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Aliases for VPS53 Gene

Aliases for VPS53 Gene

  • Vacuolar Protein Sorting 53 Homolog (S. Cerevisiae) 2 3
  • Vacuolar Protein Sorting-Associated Protein 53 Homolog 3
  • Vacuolar Protein Sorting 53 (Yeast) 2
  • HVps53L 3
  • Pp13624 3
  • HCCS1 3
  • PCH2E 3

External Ids for VPS53 Gene

Previous GeneCards Identifiers for VPS53 Gene

  • GC17M000366
  • GC17M000381

Summaries for VPS53 Gene

Entrez Gene Summary for VPS53 Gene

  • This gene encodes a protein with sequence similarity to the yeast Vps53p protein. Vps53p is involved in retrograde vesicle trafficking in late Golgi. [provided by RefSeq, Jul 2008]

GeneCards Summary for VPS53 Gene

VPS53 (Vacuolar Protein Sorting 53 Homolog (S. Cerevisiae)) is a Protein Coding gene. Diseases associated with VPS53 include pontocerebellar hypoplasia, type 2e and pontocerebellar hypoplasia type 2d.

UniProtKB/Swiss-Prot for VPS53 Gene

  • May be involved in retrograde transport of early and late endosomes to the late Golgi. 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.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VPS53 Gene

Genomics for VPS53 Gene

Regulatory Elements for VPS53 Gene

Genomic Location for VPS53 Gene

508,668 bp from pter
721,717 bp from pter
213,050 bases
Minus strand

Genomic View for VPS53 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for VPS53 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VPS53 Gene

Proteins for VPS53 Gene

  • Protein details for VPS53 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Vacuolar protein sorting-associated protein 53 homolog
    Protein Accession:
    Secondary Accessions:
    • A8K2S8
    • B3FH42
    • Q8WYW3
    • Q9BRR2
    • Q9BY02
    • Q9NV25

    Protein attributes for VPS53 Gene

    699 amino acids
    Molecular mass:
    79653 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.
    • Sequence=AAL55842.1; Type=Frameshift; Positions=562; Evidence={ECO:0000305};

    Alternative splice isoforms for VPS53 Gene


neXtProt entry for VPS53 Gene

Proteomics data for VPS53 Gene at MOPED

Post-translational modifications for VPS53 Gene

  • Ubiquitination at Lys102
  • Modification sites at PhosphoSitePlus

Antibody Products

No data available for DME Specific Peptides for VPS53 Gene

Domains for VPS53 Gene

Protein Domains for VPS53 Gene

Suggested Antigen Peptide Sequences for VPS53 Gene

Graphical View of Domain Structure for InterPro Entry



  • Q5VIR6
  • Belongs to the VPS53 family.
genes like me logo Genes that share domains with VPS53: view

No data available for Gene Families for VPS53 Gene

Function for VPS53 Gene

Molecular function for VPS53 Gene

UniProtKB/Swiss-Prot Function:
May be involved in retrograde transport of early and late endosomes to the late Golgi. 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.

Gene Ontology (GO) - Molecular Function for VPS53 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 15878329
genes like me logo Genes that share ontologies with VPS53: view

Phenotypes for VPS53 Gene

genes like me logo Genes that share phenotypes with VPS53: view

Animal Models for VPS53 Gene

MGI Knock Outs for VPS53:

Animal Model Products

miRNA for VPS53 Gene

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for VPS53

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targeting and HOMER Transcription for VPS53 Gene

Localization for VPS53 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VPS53 Gene

Golgi apparatus, trans-Golgi network membrane; Peripheral membrane protein. Endosome membrane; Peripheral membrane protein.

Subcellular locations from

Jensen Localization Image for VPS53 Gene COMPARTMENTS Subcellular localization image for VPS53 gene
Compartment Confidence
endosome 5
golgi apparatus 5
cytosol 2
nucleus 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for VPS53 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000938 GARP complex IDA 19620288
GO:0005768 endosome --
GO:0005794 Golgi apparatus IDA 15878329
GO:0010008 endosome membrane IEA --
GO:0016020 membrane --
genes like me logo Genes that share ontologies with VPS53: view

Pathways for VPS53 Gene

SuperPathways for VPS53 Gene

No Data Available

Gene Ontology (GO) - Biological Process for VPS53 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0015031 protein transport IEA --
GO:0016192 vesicle-mediated transport --
GO:0042147 retrograde transport, endosome to Golgi IBA --
genes like me logo Genes that share ontologies with VPS53: view

