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VPS39 (VPS39 subunit of HOPS complex)

Identity

Alias (NCBI)TLP
VAM6
hVam6p
HGNC (Hugo) VPS39
HGNC Alias symbKIAA0770
VAM6
HGNC Previous namevacuolar protein sorting 39 (yeast)
 vacuolar protein sorting 39 homolog (S. cerevisiae)
 VPS39, HOPS complex subunit
LocusID (NCBI) 23339
Atlas_Id 42957
Location 15q15.1  [Link to chromosome band 15q15]
Location_base_pair Starts at 42158711 and ends at 42208304 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    VPS39 subunit of HOPS complex
AliasesTLP; VAM6; hVam6p
GeneCards (Weizmann)VPS39
Ensembl hg19 (Hinxton)ENSG00000166887 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000166887 [Gene_View]  ENSG00000166887 [Sequence]  chr15:42158711-42208304 [Contig_View]  VPS39 [Vega]
ICGC DataPortalENSG00000166887
TCGA cBioPortalVPS39
AceView (NCBI)VPS39
Genatlas (Paris)VPS39
SOURCE (Princeton)VPS39
Genetics Home Reference (NIH)VPS39
Genomic and cartography
GoldenPath hg38 (UCSC)VPS39  -     chr15:42158711-42208304 -  15q15.1   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)VPS39  -     15q15.1   [Description]    (hg19-Feb_2009)
GoldenPathVPS39 - 15q15.1 [CytoView hg19]  VPS39 - 15q15.1 [CytoView hg38]
ImmunoBaseENSG00000166887
Genome Data Viewer NCBIVPS39 [Mapview hg19]  
OMIM612188   
Gene and transcription
Genbank (Entrez)AB018313 AF280814 AF281052 AK025334 AK074193
RefSeq transcript (Entrez)NM_001301138 NM_015289
Consensus coding sequences : CCDS (NCBI)VPS39
Gene ExpressionVPS39 [ NCBI-GEO ]   VPS39 [ EBI - ARRAY_EXPRESS ]   VPS39 [ SEEK ]   VPS39 [ MEM ]
Gene Expression Viewer (FireBrowse)VPS39 [ Firebrowse - Broad ]
GenevisibleExpression of VPS39 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
PhosPhoSitePlusQ96JC1
Domaine pattern : Prosite (Expaxy)CHCR (PS50236)    CNH (PS50219)   
Domains : Interpro (EBI)Clathrin_H-chain/VPS_repeat    CNH_dom    Vam6/VPS39/TRAP1    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
PDB (RSDB)6ZE9   
PDB Europe6ZE9   
PDB (PDBSum)6ZE9   
PDB (IMB)6ZE9   
Structural Biology KnowledgeBase6ZE9   
SCOP (Structural Classification of Proteins)6ZE9   
CATH (Classification of proteins structures)6ZE9   
SuperfamilyQ96JC1
AlphaFold pdb e-kbQ96JC1   
Human Protein Atlas [tissue]ENSG00000166887-VPS39 [tissue]
HPRD10300
Protein Interaction databases
DIP (DOE-UCLA)Q96JC1
IntAct (EBI)Q96JC1
BioGRIDVPS39
STRING (EMBL)VPS39
ZODIACVPS39
Ontologies - Pathways
QuickGOQ96JC1
Ontology : AmiGOprotein binding  cytoplasm  lysosomal membrane  lysosomal membrane  late endosome  intracellular protein transport  autophagy  autophagy  endosome to lysosome transport  membrane  AP-3 adaptor complex  HOPS complex  late endosome membrane  endocytic recycling  endosomal vesicle fusion  endosomal vesicle fusion  autophagosome-lysosome fusion  lysosomal HOPS complex  late endosome to lysosome transport  
Ontology : EGO-EBIprotein binding  cytoplasm  lysosomal membrane  lysosomal membrane  late endosome  intracellular protein transport  autophagy  autophagy  endosome to lysosome transport  membrane  AP-3 adaptor complex  HOPS complex  late endosome membrane  endocytic recycling  endosomal vesicle fusion  endosomal vesicle fusion  autophagosome-lysosome fusion  lysosomal HOPS complex  late endosome to lysosome transport  
NDEx NetworkVPS39
Atlas of Cancer Signalling NetworkVPS39
Wikipedia pathwaysVPS39
Orthology - Evolution
OrthoDB23339
GeneTree (enSembl)ENSG00000166887
Phylogenetic Trees/Animal Genes : TreeFamVPS39
Homologs : HomoloGeneVPS39
Homology/Alignments : Family Browser (UCSC)VPS39
Gene fusions - Rearrangements
Fusion : MitelmanCLIC2/VPS39 [Xq28/15q15.1]  
Fusion : QuiverVPS39
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerVPS39 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)VPS39
dbVarVPS39
ClinVarVPS39
MonarchVPS39
1000_GenomesVPS39 
Exome Variant ServerVPS39
GNOMAD BrowserENSG00000166887
Varsome BrowserVPS39
ACMGVPS39 variants
VarityQ96JC1
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]  
Somatic Mutations in Cancer : COSMIC3DVPS39
Mutations and Diseases : HGMDVPS39
LOVD (Leiden Open Variation Database)[gene] [transcripts] [variants]
BioMutaVPS39
DgiDB (Drug Gene Interaction Database)VPS39
DoCM (Curated mutations)VPS39
CIViC (Clinical Interpretations of Variants in Cancer)VPS39
Cancer3DVPS39
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM612188   
Orphanet
DisGeNETVPS39
MedgenVPS39
Genetic Testing Registry VPS39
NextProtQ96JC1 [Medical]
GENETestsVPS39
Target ValidationVPS39
Huge Navigator VPS39 [HugePedia]
ClinGenVPS39
Clinical trials, drugs, therapy
MyCancerGenomeVPS39
Protein Interactions : CTDVPS39
Pharm GKB GenePA134945163
PharosQ96JC1
Clinical trialVPS39
Miscellaneous
canSAR (ICR)VPS39
HarmonizomeVPS39
DataMed IndexVPS39
Probes
Litterature
PubMed52 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
EVEXVPS39
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Mon Oct 4 15:38:06 CEST 2021

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