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Aliases for VPS54 Gene

Aliases for VPS54 Gene

  • Vacuolar Protein Sorting 54 Homolog (S. Cerevisiae) 2 3
  • Hepatocellular Carcinoma Protein 8 3 4
  • Tumor Antigen HOM-HCC-8 3 4
  • Tumor Antigen SLP-8p 3 4
  • HCC8 3 4
  • Protein Phosphatase 1, Regulatory Subunit 164 3
  • Vacuolar Protein Sorting 54 (Yeast) 2
  • Regulatory Subunit 164 2
  • Protein Phosphatase 1 2
  • PPP1R164 3
  • HVps54L 3
  • SLP-8p 3
  • VPS54L 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 (Vacuolar Protein Sorting 54 Homolog (S. Cerevisiae)) is a Protein Coding gene. Diseases associated with VPS54 include amyotrophic lateral sclerosis 1. 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

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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).

Gene Ontology (GO) - Molecular Function for VPS54 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 15878329
GO:0019905 syntaxin binding IBA --
genes like me logo Genes that share ontologies with VPS54: view
genes like me logo Genes that share phenotypes with VPS54: view

Animal Model Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for VPS54

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , 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 4
endosome 2
lysosome 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:0005622 intracellular --
GO:0005654 nucleoplasm IDA --
GO:0005794 Golgi apparatus IDA 15878329
GO:0005802 trans-Golgi network IDA 25799061
genes like me logo Genes that share ontologies with VPS54: view

Pathways & Interactions for VPS54 Gene

SuperPathways for VPS54 Gene

No Data Available

Interacting Proteins for VPS54 Gene

Gene Ontology (GO) - Biological Process for VPS54 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006896 Golgi to vacuole transport IBA --
GO:0015031 protein transport IEA --
GO:0040007 growth IEA --
GO:0042147 retrograde transport, endosome to Golgi IBA --
GO:0048873 homeostasis of number of cells within a tissue IEA --
genes like me logo Genes that share ontologies with VPS54: view

No data available for Pathways by source and 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:

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for VPS54

Flow Cytometry Products

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 MAF
rs763848 -- 64,003,107(+) GATGA(A/G)AAACC intron-variant
rs933613 -- 64,019,566(-) ACGCG(A/G/T)TGTAT upstream-variant-2KB
rs992479 -- 63,949,639(-) ataac(C/T)tttat intron-variant
rs1345479 -- 63,903,097(+) AAAAA(A/G)GGAAA intron-variant
rs1362797 -- 63,901,458(+) agagt(C/T)tgcac intron-variant

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
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. 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) 23 67
  2. Identification, characterization and cytogenetic mapping of a yeast Vps54 homolog in rat and mouse. (PMID: 12039048) Walter L. … GA1nther E. (Gene 2002) 2 67
  3. EARP is a multisubunit tethering complex involved in endocytic recycling. (PMID: 25799061) Schindler C. … Bonifacino J.S. (Nat. Cell Biol. 2015) 67
  4. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 67
  5. Clozapine-induced agranulocytosis is associated with rare HLA-DQB1 and HLA-B alleles. (PMID: 25187353) Goldstein J.I. … Sullivan P.F. (Nat Commun 2014) 67

Products for VPS54 Gene

Sources for VPS54 Gene

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