No data available for Pathways by source for VPS53 Gene

Transcripts for VPS53 Gene

Unigene Clusters for VPS53 Gene

Vacuolar protein sorting 53 homolog (S. cerevisiae):
Representative Sequences:

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for VPS53

Primer Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for VPS53 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23a · 23b ^ 24 ^ 25 ^
SP1: - - -
SP2: - - - - -

ExUns: 26

Relevant External Links for VPS53 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for VPS53 Gene

mRNA expression in normal human tissues for VPS53 Gene

Protein differential expression in normal tissues for VPS53 Gene

This gene is overexpressed in Bone (18.7), Peripheral blood mononuclear cells (7.5), and Lymph node (6.8).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for VPS53 Gene

SOURCE GeneReport for Unigene cluster for VPS53 Gene Hs.461819

genes like me logo Genes that share expressions with VPS53: view

Expression partners for VPS53 Gene

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 VPS53 Gene

Orthologs for VPS53 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for VPS53 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia VPS53 35
  • 90.71 (n)
  • 97.43 (a)
VPS53 36
  • 97 (a)
(Canis familiaris)
Mammalia VPS53 35
  • 91.81 (n)
  • 97.8 (a)
VPS53 36
  • 98 (a)
(Mus musculus)
Mammalia Vps53 35
  • 89.45 (n)
  • 96.7 (a)
Vps53 16
Vps53 36
  • 97 (a)
(Pan troglodytes)
Mammalia VPS53 35
  • 99.57 (n)
  • 99.71 (a)
VPS53 36
  • 100 (a)
(Rattus norvegicus)
Mammalia Vps53 35
  • 89.2 (n)
  • 96.45 (a)
(Monodelphis domestica)
Mammalia VPS53 36
  • 95 (a)
(Ornithorhynchus anatinus)
Mammalia VPS53 36
  • 91 (a)
(Gallus gallus)
Aves VPS53 35
  • 82.52 (n)
  • 93.64 (a)
VPS53 36
  • 94 (a)
(Anolis carolinensis)
Reptilia VPS53 36
  • 91 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100496110 35
  • 75.16 (n)
  • 88.97 (a)
(Danio rerio)
Actinopterygii vps53 35
  • 77.87 (n)
  • 90.43 (a)
vps53 36
  • 90 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006623 35
  • 59.2 (n)
  • 54.38 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG3338 35
  • 57.93 (n)
  • 53.72 (a)
CG3338 36
  • 47 (a)
(Caenorhabditis elegans)
Secernentea vps-53 35
  • 49.37 (n)
  • 41.72 (a)
vps-53 36
  • 37 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VPS53 36
  • 21 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons HIT1 35
  • 48.66 (n)
  • 36.6 (a)
(Oryza sativa)
Liliopsida Os01g0906200 35
  • 47.9 (n)
  • 36.31 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU03024 35
  • 47.24 (n)
  • 33.67 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes vps53 35
  • 41.81 (n)
  • 29 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 59 (a)
Species with no ortholog for VPS53:
  • 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)
  • wheat (Triticum aestivum)

Evolution for VPS53 Gene

Gene Tree for VPS53 (if available)
Gene Tree for VPS53 (if available)

Paralogs for VPS53 Gene Pseudogenes for VPS53 Gene

genes like me logo Genes that share paralogs with VPS53: view

No data available for Paralogs for VPS53 Gene

Variants for VPS53 Gene

Sequence variations from dbSNP and Humsavar for VPS53 Gene

SNP ID Clin Chr 17 pos Sequence Context AA Info Type MAF
rs179462 -- 638,632(+) tcagc(A/G)tttgc intron-variant
rs182793 -- 682,320(-) tcttt(C/T)tgctt intron-variant
rs184539 -- 639,058(+) ccaat(A/C)agacg intron-variant
rs186681 -- 629,620(+) tagcc(A/G)ggcgt intron-variant
rs330996 -- 711,141(-) CCTCA(A/T)CCTCC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for VPS53 Gene

