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VPS39 VPS39 subunit of HOPS complex [ Homo sapiens (human) ]

Gene ID: 23339, updated on 7-Apr-2024

Summary

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Official Symbol
VPS39provided by HGNC
Official Full Name
VPS39 subunit of HOPS complexprovided by HGNC
Primary source
HGNC:HGNC:20593
See related
Ensembl:ENSG00000166887 MIM:612188; AllianceGenome:HGNC:20593
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
TLP; VAM6; hVam6p
Summary
This gene encodes a protein that may promote clustering and fusion of late endosomes and lysosomes. The protein may also act as an adaptor protein that modulates the transforming growth factor-beta response by coupling the transforming growth factor-beta receptor complex to the Smad pathway. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]
Expression
Ubiquitous expression in brain (RPKM 16.3), thyroid (RPKM 14.7) and 25 other tissues See more
Orthologs
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Genomic context

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See VPS39 in Genome Data Viewer
Location:
15q15.1
Exon count:
27
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (42158701..42208304, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (39964724..40014333, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (42450899..42500502, complement)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:42372926-42373474 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:42373475-42374022 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:42376405-42377604 Neighboring gene phospholipase A2 group IVD Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:42383636-42384610 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:42385585-42386559 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:42388958-42389458 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6373 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:42438231-42438731 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:42441913-42442700 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:42442839-42442991 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:42446257-42446767 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:42448559-42449274 Neighboring gene phospholipase A2 group IVF Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:42451565-42452064 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9296 Neighboring gene microRNA 627 Neighboring gene VPS39 divergent transcript Neighboring gene transmembrane protein 87A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9297 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9298 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:42565593-42566792 Neighboring gene glucosidase alpha, neutral C Neighboring gene BCL2 interacting protein 3 pseudogene 5

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Functional characterization of TRAP1-like protein involved in modulating fibrotic processes mediated by TGF-β/Smad signaling in hypertrophic scar fibroblasts. Wang X, et al. Exp Cell Res, 2015 Mar 15. PMID 25655281
  2. Effects of TRAP-1-like protein (TLP) gene on collagen synthesis induced by TGF-β/Smad signaling in human dermal fibroblasts. Wang X, et al. PLoS One, 2013. PMID 23418473, Free PMC Article
  3. Merkel cell polyomavirus large T antigen disrupts lysosome clustering by translocating human Vam6p from the cytoplasm to the nucleus. Liu X, et al. J Biol Chem, 2011 May 13. PMID 21454559, Free PMC Article
  4. TLP, a novel modulator of TGF-beta signaling, has opposite effects on Smad2- and Smad3-dependent signaling. Felici A, et al. EMBO J, 2003 Sep 1. PMID 12941698, Free PMC Article
  5. The SARS-CoV-2 accessory protein Orf3a is not an ion channel, but does interact with trafficking proteins. Miller AN, et al. Elife, 2023 Jan 25. PMID 36695574, Free PMC Article

See all (68) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. VPS39-deficiency observed in type 2 diabetes impairs muscle stem cell differentiation via altered autophagy and epigenetics.
    Title: VPS39-deficiency observed in type 2 diabetes impairs muscle stem cell differentiation via altered autophagy and epigenetics.
  2. TLP expression contributes to hypertrophic scar formation and contraction.
    Title: Functional characterization of TRAP1-like protein involved in modulating fibrotic processes mediated by TGF-β/Smad signaling in hypertrophic scar fibroblasts.
  3. TLP likely acts as a molecular modulator capable of altering the balance of Smad3- and Smad2-dependent signaling through regulation of phosphorylation, thus facilitating collagen synthesis in fibroblasts.
    Title: Effects of TRAP-1-like protein (TLP) gene on collagen synthesis induced by TGF-β/Smad signaling in human dermal fibroblasts.
  4. Vps39 knockdown impairs late endosome fusion and fusion between late endosomes and lysosomes.
    Title: The HOPS proteins hVps41 and hVps39 are required for homotypic and heterotypic late endosome fusion.
  5. Merkel cell polyomavirus large T antigen disrupts lysosome clustering by translocating human Vam6p from the cytoplasm to the nucleus
    Title: Merkel cell polyomavirus large T antigen disrupts lysosome clustering by translocating human Vam6p from the cytoplasm to the nucleus.
  6. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
  7. Observational study of gene-disease association. (HuGE Navigator)
    Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
  8. although only TBC1D15/Rab7-GAP altered Rab7-GTP levels, both Rab7-GAP and mVps39 regulate lysosomal morphology and play a role in maintaining growth factor dependence
    Title: Differential effects of TBC1D15 and mammalian Vps39 on Rab7 activation state, lysosomal morphology, and growth factor dependence.
  9. propose that TLP might regulate the balance of Smad2 and Smad3 signaling by localizing Smad4 intracellularly, thus contributing to cellular specificity of TGF-beta transcriptional responses in both normal and pathophysiology
    Title: TLP, a novel modulator of TGF-beta signaling, has opposite effects on Smad2- and Smad3-dependent signaling.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ21681, FLJ46546, KIAA0770

