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

    Gene ID: 23339, updated on 3-Nov-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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (42158701..42208304, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (39964724..40014333, complement)
    RS_2024_09 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 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. 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
    2. 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
    3. 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
    4. 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
    5. VPS39-deficiency observed in type 2 diabetes impairs muscle stem cell differentiation via altered autophagy and epigenetics. Davegårdh C, et al. Nat Commun, 2021 Apr 23. PMID 33893273, Free PMC Article

    See all (76) 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_2024_08

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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