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... See more...

Aliases for VPS52 Gene

Aliases for VPS52 Gene

  • VPS52 Subunit Of GARP Complex 2 3 5
  • Vacuolar Protein Sorting-Associated Protein 52 Homolog 3 4
  • SAC2 Suppressor Of Actin Mutations 2-Like Protein 3 4
  • VPS52, GARP Complex Subunit 2 3
  • SACM2L 3 4
  • ARE1 2 3
  • 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
  • VPS52 5
  • SAC2 3

External Ids for VPS52 Gene

Previous HGNC Symbols for VPS52 Gene

  • SACM2L

Previous GeneCards Identifiers for VPS52 Gene

  • GC06M033210
  • GC06M033264
  • GC06M033326
  • GC06M033218
  • GC06M032960
  • GC06M033251
  • GC06M033263

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 Subunit Of GARP Complex) is a Protein Coding gene. Diseases associated with VPS52 include Robinow Syndrome, Autosomal Dominant 2 and Prader-Willi Syndrome. Among its related pathways are Retrograde transport at the Trans-Golgi-Network and Vesicle-mediated transport. Gene Ontology (GO) annotations related to this gene include syntaxin binding.

UniProtKB/Swiss-Prot Summary 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 CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for VPS52 Gene

Genomics for VPS52 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for VPS52 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VPS52 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for VPS52

Top Transcription factor binding sites by QIAGEN in the VPS52 gene promoter:
  • AP-1
  • ATF-2
  • c-Jun
  • ER-alpha
  • HNF-4alpha1
  • Meis-1b
  • Olf-1
  • p53

Genomic Locations for VPS52 Gene

Latest Assembly
chr6:33,250,272-33,272,047
(GRCh38/hg38)
Size:
21,776 bases
Orientation:
Minus strand

Previous Assembly
chr6:33,218,049-33,239,742
(GRCh37/hg19 by Entrez Gene)
Size:
21,694 bases
Orientation:
Minus strand

chr6:33,218,049-33,239,824
(GRCh37/hg19 by Ensembl)
Size:
21,776 bases
Orientation:
Minus strand

Alternative Locations (GRCh38/hg38)

  • chr6(ALT_REF_LOCI_2):4,661,769-4,683,446 (-)
  • chr6(ALT_REF_LOCI_3):4,493,784-4,515,479 (-)
  • chr6(ALT_REF_LOCI_4):4,669,733-4,671,435 (-)
  • chr6(ALT_REF_LOCI_5):4,686,254-4,707,927 (-)
  • chr6(ALT_REF_LOCI_6):4,444,672-4,466,382 (-)
  • chr6(ALT_REF_LOCI_7):4,698,976-4,720,646 (-)

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:27440922, PubMed:15878329, PubMed:20685960). Component of the endosome-associated retrograde protein (EARP) complex, composed of VPS51, VPS52, VPS53 and VPS50/Syndetin (PubMed:25799061, PubMed:27440922). EIPR1 interacts with both EARP and GARP complexes and mediates the recruitment of the GARP complex to the trans-Golgi network (PubMed:27440922). Interacts with RAB6A and STX10 (PubMed:15878329, PubMed:20685960). Interacts with UHRF1BP1L (PubMed:20163565).
    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

Post-translational modifications for VPS52 Gene

  • Ubiquitination at Lys205
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for VPS52 Gene

Domains & Families for VPS52 Gene

Protein Domains for VPS52 Gene

InterPro:

Suggested Antigen Peptide Sequences for VPS52 Gene

GenScript: Design optimal peptide antigens:
  • Vacuolar protein sorting 52 (S. cerevisiae) (B0UYQ4_HUMAN)
  • cDNA FLJ54452, highly similar to Vacuolar protein sorting protein 52 (B4DNI9_HUMAN)
  • cDNA FLJ55499, highly similar to Vacuolar protein sorting protein 52 (B4DS44_HUMAN)
  • ARE1 protein (Q7LA74_HUMAN)
  • SAC2 suppressor of actin mutations 2-like protein (VPS52_HUMAN)

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

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).

Phenotypes From GWAS Catalog for VPS52 Gene

Gene Ontology (GO) - Molecular Function for VPS52 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 15878329
GO:0019905 syntaxin binding IPI 15878329
GO:0031267 small GTPase binding IBA --
genes like me logo Genes that share ontologies with VPS52: view
genes like me logo Genes that share phenotypes with VPS52: view

Animal Models for VPS52 Gene

MGI Knock Outs for VPS52:

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VPS52

No data available for Enzyme Numbers (IUBMB) , 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
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 VPS52 gene
Compartment Confidence
endosome 5
golgi apparatus 5
cytosol 3
plasma membrane 2
mitochondrion 2
peroxisome 2
nucleus 2
endoplasmic reticulum 2
lysosome 2
extracellular 1
cytoskeleton 1

Gene Ontology (GO) - Cellular Components for VPS52 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000938 GARP complex IBA,IDA 25799061
GO:0005768 endosome IEA --
GO:0005794 Golgi apparatus IEA,IDA 15878329
GO:0005829 cytosol IEA --
GO:0010008 endosome membrane IEA --
genes like me logo Genes that share ontologies with VPS52: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for VPS52 Gene

