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Aliases for VPS54 Gene

Aliases for VPS54 Gene

  • VPS54, GARP Complex Subunit 2 3
  • Hepatocellular Carcinoma Protein 8 3 4
  • VPS54 GARP Complex Subunit 3 5
  • Tumor Antigen HOM-HCC-8 3 4
  • Tumor Antigen SLP-8p 3 4
  • HCC8 3 4
  • Vacuolar Protein Sorting 54 Homolog (S. Cerevisiae) 2
  • Protein Phosphatase 1, Regulatory Subunit 164 3
  • Vacuolar Protein Sorting 54 (Yeast) 2
  • Vacuolar Protein Sorting 54 Homolog 3
  • Regulatory Subunit 164 2
  • Protein Phosphatase 1 2
  • PPP1R164 3
  • HVps54L 3
  • VPS54L 3
  • SLP-8p 3
  • WR 3

External Ids for VPS54 Gene

Previous GeneCards Identifiers for VPS54 Gene

  • GC02M064076
  • GC02M064093
  • GC02M064094
  • GC02M064031
  • GC02M063973
  • GC02M064119
  • GC02M063859

Summaries for VPS54 Gene

Entrez Gene Summary for VPS54 Gene

  • This gene encodes for a protein that in yeast forms part of a trimeric vacuolar-protein-sorting complex that is required for retrograde transport of proteins from prevacuoles to the late Golgi compartment. As in yeast, mammalian Vps54 proteins contain a coiled-coil region and dileucine motifs. Alternative splicing results in multiple transcript variants encoding different isoforms [provided by RefSeq, Jul 2008]

GeneCards Summary for VPS54 Gene

VPS54 (VPS54, GARP Complex Subunit) is a Protein Coding gene. Diseases associated with VPS54 include amyotrophic lateral sclerosis 1. 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 VPS54 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:18367545). Within the GARP complex, required to tether the complex to the TGN. Not involved in endocytic recycling (PubMed:25799061).

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VPS54 Gene

Genomics for VPS54 Gene

Regulatory Elements for VPS54 Gene

Promoters for VPS54 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around VPS54 on UCSC Golden Path with GeneCards custom track

Genomic Location for VPS54 Gene

Chromosome:
2
Start:
63,892,146 bp from pter
End:
64,019,080 bp from pter
Size:
126,935 bases
Orientation:
Minus strand

Genomic View for VPS54 Gene

Genes around VPS54 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VPS54 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VPS54 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VPS54 Gene

Proteins for VPS54 Gene

  • Protein details for VPS54 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9P1Q0-VPS54_HUMAN
    Recommended name:
    Vacuolar protein sorting-associated protein 54
    Protein Accession:
    Q9P1Q0
    Secondary Accessions:
    • Q5VIR5
    • Q86YF7
    • Q8N6G3
    • Q9NPV0
    • Q9NT07
    • Q9NUJ0

    Protein attributes for VPS54 Gene

    Size:
    977 amino acids
    Molecular mass:
    110589 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.
    SequenceCaution:
    • Sequence=BAA92134.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for VPS54 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VPS54 Gene

Proteomics data for VPS54 Gene at MOPED

Post-translational modifications for VPS54 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for VPS54 Gene

No data available for DME Specific Peptides for VPS54 Gene

Domains & Families for VPS54 Gene

Gene Families for VPS54 Gene

Protein Domains for VPS54 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for VPS54 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9P1Q0

UniProtKB/Swiss-Prot:

VPS54_HUMAN :
  • Belongs to the VPS54 family.
Family:
  • Belongs to the VPS54 family.
genes like me logo Genes that share domains with VPS54: view

Function for VPS54 Gene

Molecular function for VPS54 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:18367545). Within the GARP complex, required to tether the complex to the TGN. Not involved in endocytic recycling (PubMed:25799061).
genes like me logo Genes that share phenotypes with VPS54: view

Animal Model 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 VPS54 Gene

Localization for VPS54 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VPS54 Gene

Golgi apparatus, trans-Golgi network.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for VPS54 Gene COMPARTMENTS Subcellular localization image for VPS54 gene
Compartment Confidence
golgi apparatus 5
nucleus 3
cytosol 2
endosome 2
extracellular 1
lysosome 1
plasma membrane 1
vacuole 1

Gene Ontology (GO) - Cellular Components for VPS54 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000938 GARP complex IDA 19620288
GO:0005829 cytosol IMP 25799061
genes like me logo Genes that share ontologies with VPS54: view

Pathways & Interactions for VPS54 Gene

genes like me logo Genes that share pathways with VPS54: view

Interacting Proteins for VPS54 Gene

Gene Ontology (GO) - Biological Process for VPS54 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0050881 musculoskeletal movement IEA --
GO:0060052 neurofilament cytoskeleton organization IEA --
genes like me logo Genes that share ontologies with VPS54: view

No data available for SIGNOR curated interactions for VPS54 Gene

Drugs & Compounds for VPS54 Gene

No Compound Related Data Available

Transcripts for VPS54 Gene

Unigene Clusters for VPS54 Gene

Vacuolar protein sorting 54 homolog (S. cerevisiae):
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for VPS54 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14a · 14b ^ 15a · 15b ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23a · 23b
SP1: - -
SP2: -
SP3:

Relevant External Links for VPS54 Gene

GeneLoc Exon Structure for
VPS54
ECgene alternative splicing isoforms for
VPS54

Expression for VPS54 Gene

mRNA expression in normal human tissues for VPS54 Gene

Protein differential expression in normal tissues from HIPED for VPS54 Gene

This gene is overexpressed in Heart (60.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for VPS54 Gene



SOURCE GeneReport for Unigene cluster for VPS54 Gene Hs.48499

genes like me logo Genes that share expression patterns with VPS54: view

Protein tissue co-expression partners for VPS54 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 VPS54 Gene

Orthologs for VPS54 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for VPS54 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia VPS54 35
  • 95.7 (n)
  • 95.91 (a)
VPS54 36
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia VPS54 35
  • 95.56 (n)
  • 96.52 (a)
VPS54 36
  • 97 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Vps54 35
  • 91.3 (n)
  • 92.63 (a)
Vps54 16
Vps54 36
  • 93 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia VPS54 35
  • 99.83 (n)
  • 99.69 (a)
VPS54 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Vps54 35
  • 89.08 (n)
  • 91.09 (a)
oppossum
(Monodelphis domestica)
Mammalia VPS54 36
  • 91 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia VPS54 36
  • 91 (a)
OneToOne
chicken
(Gallus gallus)
Aves VPS54 35
  • 82.34 (n)
  • 86.96 (a)
VPS54 36
  • 88 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia VPS54 36
  • 86 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.19681 35
vps54 35
  • 74.14 (n)
  • 77.79 (a)
zebrafish
(Danio rerio)
Actinopterygii vps54 35
  • 63.92 (n)
  • 68.9 (a)
vps54 36
  • 65 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008353 35
  • 47.28 (n)
  • 42.5 (a)
fruit fly
(Drosophila melanogaster)
Insecta scat 35
  • 49.5 (n)
  • 41.35 (a)
scat 36
  • 35 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea vps-54 35
  • 46.31 (n)
  • 29.29 (a)
vps-54 36
  • 22 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VPS54 38
thale cress
(Arabidopsis thaliana)
eudicotyledons VPS54 35
  • 45.97 (n)
  • 34.8 (a)
rice
(Oryza sativa)
Liliopsida Os04g0212100 35
  • 42.98 (n)
  • 30.12 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.1333 36
  • 39 (a)
OneToOne
Species with no ortholog for VPS54:
  • 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)
  • bread mold (Neurospora crassa)
  • 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)
  • 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 VPS54 Gene

ENSEMBL:
Gene Tree for VPS54 (if available)
TreeFam:
Gene Tree for VPS54 (if available)

Paralogs for VPS54 Gene

No data available for Paralogs for VPS54 Gene

Variants for VPS54 Gene

Sequence variations from dbSNP and Humsavar for VPS54 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs34015596 - 63,933,730(-) TGATT(C/G)TTCAT nc-transcript-variant, reference, missense
rs11558741 - 63,897,588(-) CAGAT(G/T)TTATT nc-transcript-variant, reference, missense
rs763848 -- 64,003,107(+) GATGA(A/G)AAACC intron-variant
rs992479 -- 63,949,639(-) ataac(C/T)tttat intron-variant
rs933613 -- 64,019,566(-) ACGCG(A/G/T)TGTAT upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for VPS54 Gene

Variant ID Type Subtype PubMed ID
nsv7313 OTHER Inversion 18451855
nsv521717 CNV Gain 19592680
nsv874236 CNV Loss 21882294

Variation tolerance for VPS54 Gene

Residual Variation Intolerance Score: 9.22% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.77; 83.30% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for VPS54 Gene

HapMap Linkage Disequilibrium report
VPS54

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VPS54 Gene

Disorders for VPS54 Gene

MalaCards: The human disease database

(1) MalaCards diseases for VPS54 Gene - From: DISEASES

Disorder Aliases PubMed IDs
amyotrophic lateral sclerosis 1
  • amyotrophic lateral sclerosis
- elite association - COSMIC cancer census association via MalaCards
Search VPS54 in MalaCards View complete list of genes associated with diseases

Relevant External Links for VPS54

Genetic Association Database (GAD)
VPS54
Human Genome Epidemiology (HuGE) Navigator
VPS54
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
VPS54
genes like me logo Genes that share disorders with VPS54: view

No data available for UniProtKB/Swiss-Prot and Genatlas for VPS54 Gene

Publications for VPS54 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. 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. Identification, characterization and cytogenetic mapping of a yeast Vps54 homolog in rat and mouse. (PMID: 12039048) Walter L. … GA1nther E. (Gene 2002) 2 3
  4. EARP is a multisubunit tethering complex involved in endocytic recycling. (PMID: 25799061) Schindler C. … Bonifacino J.S. (Nat. Cell Biol. 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 VPS54 Gene

Sources for VPS54 Gene

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