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in autophagosome-lysosome fusion IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in autophagy IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in autophagy IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in endocytic recycling IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in endosomal vesicle fusion IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in endosomal vesicle fusion IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in endosomal vesicle fusion NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in endosome to lysosome transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in intracellular protein transport IEA
Inferred from Electronic Annotation
more info
  
involved_in late endosome to lysosome transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of SNARE complex assembly NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
part_of AP-3 adaptor complex IEA
Inferred from Electronic Annotation
more info
  
part_of HOPS complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of HOPS complex NAS
Non-traceable Author Statement
more info
 PubMed 
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endosome membrane TAS
Traceable Author Statement
more info
  
located_in late endosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in late endosome membrane IDA
Inferred from Direct Assay
more info
 PubMed 
part_of lysosomal HOPS complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in lysosomal membrane HDA PubMed 
located_in lysosomal membrane IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
vam6/Vps39-like protein
Names
TRAP1-like protein
VPS39, HOPS complex subunit
vacuolar protein sorting 39 homolog

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001301138.3 → NP_001288067.1  vam6/Vps39-like protein isoform a

    See identical proteins and their annotated locations for NP_001288067.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    AC036103, AF280814, AF281052, AK074193, DB461120
    Consensus CDS
    CCDS73710.1
    UniProtKB/Swiss-Prot
    O94869, Q71SQ6, Q7Z3V3, Q96B93, Q96JC1, Q96RM0
    Related
    ENSP00000335193.5, ENST00000348544.4
    Conserved Domains (4) summary
    pfam00637
    Location:599 → 746
    Clathrin; Region in Clathrin and VPS
    pfam10366
    Location:460 → 562
    Vps39_1; Vacuolar sorting protein 39 domain 1
    pfam10367
    Location:772 → 879
    Vps39_2; Vacuolar sorting protein 39 domain 2
    cl02434
    Location:20 → 291
    CNH; CNH domain

  2. NM_015289.5 → NP_056104.2  vam6/Vps39-like protein isoform b

    See identical proteins and their annotated locations for NP_056104.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (b) that is shorter than isoform a.
    Source sequence(s)
    AC036103, AF281052, AK074193, DB461120
    Consensus CDS
    CCDS10083.1
    Related
    ENSP00000326534.5, ENST00000318006.10
    Conserved Domains (4) summary
    pfam10366
    Location:449 → 551
    Vps39_1; Vacuolar sorting protein 39 domain 1
    pfam10367
    Location:761 → 868
    Vps39_2; Vacuolar sorting protein 39 domain 2
    cl02434
    Location:20 → 280
    CNH; CNH domain
    cl26078
    Location:650 → 736
    Clathrin; Region in Clathrin and VPS

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    42158701..42208304 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011521404.3 → XP_011519706.1  vam6/Vps39-like protein isoform X2

    Conserved Domains (4) summary
    pfam00637
    Location:588 → 735
    Clathrin; Region in Clathrin and VPS
    pfam10366
    Location:449 → 551
    Vps39_1; Vacuolar sorting protein 39 domain 1
    pfam10367
    Location:761 → 851
    Vps39_2; Vacuolar sorting protein 39 domain 2
    cl02434
    Location:20 → 280
    CNH; CNH domain

  2. XM_011521403.3 → XP_011519705.1  vam6/Vps39-like protein isoform X1

    Conserved Domains (4) summary
    pfam00637
    Location:599 → 746
    Clathrin; Region in Clathrin and VPS
    pfam10366
    Location:460 → 562
    Vps39_1; Vacuolar sorting protein 39 domain 1
    pfam10367
    Location:772 → 862
    Vps39_2; Vacuolar sorting protein 39 domain 2
    cl02434
    Location:20 → 291
    CNH; CNH domain

  3. XM_047432322.1 → XP_047288278.1  vam6/Vps39-like protein isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    39964724..40014333 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054377624.1 → XP_054233599.1  vam6/Vps39-like protein isoform X2

  2. XM_054377623.1 → XP_054233598.1  vam6/Vps39-like protein isoform X1

  3. XM_054377625.1 → XP_054233600.1  vam6/Vps39-like protein isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96JC1.2 GenPept UniProtKB/Swiss-Prot:Q96JC1

Gene LinkOut

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