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VPS39 (VPS39, HOPS complex subunit)

Identity

Alias_namesvacuolar protein sorting 39 (yeast)
vacuolar protein sorting 39 homolog (S. cerevisiae)
Alias_symbol (synonym)KIAA0770
VAM6
Other aliasTLP
hVam6p
HGNC (Hugo) VPS39
LocusID (NCBI) 23339
Atlas_Id 42957
Location 15q15.1  [Link to chromosome band 15q15]
Location_base_pair Starts at 42158701 and ends at 42208326 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
CLIC2 (Xq28) / VPS39 (15q15.1)HNRNPU (1q44) / VPS39 (15q15.1)TUBA1C (12q13.12) / VPS39 (15q15.1)
VPS39 (15q15.1) / VPS39 (15q15.1)CLIC2 Xq28 / VPS39 15q15.1

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


External links

Nomenclature
HGNC (Hugo)VPS39   20593
Cards
Entrez_Gene (NCBI)VPS39  23339  VPS39, HOPS complex subunit
AliasesTLP; VAM6; hVam6p
GeneCards (Weizmann)VPS39
Ensembl hg19 (Hinxton)ENSG00000166887 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000166887 [Gene_View]  chr15:42158701-42208326 [Contig_View]  VPS39 [Vega]
ICGC DataPortalENSG00000166887
TCGA cBioPortalVPS39
AceView (NCBI)VPS39
Genatlas (Paris)VPS39
WikiGenes23339
SOURCE (Princeton)VPS39
Genetics Home Reference (NIH)VPS39
Genomic and cartography
GoldenPath hg38 (UCSC)VPS39  -     chr15:42158701-42208326 -  15q15.1   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)VPS39  -     15q15.1   [Description]    (hg19-Feb_2009)
EnsemblVPS39 - 15q15.1 [CytoView hg19]  VPS39 - 15q15.1 [CytoView hg38]
Mapping of homologs : NCBIVPS39 [Mapview hg19]  VPS39 [Mapview hg38]
OMIM612188   
Gene and transcription
Genbank (Entrez)AB018313 AF280814 AF281052 AK025334 AK074193
RefSeq transcript (Entrez)NM_001301138 NM_015289
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)VPS39
Cluster EST : UnigeneHs.88025 [ NCBI ]
CGAP (NCI)Hs.88025
Alternative Splicing GalleryENSG00000166887
Gene ExpressionVPS39 [ NCBI-GEO ]   VPS39 [ EBI - ARRAY_EXPRESS ]   VPS39 [ SEEK ]   VPS39 [ MEM ]
Gene Expression Viewer (FireBrowse)VPS39 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)23339
GTEX Portal (Tissue expression)VPS39
Human Protein AtlasENSG00000166887-VPS39 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ96JC1   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ96JC1  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ96JC1
Splice isoforms : SwissVarQ96JC1
PhosPhoSitePlusQ96JC1
Domaine pattern : Prosite (Expaxy)CHCR (PS50236)    CNH (PS50219)   
Domains : Interpro (EBI)Clathrin_H-chain/VPS_repeat    CNH_dom    VAM6/VPS39    VPS39/TGF_beta_rcpt-assoc_1    VPS39/TGF_beta_rcpt-assoc_2   
Domain families : Pfam (Sanger)CNH (PF00780)    Vps39_1 (PF10366)    Vps39_2 (PF10367)   
Domain families : Pfam (NCBI)pfam00780    pfam10366    pfam10367   
Domain families : Smart (EMBL)CNH (SM00036)  
Conserved Domain (NCBI)VPS39
DMDM Disease mutations23339
Blocks (Seattle)VPS39
SuperfamilyQ96JC1
Human Protein Atlas [tissue]ENSG00000166887-VPS39 [tissue]
Peptide AtlasQ96JC1
HPRD10300
IPIIPI00328236   IPI00332744   
Protein Interaction databases
DIP (DOE-UCLA)Q96JC1
IntAct (EBI)Q96JC1
FunCoupENSG00000166887
BioGRIDVPS39
STRING (EMBL)VPS39
ZODIACVPS39
Ontologies - Pathways
QuickGOQ96JC1
Ontology : AmiGOlysosome  lysosomal membrane  late endosome  intracellular protein transport  autophagy  endosome to lysosome transport  AP-3 adaptor complex  HOPS complex  late endosome membrane  endosomal vesicle fusion  vacuole fusion  late endosome to lysosome transport  retrograde transport, endosome to plasma membrane  
Ontology : EGO-EBIlysosome  lysosomal membrane  late endosome  intracellular protein transport  autophagy  endosome to lysosome transport  AP-3 adaptor complex  HOPS complex  late endosome membrane  endosomal vesicle fusion  vacuole fusion  late endosome to lysosome transport  retrograde transport, endosome to plasma membrane  
NDEx NetworkVPS39
Atlas of Cancer Signalling NetworkVPS39
Wikipedia pathwaysVPS39
Orthology - Evolution
OrthoDB23339
GeneTree (enSembl)ENSG00000166887
Phylogenetic Trees/Animal Genes : TreeFamVPS39
HOVERGENQ96JC1
HOGENOMQ96JC1
Homologs : HomoloGeneVPS39
Homology/Alignments : Family Browser (UCSC)VPS39
Gene fusions - Rearrangements
Fusion : MitelmanCLIC2/VPS39 [Xq28/15q15.1]  [t(X;15)(q28;q15)]  
Fusion: TCGA_MDACCCLIC2 Xq28 VPS39 15q15.1 LUAD
Tumor Fusion PortalVPS39
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerVPS39 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)VPS39
dbVarVPS39
ClinVarVPS39
1000_GenomesVPS39 
Exome Variant ServerVPS39
ExAC (Exome Aggregation Consortium)ENSG00000166887
GNOMAD BrowserENSG00000166887
Genetic variants : HAPMAP23339
Genomic Variants (DGV)VPS39 [DGVbeta]
DECIPHERVPS39 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisVPS39 
Mutations
ICGC Data PortalVPS39 
TCGA Data PortalVPS39 
Broad Tumor PortalVPS39
OASIS PortalVPS39 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICVPS39  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDVPS39
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch VPS39
DgiDB (Drug Gene Interaction Database)VPS39
DoCM (Curated mutations)VPS39 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)VPS39 (select a term)
intoGenVPS39
Cancer3DVPS39(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM612188   
Orphanet
DisGeNETVPS39
MedgenVPS39
Genetic Testing Registry VPS39
NextProtQ96JC1 [Medical]
TSGene23339
GENETestsVPS39
Target ValidationVPS39
Huge Navigator VPS39 [HugePedia]
snp3D : Map Gene to Disease23339
BioCentury BCIQVPS39
ClinGenVPS39
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD23339
Chemical/Pharm GKB GenePA134945163
Clinical trialVPS39
Miscellaneous
canSAR (ICR)VPS39 (select the gene name)
Probes
Litterature
PubMed36 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineVPS39
EVEXVPS39
GoPubMedVPS39
iHOPVPS39
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Nov 21 14:41:25 CET 2017

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