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Aliases for VPS39 Gene

Aliases for VPS39 Gene

  • VPS39, HOPS Complex Subunit 2 3 5
  • TRAP1-Like Protein 3 4
  • HVam6p 3 4
  • VAM6 3 4
  • TLP 3 4
  • Vacuolar Protein Sorting 39 Homolog (S. Cerevisiae) 2
  • Vacuolar Protein Sorting 39 Homolog 3
  • Vacuolar Protein Sorting 39 (Yeast) 2
  • Vam6/Vps39-Like Protein 3
  • KIAA0770 4

External Ids for VPS39 Gene

Previous GeneCards Identifiers for VPS39 Gene

  • GC15M037818
  • GC15M035346
  • GC15M040030
  • GC15M040166
  • GC15M040238
  • GC15M042450
  • GC15M019299

Summaries for VPS39 Gene

Entrez Gene Summary for VPS39 Gene

  • 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]

GeneCards Summary for VPS39 Gene

VPS39 (VPS39, HOPS Complex Subunit) is a Protein Coding gene. Diseases associated with VPS39 include Arthrogryposis, Renal Dysfunction, And Cholestasis 1. An important paralog of this gene is TGFBRAP1.

UniProtKB/Swiss-Prot for VPS39 Gene

  • Regulator of TGF-beta/activin signaling, inhibiting SMAD3- and activating SMAD2-dependent transcription. Acts by interfering with SMAD3/SMAD4 complex formation, this would lead to inhibition of SMAD3-dependent transcription and relieve SMAD3 inhibition of SMAD2-dependent promoters, thus increasing SMAD2-dependent transcription. Does not affect TGF-beta-induced SMAD2 or SMAD3 phosphorylation, nor SMAD2/SMAD4 complex formation.

  • Plays a role in vesicle-mediated protein trafficking to lysosomal compartments including the endocytic membrane transport and autophagic pathways. Believed to act in part as a component of the putative HOPS endosomal tethering complex which is proposed to be involved in the Rab5-to-Rab7 endosome conversion probably implicating MON1A/B, and via binding SNAREs and SNARE complexes to mediate tethering and docking events during SNARE-mediated membrane fusion. The HOPS complex is proposed to be recruited to Rab7 on the late endosomal membrane and to regulate late endocytic, phagocytic and autophagic traffic towards lysosomes (PubMed:23351085). Involved in homotypic vesicle fusions between late endosomes and in heterotypic fusions between late endosomes and lysosomes (PubMed:11448994, PubMed:23351085, PubMed:23167963). Required for fusion of endosomes and autophagosomes with lysosomes (PubMed:25783203).

Gene Wiki entry for VPS39 Gene

Additional gene information for VPS39 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VPS39 Gene

Genomics for VPS39 Gene

GeneHancer (GH) Regulatory Elements for VPS39 Gene

Promoters and enhancers for VPS39 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH15J042206 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 650.7 +0.3 317 2.1 HDGF PKNOX1 ATF1 SMAD1 ARID4B SIN3A DMAP1 ZNF48 YY1 POLR2B VPS39 LOC105370795 GANC TMEM87A MIR627
GH15J041772 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 21.8 +432.3 432328 6.4 DMAP1 IRF4 YY1 SLC30A9 ZNF213 ZNF143 SP3 NFYC SSRP1 ZNF610 MAPKBP1 JMJD7 MGA CDAN1 SPTBN5 VPS39 INO80 ENSG00000260814 JMJD7-PLA2G4B ENSG00000250379
GH15J041330 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 19.3 +875.3 875331 4.1 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 OIP5 NUSAP1 NDUFAF1 DNAJC17 ENSG00000259211 INO80 LOC105370795 GANC VPS39 BAHD1
GH15J041492 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 15.2 +713.5 713506 5.1 FOXA2 ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 POLR2B ZNF766 ITPKA NDUFAF1 MGA INO80 DNAJC17 RPAP1 RTF1 RAD51-AS1 VPS39 LOC105370795
GH15J041659 Promoter/Enhancer 1.9 FANTOM5 Ensembl ENCODE 19.3 +547.3 547306 3.6 HDGF PKNOX1 SMAD1 FOXA2 MLX ZFP64 ARID4B SIN3A FEZF1 DMAP1 INO80 MGA DNAJC17 JMJD7 RAD51-AS1 LRRC57 LOC105370795 GANC ENSG00000260814 VPS39
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VPS39 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the VPS39 gene promoter:
  • FOXJ2 (long isoform)
  • FOXJ2
  • c-Ets-1
  • RORalpha2
  • AML1a
  • FOXO1
  • FOXO1a
  • RP58
  • HTF
  • En-1

