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Aliases for VPS52 Gene

Aliases for VPS52 Gene

  • VPS52, GARP Complex Subunit 2 3
  • SAC2 Suppressor Of Actin Mutations 2-Like Protein 3 4
  • VPS52 GARP Complex Subunit 3 5
  • SACM2L 3 4
  • Vacuolar Protein Sorting 52 Homolog (S. Cerevisiae) 2
  • SAC2 Suppressor Of Actin Mutations 2-Like (Yeast) 2
  • Vacuolar Protein Sorting 52 (Yeast) 2
  • Vacuolar Protein Sorting 52 Homolog 3
  • DJ1033B10.5 3
  • SAC2 3
  • ARE1 3

External Ids for VPS52 Gene

Previous HGNC Symbols for VPS52 Gene

  • SACM2L

Previous GeneCards Identifiers for VPS52 Gene

  • GC06M033210
  • GC06M033264
  • GC06M033326
  • GC06M033218
  • GC06M032960

Summaries for VPS52 Gene

Entrez Gene Summary for VPS52 Gene

  • This gene encodes a protein that is similar to the yeast suppressor of actin mutations 2 gene. The yeast protein forms a subunit of the tetrameric Golgi-associated retrograde protein complex that is involved in vesicle trafficking from from both early and late endosomes, back to the trans-Golgi network. This gene is located on chromosome 6 in a head-to-head orientation with the gene encoding ribosomal protein S18. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]

GeneCards Summary for VPS52 Gene

VPS52 (VPS52, GARP Complex Subunit) is a Protein Coding gene. Among its related pathways are Vesicle-mediated transport and Golgi-to-ER retrograde transport. GO annotations related to this gene include syntaxin binding.

UniProtKB/Swiss-Prot for VPS52 Gene

  • Acts as component of the GARP complex that is involved in retrograde transport from early and late endosomes to the trans-Golgi network (TGN). The GARP complex is required for the maintenance of the cycling of mannose 6-phosphate receptors between the TGN and endosomes, this cycling is necessary for proper lysosomal sorting of acid hydrolases such as CTSD (PubMed:15878329, PubMed:18367545). Acts as component of the EARP complex that is involved in endocytic recycling. The EARP complex associates with Rab4-positive endosomes and promotes recycling of internalized transferrin receptor (TFRC) to the plasma membrane (PubMed:25799061).

Gene Wiki entry for VPS52 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VPS52 Gene

Genomics for VPS52 Gene

Regulatory Elements for VPS52 Gene

Promoters for VPS52 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around VPS52 on UCSC Golden Path with GeneCards custom track

Genomic Location for VPS52 Gene

Chromosome:
6
Start:
33,250,272 bp from pter
End:
33,272,047 bp from pter
Size:
21,776 bases
Orientation:
Minus strand

Genomic View for VPS52 Gene

Genes around VPS52 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VPS52 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VPS52 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

Proteins for VPS52 Gene

  • Protein details for VPS52 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8N1B4-VPS52_HUMAN
    Recommended name:
    Vacuolar protein sorting-associated protein 52 homolog
    Protein Accession:
    Q8N1B4
    Secondary Accessions:
    • A2BF38
    • B0UZZ4
    • B4DNI9
    • Q53GR4
    • Q5JPA0
    • Q5SQW1
    • Q8IUN6
    • Q9NPT5

    Protein attributes for VPS52 Gene

    Size:
    723 amino acids
    Molecular mass:
    82221 Da
    Quaternary structure:
    • Component of the Golgi-associated retrograde protein (GARP) complex, also called VFT (VPS fifty-three) complex, composed of VPS51, VPS52, VPS53 and VPS54 (PubMed:15878329, PubMed:20685960). Component of the endosome-associated retrograde protein (EARP) complex, composed of VPS51, VPS52, VPS53 and VPS50/Syndetin (PubMed:25799061). Interacts with RAB6A and STX10 (PubMed:15878329, PubMed:20685960).
    SequenceCaution:
    • Sequence=CAI95619.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Alternative splice isoforms for VPS52 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VPS52 Gene

