Free for academic non-profit institutions. Other users need a Commercial license

Aliases for VPS54 Gene

Aliases for VPS54 Gene

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

Additional gene information for VPS54 Gene

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

Genomics for VPS54 Gene

GeneHancer (GH) Regulatory Elements for VPS54 Gene

Promoters and enhancers for VPS54 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02I064017 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 550.8 0.0 -42 3.4 HDGF PKNOX1 SMAD1 FOXA2 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 VPS54 WDPCP ENSG00000228079 GC02M063958
GH02I064635 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 29.1 -628.9 -628918 24.5 MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 ZNF213 ZNF143 SP3 PPARGC1A SERTAD2 VPS54 AFTPH LINC02576 ENSG00000251775 LOC105374775 RPS10P9
GH02I063587 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 36.5 +429.2 429156 5.3 CLOCK FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 ZNF548 MDH1 WDPCP VPS54 AFTPH PIR47439
GH02I064857 Promoter/Enhancer 2.1 FANTOM5 Ensembl ENCODE dbSUPER 26.5 -842.8 -842805 8.7 HDGF PKNOX1 MLX ARID4B SIN3A ZNF766 ZNF143 DEK SP3 SP5 LINC01800 VPS54 SERTAD2 ACTR2 AFTPH RAB1A SLC1A4 GC02P064841
GH02I063048 Promoter/Enhancer 2.4 VISTA EPDnew Ensembl ENCODE 18.4 +969.3 969272 3.7 PKNOX1 ARID4B SIN3A FEZF1 DMAP1 SLC30A9 POLR2B ZNF213 ZNF143 FOS LOC100132215 OTX1 VPS54 WDPCP
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around VPS54 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the VPS54 gene promoter:

Genomic Locations for VPS54 Gene

Genomic Locations for VPS54 Gene
chr2:63,892,146-64,019,080
(GRCh38/hg38)
Size:
126,935 bases
Orientation:
Minus strand
chr2:64,119,280-64,246,214
(GRCh37/hg19)

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

Post-translational modifications for VPS54 Gene

No Post-translational modifications

Other Protein References for VPS54 Gene

No data available for DME Specific Peptides for VPS54 Gene

Domains & 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).

Phenotypes From GWAS Catalog for VPS54 Gene

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

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , 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
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 VPS54 gene
Compartment Confidence
nucleus 5
golgi apparatus 5
cytosol 3
endosome 2
plasma membrane 1
extracellular 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (4)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for VPS54 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000938 GARP complex IDA 19620288
GO:0005654 nucleoplasm IDA --
GO:0005794 Golgi apparatus IEA,IDA 15878329
GO:0005802 trans-Golgi network IMP 25795912
GO:0005829 cytosol IEA --
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

Gene Ontology (GO) - Biological Process for VPS54 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0006896 Golgi to vacuole transport IBA --
GO:0007041 lysosomal transport IMP 25799061
GO:0015031 protein transport IEA --
GO:0040007 growth 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:

CRISPR Products

Inhibitory RNA 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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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, MaxQB, and MOPED for VPS54 Gene



Protein tissue co-expression partners for VPS54 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of VPS54 Gene:

VPS54

SOURCE GeneReport for Unigene cluster for VPS54 Gene:

Hs.48499

Evidence on tissue expression from TISSUES for VPS54 Gene

  • Skin(4.2)
  • Nervous system(2.2)
genes like me logo Genes that share expression patterns with VPS54: view

Primer Products

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 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
chimpanzee
(Pan troglodytes)
Mammalia VPS54 33 34
  • 99.83 (n)
cow
(Bos Taurus)
Mammalia VPS54 33 34
  • 95.7 (n)
dog
(Canis familiaris)
Mammalia VPS54 33 34
  • 95.56 (n)
mouse
(Mus musculus)
Mammalia Vps54 33 16 34
  • 91.3 (n)
oppossum
(Monodelphis domestica)
Mammalia VPS54 34
  • 91 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia VPS54 34
  • 91 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Vps54 33
  • 89.08 (n)
chicken
(Gallus gallus)
Aves VPS54 33 34
  • 82.34 (n)
lizard
(Anolis carolinensis)
Reptilia VPS54 34
  • 86 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vps54 33
  • 74.14 (n)
Str.19681 33
zebrafish
(Danio rerio)
Actinopterygii vps54 33 34
  • 63.92 (n)
fruit fly
(Drosophila melanogaster)
Insecta scat 33 34
  • 49.5 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008353 33
  • 47.28 (n)
worm
(Caenorhabditis elegans)
Secernentea vps-54 33 34
  • 46.31 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VPS54 36
thale cress
(Arabidopsis thaliana)
eudicotyledons VPS54 33
  • 45.97 (n)
rice
(Oryza sativa)
Liliopsida Os04g0212100 33
  • 42.98 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.1333 34
  • 39 (a)
OneToOne
Species where no ortholog for VPS54 was found in the sources mined by GeneCards:
  • 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 Variation AA Info Type
rs1000004378 -- 63,970,695(-) A/G intron_variant
rs1000035797 -- 63,995,674(-) G/A intron_variant
rs1000047525 -- 63,902,352(-) A/G intron_variant
rs1000052236 -- 64,014,397(-) G/A intron_variant
rs1000105195 -- 64,010,106(-) T/C intron_variant

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

Variant ID Type Subtype PubMed ID
nsv7313 OTHER inversion 18451855
nsv582127 CNV gain 21841781
nsv582126 CNV gain 21841781
nsv521717 CNV gain 19592680
nsv1013132 CNV loss 25217958
nsv1002209 CNV loss 25217958
esv3591068 CNV loss 21293372
esv3591067 CNV loss 21293372
esv2763643 CNV gain 21179565

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)

Additional Variant Information for VPS54 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
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
  • als1
- elite association - COSMIC cancer census association via MalaCards
Search VPS54 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for VPS54

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 (Experimental cell research 2005) 2 3 4 58
  2. EARP is a multisubunit tethering complex involved in endocytic recycling. (PMID: 25799061) Schindler C … Bonifacino JS (Nature cell biology 2015) 3 4 58
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  4. Ang2/fat-free is a conserved subunit of the Golgi-associated retrograde protein complex. (PMID: 20685960) Pérez-Victoria FJ … Bonifacino JS (Molecular biology of the cell 2010) 3 4 58
  5. Dual roles of the mammalian GARP complex in tethering and SNARE complex assembly at the trans-golgi network. (PMID: 19620288) Pérez-Victoria FJ … Bonifacino JS (Molecular and cellular biology 2009) 3 22 58

Products for VPS54 Gene

Sources for VPS54 Gene

Content
Loading form....