Genomic Locations for VPS39 Gene

Genomic Locations for VPS39 Gene
chr15:42,158,701-42,208,326
(GRCh38/hg38)
Size:
49,626 bases
Orientation:
Minus strand
chr15:42,450,899-42,500,514
(GRCh37/hg19)
Size:
49,616 bases
Orientation:
Minus strand

Genomic View for VPS39 Gene

Genes around VPS39 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VPS39 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VPS39 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VPS39 Gene

Proteins for VPS39 Gene

  • Protein details for VPS39 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96JC1-VPS39_HUMAN
    Recommended name:
    Vam6/Vps39-like protein
    Protein Accession:
    Q96JC1
    Secondary Accessions:
    • O94869
    • Q71SQ6
    • Q7Z3V3
    • Q96B93
    • Q96RM0

    Protein attributes for VPS39 Gene

    Size:
    886 amino acids
    Molecular mass:
    101809 Da
    Quaternary structure:
    • Homooligomer (PubMed:11448994). Interacts with TGFBR2 and, less efficiently, with TGFBR1; interaction with TGFBR2 is independent of the receptor kinase activity and of the presence of TGF-beta. Also interacts with ACVR2B, but not with BMPR2. Interacts with SMAD4, preferentially following TGF-beta treatment. Does not interact with SAMD2 or SMAD3 (PubMed:12941698). Component of the putative homotypic fusion and vacuole protein sorting (HOPS) complex; the core of which composed of the class C Vps proteins VPS11, VPS16, VPS18 and VPS33A, is associated with VPS39 and VPS41 (PubMed:23351085, PubMed:23901104, PubMed:25908847). Interacts with PLEKHM2; involved in VPS39 recruitment to ARL8B-containing lysosomes (PubMed:25908847). Associates with adaptor protein complex 3 (AP-3) and clathrin:AP-3 complexes (By similarity).
    SequenceCaution:
    • Sequence=BAA34490.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for VPS39 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VPS39 Gene

Post-translational modifications for VPS39 Gene

  • Ubiquitination at posLast=843843
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for VPS39 Gene

Domains & Families for VPS39 Gene

Gene Families for VPS39 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for VPS39 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q96JC1

UniProtKB/Swiss-Prot:

VPS39_HUMAN :
  • Belongs to the VAM6/VPS39 family.
Family:
  • Belongs to the VAM6/VPS39 family.
genes like me logo Genes that share domains with VPS39: view

Function for VPS39 Gene

Molecular function for VPS39 Gene

UniProtKB/Swiss-Prot Function:
Regulator of TGF-beta/activin signaling, inhibiting SMAD3- and activating SMAD2-dependent transcription. Acts by interfering with SMAD3/SMAD4 complex formation, this would lead to inhibition of SMAD3-dependent transcription and relieve SMAD3 inhibition of SMAD2-dependent promoters, thus increasing SMAD2-dependent transcription. Does not affect TGF-beta-induced SMAD2 or SMAD3 phosphorylation, nor SMAD2/SMAD4 complex formation.
UniProtKB/Swiss-Prot Function:
Plays a role in vesicle-mediated protein trafficking to lysosomal compartments including the endocytic membrane transport and autophagic pathways. Believed to act in part as a component of the putative HOPS endosomal tethering complex which is proposed to be involved in the Rab5-to-Rab7 endosome conversion probably implicating MON1A/B, and via binding SNAREs and SNARE complexes to mediate tethering and docking events during SNARE-mediated membrane fusion. The HOPS complex is proposed to be recruited to Rab7 on the late endosomal membrane and to regulate late endocytic, phagocytic and autophagic traffic towards lysosomes (PubMed:23351085). Involved in homotypic vesicle fusions between late endosomes and in heterotypic fusions between late endosomes and lysosomes (PubMed:11448994, PubMed:23351085, PubMed:23167963). Required for fusion of endosomes and autophagosomes with lysosomes (PubMed:25783203).

