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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 (Yeast) 2
  • Vacuolar Protein Sorting 39 Homolog 3
  • 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

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

Genomics for VPS39 Gene

Regulatory Elements for VPS39 Gene

Enhancers for VPS39 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH15G042286 1.2 ENCODE dbSUPER 5.7 -78.9 -78923 2.3 HNRNPUL1 PKNOX1 FOXA2 MLX ARID4B YY1 CBX5 ZNF143 PPARG TBX21 GANC CAPN3 PLA2G4F VPS39 TMEM87A BNIP3P5
GH15G042401 1.2 Ensembl ENCODE dbSUPER 5 -193.7 -193743 1.6 NFYA L3MBTL2 NR2F1 ETV1 ZBTB40 GABPA POLR2A NFYB NR2C1 ZNF24 GANC TMEM87A ADAL VPS39 GC15P042409 PIR36482 PIR50861
GH15G042165 0.5 ENCODE 11 +43.1 43089 0.2 POLR2A SIN3A CHD7 NR2F2 MIR627 VPS39 CAPN3 PIR62541 GC15M042161 PIR49567
GH15G042403 0.9 ENCODE dbSUPER 5.3 -196.9 -196882 3.6 ATF1 CEBPG RAD21 ZNF644 ATF2 HNF4G ZNF24 HNF4A SMAD4 RXRB GANC CAPN3 TMEM87A ADAL VPS39 PIR36482 GC15P042409 PIR50861
GH15G041931 1.9 FANTOM5 Ensembl ENCODE dbSUPER 1.6 +266.7 266733 19.4 PKNOX1 FOXA2 SIN3A ARID4B GATA2 ZNF207 FOS DEK TBX21 MAFF EHD4 LTK PLA2G4E-AS1 SPTBN5 LOC105370792 MAPKBP1 PLA2G4E RPAP1 TYRO3 OIP5
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around VPS39 on UCSC Golden Path with GeneCards custom track

Promoters for VPS39 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000075736 326 1201 HDGF PKNOX1 ARNT CREB3L1 WRNIP1 ARID4B SIN3A DMAP1 FEZF1 YY1

Genomic Location for VPS39 Gene

Chromosome:
15
Start:
42,158,701 bp from pter
End:
42,208,326 bp from pter
Size:
49,626 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 Lys843
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for VPS39 Gene

Domains & Families for VPS39 Gene

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

No data available for Gene Families for VPS39 Gene

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

Animal Model Products

CRISPR Products

Inhibitory RNA 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.

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:0005737 cytoplasm IEA --
GO:0005764 lysosome IEA --
GO:0005765 lysosomal membrane IDA,IEA 17897319
GO:0005768 endosome IEA --
GO:0005770 late endosome IEA --
genes like me logo Genes that share ontologies with VPS39: view

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:0006810 transport IEA --
GO:0006886 intracellular protein transport IEA --
GO:0006914 autophagy IMP 24554770
GO:0008333 endosome to lysosome transport IMP 25266290
GO:0015031 protein transport 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:

CRISPR Products

Inhibitory RNA Products

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, PaxDb, 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

Primer Products

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 35
  • 99.66 (n)
oppossum
(Monodelphis domestica)
Mammalia VPS39 35
  • 93 (a)
OneToOne
dog
(Canis familiaris)
Mammalia VPS39 34 35
  • 92.76 (n)
cow
(Bos Taurus)
Mammalia VPS39 34 35
  • 92.3 (n)
mouse
(Mus musculus)
Mammalia Vps39 34 16 35
  • 91.05 (n)
rat
(Rattus norvegicus)
Mammalia Vps39 34
  • 89.98 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia VPS39 35
  • 88 (a)
OneToOne
chicken
(Gallus gallus)
Aves VPS39 34 35
  • 82.06 (n)
lizard
(Anolis carolinensis)
Reptilia VPS39 35
  • 93 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii vps39 34 35
  • 75.87 (n)
Dr.18700 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002498 34
  • 53.21 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG7146 36 34 35
  • 49.48 (n)
worm
(Caenorhabditis elegans)
Secernentea vps-39 34 35
  • 43.92 (n)
T08G5.5 36
  • 30 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VAM6 35 37
  • 18 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons EMB2754 34
  • 44.67 (n)
rice
(Oryza sativa)
Liliopsida Os03g0715500 34
  • 44.54 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 47 (a)
OneToOne
bread mold
(Neurospora crassa)
Ascomycetes NCU01539 34
  • 46.09 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes vam6 34
  • 40.65 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.986 34
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)

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 Sequence Context AA Info Type
rs1000119857 -- 42,163,858(+) GGTTT(C/T)TCTTC intron-variant
rs1000283906 -- 42,185,118(+) TTACA(C/T)AAACG intron-variant
rs1000296486 -- 42,177,996(+) TATTA(C/T)TAGAA intron-variant
rs1000308133 -- 42,186,594(+) TATAG(C/T)ATGCA intron-variant
rs1000358329 -- 42,186,373(+) GAGAC(A/G)GAGGC 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)

Relevant External Links for VPS39 Gene

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

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: DISEASES and GeneCards

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

Relevant External Links for VPS39

Genetic Association Database (GAD)
VPS39
Human Genome Epidemiology (HuGE) Navigator
VPS39
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
VPS39
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 J.S. (J. Cell Biol. 2001) 2 3 4 22 64
  2. Characterization of the Mammalian CORVET and HOPS Complexes and Their Modular Restructuring for Endosome Specificity. (PMID: 26463206) van der Kant R. … Neefjes J. (J. Biol. Chem. 2015) 2 3 64
  3. Recruitment of VPS33A to HOPS by VPS16 Is Required for Lysosome Fusion with Endosomes and Autophagosomes. (PMID: 25783203) Wartosch L. … Luzio J.P. (Traffic 2015) 3 4 64
  4. The HOPS proteins hVps41 and hVps39 are required for homotypic and heterotypic late endosome fusion. (PMID: 23167963) Pols M.S. … Klumperman J. (Traffic 2013) 3 4 64
  5. Structural basis of Vps33A recruitment to the human HOPS complex by Vps16. (PMID: 23901104) Graham S.C. … Owen D.J. (Proc. Natl. Acad. Sci. U.S.A. 2013) 3 4 64

Products for VPS39 Gene

Sources for VPS39 Gene

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