Variant ID Type Subtype PubMed ID
nsv907452 CNV Gain 21882294
nsv457627 CNV Gain 19166990
esv2422420 CNV Duplication 17116639
nsv522031 CNV Gain 19592680
dgv924e1 CNV Complex 17122850
nsv428332 CNV Loss 18775914
esv28623 CNV Gain 19812545
esv2715313 CNV Deletion 23290073
esv2052813 CNV Deletion 18987734
esv2715314 CNV Deletion 23290073
esv1004113 CNV Deletion 20482838
esv2715315 CNV Deletion 23290073
esv1545947 CNV Deletion 17803354
esv2715316 CNV Deletion 23290073
esv1753121 CNV Insertion 17803354
esv2540286 CNV Insertion 19546169
esv1159433 CNV Insertion 17803354
esv1679501 CNV Insertion 17803354
esv21577 CNV Loss 19812545
esv2332044 CNV Deletion 18987734
esv2715317 CNV Deletion 23290073
nsv469805 CNV Complex 16826518
esv2715319 CNV Deletion 23290073
esv1467116 CNV Insertion 17803354
esv2715320 CNV Deletion 23290073
esv2715321 CNV Deletion 23290073
esv2715322 CNV Deletion 23290073
esv1350659 CNV Insertion 17803354
esv1749886 CNV Insertion 17803354
nsv111966 CNV Loss 16902084
esv2031997 CNV Deletion 18987734
esv2715323 CNV Deletion 23290073
esv2715324 CNV Deletion 23290073
esv2630451 CNV Deletion 19546169
esv2212170 CNV Deletion 18987734
esv4014 CNV Deletion 18987735
esv997699 CNV Deletion 20482838
esv2715325 CNV Deletion 23290073
esv1520334 CNV Deletion 17803354
esv1357787 CNV Deletion 17803354
esv2715326 CNV Deletion 23290073
esv26118 CNV Gain 19812545
esv2674580 CNV Deletion 23128226
esv1215226 CNV Insertion 17803354
dgv521e199 CNV Deletion 23128226
esv5641 CNV Loss 19470904
esv2715327 CNV Deletion 23290073
esv2661341 CNV Deletion 23128226
nsv9485 CNV Gain 18304495
esv1335456 CNV Deletion 17803354
esv2715328 CNV Deletion 23290073
esv2715330 CNV Deletion 23290073
esv24077 CNV Loss 19812545
esv2715331 CNV Deletion 23290073
esv1395254 CNV Deletion 17803354
esv1392031 CNV Deletion 17803354
esv1712223 CNV Deletion 17803354
nsv1940 CNV Insertion 18451855
nsv457631 CNV Gain 19166990
esv2715332 CNV Deletion 23290073
esv27374 CNV Gain+Loss 19812545
esv1330743 CNV Deletion 17803354
esv2715333 CNV Deletion 23290073
esv1001912 CNV Deletion 20482838
esv1714830 CNV Deletion 17803354
esv2715334 CNV Deletion 23290073
esv1490863 CNV Deletion 17803354
esv2261698 CNV Deletion 18987734
esv2715335 CNV Deletion 23290073
esv2715336 CNV Deletion 23290073
esv2715337 CNV Deletion 23290073
esv2715338 CNV Deletion 23290073
esv2715339 CNV Deletion 23290073
esv2715341 CNV Deletion 23290073
esv2715342 CNV Deletion 23290073
esv2715343 CNV Deletion 23290073
esv2715344 CNV Deletion 23290073
esv2396313 CNV Deletion 18987734
esv2715345 CNV Deletion 23290073
esv2715346 CNV Deletion 23290073
nsv469891 CNV Complex 16826518
esv2715347 CNV Deletion 23290073
esv2662231 CNV Deletion 23128226

Relevant External Links for VPS53 Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VPS53 Gene

Disorders for VPS53 Gene

MalaCards: The human disease database

MalaCards: The human disease database.

Search for VPS53 Gene in MalaCards »

(2) Diseases for VPS53 Gene including...


  • Pontocerebellar hypoplasia 2E (PCH2E) [MIM:615851]: A neurodegenerative disorder characterized by progressive cerebello-cerebral atrophy, profound mental retardation, progressive microcephaly, spasticity, and early-onset epilepsy. {ECO:0000269 PubMed:24577744}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for VPS53

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with VPS53: view

No data available for OMIM , University of Copenhagen DISEASES , Novoseek inferred disease relationships and Genatlas for VPS53 Gene

Publications for VPS53 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
  2. Dual roles of the mammalian GARP complex in tethering and SNARE complex assembly at the trans-golgi network. (PMID: 19620288) PAcrez-Victoria F.J. … Bonifacino J.S. (Mol. Cell. Biol. 2009) 3 23
  3. The minimum LOH region defined on chromosome 17p13.3 in human hepatocellular carcinoma with gene content analysis. (PMID: 12565177) Zhao X. … Gu J. (Cancer Lett. 2003) 3 4
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4

Products for VPS53 Gene

Sources for VPS53 Gene

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