Proteomics data for VPS52 Gene at MOPED

Post-translational modifications for VPS52 Gene

  • Ubiquitination at Lys 205
  • Modification sites at PhosphoSitePlus

Other Protein References for VPS52 Gene

Antibody Products

No data available for DME Specific Peptides for VPS52 Gene

Domains & Families for VPS52 Gene

Protein Domains for VPS52 Gene

InterPro:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

Q8N1B4

UniProtKB/Swiss-Prot:

VPS52_HUMAN :
  • Belongs to the VPS52 family.
Family:
  • Belongs to the VPS52 family.
genes like me logo Genes that share domains with VPS52: view

No data available for Gene Families for VPS52 Gene

Function for VPS52 Gene

Molecular function for VPS52 Gene

UniProtKB/Swiss-Prot Function:
Acts as component of the GARP complex that is involved in retrograde transport from early and late endosomes to the trans-Golgi network (TGN). The GARP complex is required for the maintenance of the cycling of mannose 6-phosphate receptors between the TGN and endosomes, this cycling is necessary for proper lysosomal sorting of acid hydrolases such as CTSD (PubMed:15878329, PubMed:18367545). Acts as component of the EARP complex that is involved in endocytic recycling. The EARP complex associates with Rab4-positive endosomes and promotes recycling of internalized transferrin receptor (TFRC) to the plasma membrane (PubMed:25799061).
genes like me logo Genes that share phenotypes with VPS52: view

Animal Models for VPS52 Gene

MGI Knock Outs for VPS52:

Animal Model Products

  • Taconic Biosciences Mouse Models for VPS52

Inhibitory RNA Products

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for VPS52 Gene

Localization for VPS52 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VPS52 Gene

Golgi apparatus, trans-Golgi network membrane; Peripheral membrane protein. Endosome membrane; Peripheral membrane protein. Recycling endosome. Note=Localizes to the trans-Golgi network as part of the GARP complex, while it localizes to recycling endosomes as part of the EARP complex (PubMed:25799061). {ECO:0000269 PubMed:25799061}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for VPS52 Gene COMPARTMENTS Subcellular localization image for VPS52 gene
Compartment Confidence
endosome 5
golgi apparatus 5
cytosol 2
nucleus 2
endoplasmic reticulum 1
lysosome 1
mitochondrion 1
peroxisome 1
plasma membrane 1
vacuole 1

Gene Ontology (GO) - Cellular Components for VPS52 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000938 GARP complex IDA 25799061
genes like me logo Genes that share ontologies with VPS52: view

Pathways & Interactions for VPS52 Gene

genes like me logo Genes that share pathways with VPS52: view

Gene Ontology (GO) - Biological Process for VPS52 Gene

None

No data available for SIGNOR curated interactions for VPS52 Gene

Drugs & Compounds for VPS52 Gene

No Compound Related Data Available

Transcripts for VPS52 Gene

Unigene Clusters for VPS52 Gene

Vacuolar protein sorting 52 homolog (S. cerevisiae):
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for VPS52 Gene

No ASD Table

Relevant External Links for VPS52 Gene

GeneLoc Exon Structure for
VPS52
ECgene alternative splicing isoforms for
VPS52

Expression for VPS52 Gene

mRNA expression in normal human tissues for VPS52 Gene

Protein differential expression in normal tissues from HIPED for VPS52 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (12.7) and Bone (9.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for VPS52 Gene



SOURCE GeneReport for Unigene cluster for VPS52 Gene Hs.480356

genes like me logo Genes that share expression patterns with VPS52: view

Protein tissue co-expression partners for VPS52 Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for VPS52 Gene

