide-disulphide oxidoreductase domain 2	485							oxidoreductase activity (GO:0016491)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	12						CCTCGATGCAATCAAACACTG	0.483																																						ENST00000370575.4											0			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	12						c.(1453-1455)gaT>gaC	pyridine nucleotide-disulphide oxidoreductase domain 2						91.0	86.0	88.0					10																	100147057		2203	4300	6503	SO:0001819	synonymous_variant	84795					oxidoreductase activity	g.chr10:100147057A>G	AK074429	AK074429	CCDS7474.1	CCDS7474.1	10q24.2	2009-04-22	2009-04-22	2009-04-22	2009-04-22	2009-04-22	2009-04-22	ENSG00000119943	ENSG00000119943	ENSG00000119943	ENSG00000119943				23517	23517	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product					"""chromosome 10 open reading frame 33"""	C10orf33	"""chromosome 10 open reading frame 33"""	C10orf33				Standard	Standard	NM_032709	NM_032709		Approved	FLJ23849	uc001kpc.3	uc001kpc.3	Q8N2H3	Q8N2H3	OTTHUMG00000018877	OTTHUMG00000018877	ENST00000370575.4:c.1455T>C	10.37:g.100147057A>G			PYROXD2_ENST00000483923.1_5'UTR	p.D485D	NM_032709.2	NP_116098.2	Q8N2H3	PYRD2_HUMAN			14	1503	-			485		D3DR61|Q5TAA9|Q9BRQ1	Silent	SNP	ENST00000370575.4	37	c.1455T>C	CCDS7474.1																																																																																									0.483	PYROXD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049782.2		50.793909	-19	-19	65	65	NM_032709		16	51.000537	51.000537	22	0.421053	0	0	0	1	0	16	22	0.421053
MUC3A	4584	broad.mit.edu	37	7	100609626	100609626	+	Silent	SNP	C	C	A			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr7:100609626C>A	ENST00000319509.7	+	8	2358	c.2358C>A	c.(2356-2358)gcC>gcA	p.A786A	RP11-395B7.2_ENST00000434775.1_RNA|RP11-395B7.2_ENST00000420080.1_RNA			Q02505	MUC3A_HUMAN	mucin 3A, cell surface associated	2451	Ser-rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|extracellular matrix structural constituent (GO:0005201)			breast(3)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(32)|prostate(3)	44						GCCTGACGGCCGGCGCCGCGC	0.766																																						ENST00000319509.7											0			breast(3)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(32)|prostate(3)	44						c.(2356-2358)gcC>gcA	mucin 3A, cell surface associated						7.0	7.0	7.0					7																	100609626		860	1954	2814	SO:0001819	synonymous_variant	4584						g.chr7:100609626C>A	AF113616	AF113616			7q22.1	2012-04-20	2006-03-14		2012-04-20	2006-03-14		ENSG00000169894	ENSG00000169894	ENSG00000169894	ENSG00000169894		"""Mucins"""	"""Mucins"""	7513	7513	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			158371	158371	"""mucin 3A, intestinal"""	MUC3	"""mucin 3A, intestinal"""	MUC3		2393399, 10973822	2393399, 10973822	Standard	Standard	XM_006710192	XM_006710192		Approved		uc003uxl.1	uc003uxl.1	Q02505	Q02505	OTTHUMG00000157038	OTTHUMG00000157038	ENST00000319509.7:c.2358C>A	7.37:g.100609626C>A			RP11-395B7.2_ENST00000420080.1_RNA	p.A786A							8	2358	+					O14650|O14651|O43418|O43421|Q02506|Q6W763|Q9H3Q7|Q9UKW9|Q9UN93|Q9UN94|Q9UN95	Silent	SNP	ENST00000319509.7	37	c.2358C>A																																																																																										0.766	MUC3A-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000347215.1		7.722693	-3	-3	10	10	XM_001725354		3	8.773991	8.773991	11	0.214286	1	0	1	1	1	3	11	0.214286