Phenotypes From GWAS Catalog for VPS39 Gene

genes like me logo Genes that share phenotypes with VPS39: view

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for VPS39 Gene

Localization for VPS39 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VPS39 Gene

Cytoplasm. Lysosome membrane; Peripheral membrane protein. Late endosome membrane; Peripheral membrane protein. Late endosome. Lysosome. Note=Colocalizes with TGFBR1 and TGFBR2 in cytoplasmic vesicular structures and most prominently in cortical vesicles. {ECO:0000269 PubMed:12941698}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for VPS39 gene
Compartment Confidence
lysosome 5
endosome 5
nucleus 2
cytosol 2
peroxisome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for VPS39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005737 cytoplasm IEA --
GO:0005764 lysosome IEA --
GO:0005765 lysosomal membrane IDA,IEA 23167963
GO:0005768 endosome IEA --
genes like me logo Genes that share ontologies with VPS39: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for VPS39 Gene

Pathways & Interactions for VPS39 Gene

SuperPathways for VPS39 Gene

No Data Available

Gene Ontology (GO) - Biological Process for VPS39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006886 intracellular protein transport IEA --
GO:0006914 autophagy IMP 24554770
GO:0008333 endosome to lysosome transport IMP 25266290
GO:0015031 protein transport IEA --
GO:0016192 vesicle-mediated transport IBA,IEA --
genes like me logo Genes that share ontologies with VPS39: view

No data available for Pathways by source and SIGNOR curated interactions for VPS39 Gene

Drugs & Compounds for VPS39 Gene

No Compound Related Data Available

Transcripts for VPS39 Gene

Unigene Clusters for VPS39 Gene

Vacuolar protein sorting 39 homolog (S. cerevisiae):
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for VPS39 Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16a · 16b ^ 17 ^ 18 ^ 19a · 19b ^ 20a · 20b ^ 21 ^
SP1: - - - -
SP2: -
SP3:
SP4:
SP5:
SP6:
SP7:

ExUns: 22a · 22b ^ 23a · 23b ^ 24a · 24b ^ 25a · 25b
SP1: -
SP2: -
SP3:
SP4:
SP5:
SP6:
SP7:

Relevant External Links for VPS39 Gene

GeneLoc Exon Structure for
VPS39
ECgene alternative splicing isoforms for
VPS39

Expression for VPS39 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for VPS39 Gene

Protein differential expression in normal tissues from HIPED for VPS39 Gene

This gene is overexpressed in Lymph node (13.9) and Peripheral blood mononuclear cells (12.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for VPS39 Gene



Protein tissue co-expression partners for VPS39 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of VPS39 Gene:

VPS39

SOURCE GeneReport for Unigene cluster for VPS39 Gene:

Hs.88025

mRNA Expression by UniProt/SwissProt for VPS39 Gene:

Q96JC1-VPS39_HUMAN
Tissue specificity: Widely expressed, with highest levels in heart, skeletal muscle, kidney, pancreas, brain, placenta and spleen.

Evidence on tissue expression from TISSUES for VPS39 Gene

  • Nervous system(4.7)
  • Lung(4.3)
  • Skin(2.1)
genes like me logo Genes that share expression patterns with VPS39: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for VPS39 Gene