Orthologs for VPS52 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for VPS52 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia VPS52 35
  • 90.47 (n)
  • 99.07 (a)
VPS52 36
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia VPS52 35
  • 91.96 (n)
  • 98.61 (a)
VPS52 36
  • 98 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Vps52 35
  • 88.92 (n)
  • 98.61 (a)
Vps52 16
Vps52 36
  • 98 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia VPS52 35
  • 99.9 (n)
  • 100 (a)
VPS52 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Vps52 35
  • 88.25 (n)
  • 98.76 (a)
oppossum
(Monodelphis domestica)
Mammalia -- 36
  • 81 (a)
OneToMany
-- 36
  • 89 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia VPS52 36
  • 76 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vps52 35
  • 69.91 (n)
  • 76.2 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.11507 35
zebrafish
(Danio rerio)
Actinopterygii vps52 35
  • 69.55 (n)
  • 75.58 (a)
vps52 36
  • 72 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009739 35
  • 56.88 (n)
  • 49.45 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG7371 35
  • 57.18 (n)
  • 51.73 (a)
CG7371 36
  • 50 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea vps-52 35
  • 46.75 (n)
  • 36.69 (a)
vps-52 36
  • 35 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VPS52 36
  • 19 (a)
OneToOne
thale cress
(Arabidopsis thaliana)
eudicotyledons POK 35
  • 49.34 (n)
  • 36.69 (a)
rice
(Oryza sativa)
Liliopsida Os03g0417900 35
  • 47.51 (n)
  • 36.85 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.7505 35
sea squirt
(Ciona savignyi)
Ascidiacea CSA.6752 36
  • 47 (a)
OneToOne
Species with no ortholog for VPS52:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • 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)
  • platypus (Ornithorhynchus anatinus)
  • 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)
  • wheat (Triticum aestivum)

Evolution for VPS52 Gene

ENSEMBL:
Gene Tree for VPS52 (if available)
TreeFam:
Gene Tree for VPS52 (if available)

Paralogs for VPS52 Gene

No data available for Paralogs for VPS52 Gene

Variants for VPS52 Gene

Sequence variations from dbSNP and Humsavar for VPS52 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs213199 -- 33,267,978(-) TTCTG(C/T)TGGGC reference, synonymous-codon
rs213200 -- 33,265,612(-) GGAAG(A/G)TTGCT intron-variant
rs213201 -- 33,264,744(-) GCCAC(A/G)AACTC intron-variant
rs213202 -- 33,264,278(-) GGCCA(C/T)GCTAT intron-variant
rs213218 -- 33,255,649(+) atacc(A/G)ggcat intron-variant

Structural Variations from Database of Genomic Variants (DGV) for VPS52 Gene

Variant ID Type Subtype PubMed ID
nsv830634 CNV Loss 17160897
nsv5249 CNV Loss 18451855
nsv830635 CNV Loss 17160897

Variation tolerance for VPS52 Gene

Residual Variation Intolerance Score: 19.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.64; 31.49% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for VPS52 Gene

HapMap Linkage Disequilibrium report
VPS52

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VPS52 Gene

Disorders for VPS52 Gene

Relevant External Links for VPS52

Genetic Association Database (GAD)
VPS52
Human Genome Epidemiology (HuGE) Navigator
VPS52
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
VPS52

No disorders were found for VPS52 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for VPS52 Gene

Publications for VPS52 Gene

  1. Characterization of the human GARP (Golgi associated retrograde protein) complex. (PMID: 15878329) Liewen H. … Stenner-Liewen F. (Exp. Cell Res. 2005) 2 3 4 67
  2. Identification of a novel highly conserved gene in the centromeric part of the major histocompatibility complex. (PMID: 9790748) Walter L. … Guenther E. (Genomics 1998) 2 3 23
  3. EARP is a multisubunit tethering complex involved in endocytic recycling. (PMID: 25799061) Schindler C. … Bonifacino J.S. (Nat. Cell Biol. 2015) 3
  4. Temporal proteomics of NGF-TrkA signaling identifies an inhibitory role for the E3 ligase Cbl-b in neuroblastoma cell differentiation. (PMID: 25921289) Emdal K.B. … Olsen J.V. (Sci Signal 2015) 3
  5. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3

Products for VPS52 Gene

Sources for VPS52 Gene

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