USP13	8975	broad.mit.edu	37	3	179448030	179448030	+	Missense_Mutation	SNP	A	A	T			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr3:179448030A>T	ENST00000263966.3	+	9	1613	c.1142A>T	c.(1141-1143)cAa>cTa	p.Q381L	USP13_ENST00000482333.1_3'UTR|USP13_ENST00000496897.1_Missense_Mutation_p.Q316L	NM_003940.2	NP_003931.2	Q92995	UBP13_HUMAN	ubiquitin specific peptidase 13 (isopeptidase T-3)	381	USP.				autophagy (GO:0006914)|cell proliferation (GO:0008283)|melanocyte differentiation (GO:0030318)|protein K63-linked deubiquitination (GO:0070536)|protein stabilization (GO:0050821)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type endopeptidase activity (GO:0004197)|omega peptidase activity (GO:0008242)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	46	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)			GATCCAACACAAGATTTCAAC	0.343																																						ENST00000263966.3											0			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	46						c.(1141-1143)cAa>cTa	ubiquitin specific peptidase 13 (isopeptidase T-3)						124.0	122.0	122.0					3																	179448030		2203	4300	6503	SO:0001583	missense	8975			ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding	g.chr3:179448030A>T	U75362	U75362	CCDS3235.1	CCDS3235.1	3q26.2-q26.3	2008-04-11	2005-08-08		2008-04-11	2005-08-08		ENSG00000058056	ENSG00000058056	ENSG00000058056	ENSG00000058056		"""Ubiquitin-specific peptidases"""	"""Ubiquitin-specific peptidases"""	12611	12611	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			603591	603591	"""ubiquitin specific protease 13 (isopeptidase T-3)"""		"""ubiquitin specific protease 13 (isopeptidase T-3)"""			12838346	12838346	Standard	Standard	NM_003940	NM_003940		Approved	IsoT-3	uc003fkh.3	uc003fkh.3	Q92995	Q92995	OTTHUMG00000157783	OTTHUMG00000157783	ENST00000263966.3:c.1142A>T	3.37:g.179448030A>T	ENSP00000263966:p.Gln381Leu		USP13_ENST00000496897.1_Missense_Mutation_p.Q316L|USP13_ENST00000482333.1_3'UTR	p.Q381L	NM_003940.2	NP_003931.2	Q92995	UBP13_HUMAN	OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)		9	1613	+	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		381		A8K2S3|B4DYF3|D3DNS2|Q96B25	Missense_Mutation	SNP	ENST00000263966.3	37	c.1142A>T	CCDS3235.1	.	.	.	.	.	.	.	.	.	.	A	15.20	2.763128	0.49574	.	.	ENSG00000058056	ENST00000263966;ENST00000496897;ENST00000497155	T;T;T	0.33438	1.41;1.41;1.41	5.69	5.69	0.88448	5.69	5.69	0.88448	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.48077	0.1480	L	0.61036	1.89	0.80722	D	1	D;B	0.56035	0.974;0.03	P;B	0.57960	0.83;0.036	T	0.36138	-0.9760	10	0.33940	T	0.23	-16.1905	15.9458	0.79792	1.0:0.0:0.0:0.0	.	381;381	Q92995;A8K2S3	UBP13_HUMAN;.	L	381;316;27	ENSP00000263966:Q381L;ENSP00000417146:Q316L;ENSP00000420057:Q27L	ENSP00000263966:Q381L	Q	+	2	0	0	USP13	180930724	180930724	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.339000	0.96797	2.162000	0.67917	0.459000	0.35465	CAA		0.343	USP13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349617.1		86.258571	31	31	126	126			29	86.642034	86.642034	40	0.420290	0	0	0	1	0	29	40	0.42029
MGME1	92667	broad.mit.edu	37	20	17968940	17968940	+	Splice_Site	SNP	A	A	T			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr20:17968940A>T	ENST00000377710.5	+	4	1151	c.863A>T	c.(862-864)cAg>cTg	p.Q288L	MGME1_ENST00000377704.4_Intron|MGME1_ENST00000467391.1_3'UTR|MGME1_ENST00000377709.1_Splice_Site_p.Q208L	NM_052865.2	NP_443097.1			mitochondrial genome maintenance exonuclease 1																		TACAGCTTTCAGGTCAGGACA	0.453																																						ENST00000377710.5											0										c.