Orthologs for VPS39 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for VPS39 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VPS39 34 33
  • 99.66 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia VPS39 34
  • 93 (a)
OneToOne
dog
(Canis familiaris)
Mammalia VPS39 34 33
  • 92.76 (n)
OneToOne
cow
(Bos Taurus)
Mammalia VPS39 34 33
  • 92.3 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Vps39 16 34 33
  • 91.05 (n)
rat
(Rattus norvegicus)
Mammalia Vps39 33
  • 89.98 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia VPS39 34
  • 88 (a)
OneToOne
chicken
(Gallus gallus)
Aves VPS39 34 33
  • 82.06 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia VPS39 34
  • 93 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii vps39 34 33
  • 75.87 (n)
OneToOne
Dr.18700 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002498 33
  • 53.21 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG7146 34 35 33
  • 49.48 (n)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea vps-39 34 33
  • 43.92 (n)
OneToMany
T08G5.5 35
  • 30 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VAM6 36 34
  • 18 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons EMB2754 33
  • 44.67 (n)
rice
(Oryza sativa)
Liliopsida Os03g0715500 33
  • 44.54 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 47 (a)
OneToOne
Cin.986 33
bread mold
(Neurospora crassa)
Ascomycetes NCU01539 33
  • 46.09 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes vam6 33
  • 40.65 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.986 33
Species where no ortholog for VPS39 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for VPS39 Gene

ENSEMBL:
Gene Tree for VPS39 (if available)
TreeFam:
Gene Tree for VPS39 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for VPS39: view image

Paralogs for VPS39 Gene

Paralogs for VPS39 Gene

genes like me logo Genes that share paralogs with VPS39: view

Variants for VPS39 Gene

Sequence variations from dbSNP and Humsavar for VPS39 Gene

SNP ID Clin Chr 15 pos Variation AA Info Type
rs1000119857 -- 42,163,858(-) T/C intron_variant
rs1000283906 -- 42,185,118(-) C/T intron_variant
rs1000296486 -- 42,177,996(-) C/A/T intron_variant
rs1000308133 -- 42,186,594(-) T/C intron_variant
rs1000358329 -- 42,186,373(-) G/A intron_variant

Structural Variations from Database of Genomic Variants (DGV) for VPS39 Gene

Variant ID Type Subtype PubMed ID
nsv1054102 CNV gain 25217958
nsv1507 CNV insertion 18451855
nsv471683 CNV gain+loss 15918152
nsv832985 CNV loss 17160897
nsv9245 CNV gain 18304495
nsv952614 CNV deletion 24416366

Variation tolerance for VPS39 Gene

Residual Variation Intolerance Score: 15.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.63; 45.37% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VPS39 Gene

Human Gene Mutation Database (HGMD)
VPS39
SNPedia medical, phenotypic, and genealogical associations of SNPs for
VPS39

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VPS39 Gene

Disorders for VPS39 Gene

MalaCards: The human disease database

(1) MalaCards diseases for VPS39 Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
arthrogryposis, renal dysfunction, and cholestasis 1
  • arcs1
- elite association - COSMIC cancer census association via MalaCards
Search VPS39 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for VPS39

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with VPS39: view

No data available for UniProtKB/Swiss-Prot and Genatlas for VPS39 Gene

Publications for VPS39 Gene

  1. Human Vam6p promotes lysosome clustering and fusion in vivo. (PMID: 11448994) Caplan S … Bonifacino JS (The Journal of cell biology 2001) 2 3 4 22 58
  2. Characterization of the Mammalian CORVET and HOPS Complexes and Their Modular Restructuring for Endosome Specificity. (PMID: 26463206) van der Kant R … Neefjes J (The Journal of biological chemistry 2015) 2 3 58
  3. Recruitment of VPS33A to HOPS by VPS16 Is Required for Lysosome Fusion with Endosomes and Autophagosomes. (PMID: 25783203) Wartosch L … Luzio JP (Traffic (Copenhagen, Denmark) 2015) 3 4 58
  4. Structural basis of Vps33A recruitment to the human HOPS complex by Vps16. (PMID: 23901104) Graham SC … Owen DJ (Proceedings of the National Academy of Sciences of the United States of America 2013) 3 4 58
  5. The HOPS proteins hVps41 and hVps39 are required for homotypic and heterotypic late endosome fusion. (PMID: 23167963) Pols MS … Klumperman J (Traffic (Copenhagen, Denmark) 2013) 3 4 58

Products for VPS39 Gene

Sources for VPS39 Gene

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