Pathways & Interactions for VPS52 Gene

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

Gene Ontology (GO) - Biological Process for VPS52 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006896 Golgi to vacuole transport IBA 21873635
GO:0007041 lysosomal transport IBA,IDA 25799061
GO:0010668 ectodermal cell differentiation IEA --
GO:0015031 protein transport IEA --
GO:0032456 endocytic recycling IBA,IMP 25799061
genes like me logo Genes that share ontologies with VPS52: view

No data available for SIGNOR curated interactions for VPS52 Gene

Drugs & Compounds for VPS52 Gene

No Compound Related Data Available

Transcripts for VPS52 Gene

mRNA/cDNA for VPS52 Gene

4 REFSEQ mRNAs :
19 NCBI additional mRNA sequence :
11 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VPS52

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

No ASD Table

Relevant External Links for VPS52 Gene

GeneLoc Exon Structure for
VPS52

Expression for VPS52 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE 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, MaxQB, and MOPED for VPS52 Gene



Protein tissue co-expression partners for VPS52 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for VPS52

SOURCE GeneReport for Unigene cluster for VPS52 Gene:

Hs.480356

Evidence on tissue expression from TISSUES for VPS52 Gene

  • Nervous system(4.9)
  • Liver(4.6)
  • Intestine(4.5)
  • Skin(3.6)
  • Muscle(3)
  • Kidney(2.9)
  • Heart(2.4)
  • Lung(2.2)
  • Stomach(2.1)
  • Blood(2.1)
genes like me logo Genes that share expression patterns with VPS52: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
Chimpanzee
(Pan troglodytes)
Mammalia VPS52 29 30
  • 99.9 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia VPS52 29 30
  • 91.96 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia VPS52 29 30
  • 90.47 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia -- 30
  • 89 (a)
OneToMany
-- 30
  • 81 (a)
OneToMany
Mouse
(Mus musculus)
Mammalia Vps52 29 16 30
  • 88.92 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Vps52 29
  • 88.25 (n)
Lizard
(Anolis carolinensis)
Reptilia VPS52 30
  • 76 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia vps52 29
  • 69.91 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.11507 29
Zebrafish
(Danio rerio)
Actinopterygii vps52 29 30
  • 69.55 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta CG7371 29 30
  • 57.18 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009739 29
  • 56.88 (n)
Worm
(Caenorhabditis elegans)
Secernentea vps-52 29 30
  • 46.75 (n)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VPS52 30
  • 19 (a)
OneToOne
Thale Cress
(Arabidopsis thaliana)
eudicotyledons POK 29
  • 49.34 (n)
Rice
(Oryza sativa)
Liliopsida Os03g0417900 29
  • 47.51 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.6752 30
  • 47 (a)
OneToOne
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.7505 29
Species where no ortholog for VPS52 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
Aminode:
Evolutionary constrained regions (ECRs) for VPS52: view image
Alliance of Genome Resources:
Additional Orthologs for VPS52

Paralogs for VPS52 Gene

No data available for Paralogs for VPS52 Gene

Variants for VPS52 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for VPS52 Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
rs114441919 Benign: not provided 33,264,910(-) T/A
NM_022553.6(VPS52):c.1282-10A>T
INTRON
rs141154095 Benign: not provided 33,266,665(-) G/A
NM_022553.6(VPS52):c.1173C>T (p.Asp391=)
SYNONYMOUS
rs34933266 Benign: not provided 33,266,677(-) G/A
NM_022553.6(VPS52):c.1161C>T (p.Tyr387=)
SYNONYMOUS

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for VPS52 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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

Variant ID Type Subtype PubMed ID
dgv10609n54 CNV loss 21841781
nsv1073969 CNV deletion 25765185
nsv1112900 CNV deletion 24896259
nsv1119076 CNV deletion 24896259
nsv5249 CNV deletion 18451855
nsv830634 CNV loss 17160897
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)

Additional Variant Information for VPS52 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
VPS52
Leiden Open Variation Database (LOVD)
VPS52

SNP Genotyping and Copy Number Assays for research

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

Disorders for VPS52 Gene

MalaCards: The human disease database

(2) MalaCards diseases for VPS52 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
robinow syndrome, autosomal dominant 2
  • drs2
prader-willi syndrome
  • pws
- elite association - COSMIC cancer census association via MalaCards
Search VPS52 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for VPS52

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with VPS52: view

No data available for 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 (Experimental cell research 2005) 2 3 4
  2. Identification of a novel highly conserved gene in the centromeric part of the major histocompatibility complex. (PMID: 9790748) Walter L … Günther E (Genomics 1998) 2 3 22
  3. TSSC1 is novel component of the endosomal retrieval machinery. (PMID: 27440922) Gershlick DC … Bonifacino JS (Molecular biology of the cell 2016) 3 4
  4. EARP is a multisubunit tethering complex involved in endocytic recycling. (PMID: 25799061) Schindler C … Bonifacino JS (Nature cell biology 2015) 3 4
  5. A novel syntaxin 6-interacting protein, SHIP164, regulates syntaxin 6-dependent sorting from early endosomes. (PMID: 20163565) Otto GP … Tooze SA (Traffic (Copenhagen, Denmark) 2010) 3 4

Products for VPS52 Gene

Sources for VPS52 Gene