(862-864)cAg>cTg	mitochondrial genome maintenance exonuclease 1						96.0	87.0	90.0					20																	17968940		2203	4300	6503	SO:0001630	splice_region_variant	92667						g.chr20:17968940A>T			CCDS13131.1	CCDS13131.1	20p11.23	2013-08-29	2013-01-11	2013-01-11	2013-08-29	2013-01-11	2013-01-11	ENSG00000125871	ENSG00000125871	ENSG00000125871	ENSG00000125871				16205	16205	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product			615076	615076	"""chromosome 20 open reading frame 72"""	C20orf72	"""chromosome 20 open reading frame 72"""	C20orf72		23313956, 23358826, 23434322	23313956, 23358826, 23434322	Standard	Standard	NM_052865	NM_052865		Approved	bA504H3.4, DDK1	uc002wqh.3	uc002wqh.3	Q9BQP7	Q9BQP7	OTTHUMG00000031955	OTTHUMG00000031955	ENST00000377710.5:c.864+1A>T	20.37:g.17968940A>T			MGME1_ENST00000377709.1_Splice_Site_p.Q208L|MGME1_ENST00000377704.4_Intron|MGME1_ENST00000467391.1_3'UTR	p.Q288L	NM_052865.2	NP_443097.1					4	1151	+						Splice_Site	SNP	ENST00000377710.5	37	c.863A>T	CCDS13131.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.413106	0.83449	.	.	ENSG00000125871	ENST00000377710;ENST00000377709	T;T	0.49720	0.77;0.83	5.62	5.62	0.85841	5.62	5.62	0.85841	.	0.102324	0.64402	D	0.000001	T	0.66197	0.2765	M	0.70903	2.155	0.80722	D	1	D	0.76494	0.999	D	0.65874	0.939	T	0.67205	-0.5729	10	0.45353	T	0.12	-12.6793	15.4826	0.75539	1.0:0.0:0.0:0.0	.	288	Q9BQP7	CT072_HUMAN	L	288;208	ENSP00000366939:Q288L;ENSP00000366938:Q208L	ENSP00000366938:Q208L	Q	+	2	0	0	C20orf72	17916940	17916940	1.000000	0.71417	1.000000	0.80357	0.593000	0.36681	8.721000	0.91446	2.137000	0.66172	0.379000	0.24179	CAG		0.453	MGME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078139.1		-9.538392	9	9	105	105	NM_052865	Missense_Mutation	3	6.717945	6.717945	69	0.041667	0	0	0	1	0	3	69	0.041667
ALG1L	200810	broad.mit.edu	37	3	125651539	125651539	+	Silent	SNP	A	A	C			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr3:125651539A>C	ENST00000340333.3	-	3	277	c.114T>G	c.(112-114)ctT>ctG	p.L38L	FAM86JP_ENST00000485843.1_RNA	NM_001015050.2|NM_001195223.1	NP_001015050.2|NP_001182152.1	Q6GMV1	ALG1L_HUMAN	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase-like	38							transferase activity, transferring glycosyl groups (GO:0016757)			large_intestine(2)|lung(2)	4						CATCAAGAGTAAGTTGTTCAA	0.423																																						ENST00000340333.3											0			large_intestine(2)|lung(2)	4						c.(112-114)ctT>ctG	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase-like						89.0	82.0	85.0					3																	125651539		2203	4300	6503	SO:0001819	synonymous_variant	200810					transferase activity, transferring glycosyl groups	g.chr3:125651539A>C	BC073816	BC073816	CCDS33840.1, CCDS74998.1	CCDS33840.1, CCDS74998.1	3q21.2	2013-02-22	2013-02-22		2013-02-22	2013-02-22		ENSG00000189366	ENSG00000189366	ENSG00000189366	ENSG00000189366		"""Glycosyltransferase group 1 domain containing"""	"""Glycosyltransferase group 1 domain containing"""	33721	33721	protein-coding gene	gene with protein product	protein-coding gene	gene with protein product	"""asparagine-linked glycosylation 1-like 1"""	"""asparagine-linked glycosylation 1-like 1"""			"""asparagine-linked glycosylation 1-like"""		"""asparagine-linked glycosylation 1-like"""					Standard	Standard	NM_001015050	NM_001015050		Approved	ALG1L1	uc003eig.2	uc003eig.2	Q6GMV1	Q6GMV1	OTTHUMG00000159588	OTTHUMG00000159588	ENST00000340333.3:c.114T>G	3.37:g.125651539A>C				p.L38L	NM_001015050.2|NM_001195223.1	NP_001015050.2|NP_001182152.1	Q6GMV1	ALG1L_HUMAN			3	277	-			38		D3DNA5	Silent	SNP	ENST00000340333.3	37	c.114T>G	CCDS33840.1																																																																																									0.423	ALG1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356347.1		-7.463182	5	5	99	99	NM_001015050		4	9.159825	9.159825	74	0.051282	0	0	0	1	0	4	74	0.051282
