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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 Retrograde transport at the Trans-Golgi-Network. 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 CIViC summary , 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

Enhancers for VPS54 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH02G064200 1.4 Ensembl ENCODE dbSUPER 6.6 -184.0 -184018 5.2 HDGF FOXA2 PKNOX1 TBL1XR1 BMI1 ZBTB40 YY1 SCRT2 ZNF143 RELB LOC100507006 PELI1 LGALSL LOC105374771 ENSG00000237217 VPS54 LINC00309 GC02P064150
GH02G064017 1.1 ENCODE 0.7 0.0 -42 3.4 HDGF PKNOX1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 WDPCP VPS54 ENSG00000228079
GH02G064021 0.8 ENCODE 0.7 -2.7 -2722 0.2 ELF3 SOX13 FOXA2 SAP130 ARID4B RARA TEAD3 GATA3 NR2F6 HOMEZ VPS54 ENSG00000228079
GH02G064016 0.7 Ensembl 0.7 +2.3 2280 0.4 MAX RAD21 YY1 NR2F2 TEAD3 RARA JUND ATF3 HMBOX1 NR2F6 VPS54 PIR48907 GC02M064016
GH02G064023 0.9 ENCODE 0.4 -5.4 -5397 1.7 HNRNPUL1 FOXA2 MLX DMAP1 YY1 PPARG MIER3 ATF4 ETV4 KDM1A LOC100507006 VPS54 ENSG00000228079
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around VPS54 on UCSC Golden Path with GeneCards custom track

Promoters for VPS54 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000117897 480 2001 HDGF PKNOX1 ATF1 ARNT ARID4B SIN3A DMAP1 ZNF2 ZNF48 YY1

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

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

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

CRISPR Products

Inhibitory RNA Products

Clone 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

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 IDA 25799061
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

Clone 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 34 35
  • 99.83 (n)
cow
(Bos Taurus)
Mammalia VPS54 34 35
  • 95.7 (n)
dog
(Canis familiaris)
Mammalia VPS54 34 35
  • 95.56 (n)
mouse
(Mus musculus)
Mammalia Vps54 34 16 35
  • 91.3 (n)
oppossum
(Monodelphis domestica)
Mammalia VPS54 35
  • 91 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia VPS54 35
  • 91 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Vps54 34
  • 89.08 (n)
chicken
(Gallus gallus)
Aves VPS54 34 35
  • 82.34 (n)
lizard
(Anolis carolinensis)
Reptilia VPS54 35
  • 86 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vps54 34
  • 74.14 (n)
Str.19681 34
zebrafish
(Danio rerio)
Actinopterygii vps54 34 35
  • 63.92 (n)
fruit fly
(Drosophila melanogaster)
Insecta scat 34 35
  • 49.5 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008353 34
  • 47.28 (n)
worm
(Caenorhabditis elegans)
Secernentea vps-54 34 35
  • 46.31 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VPS54 37
thale cress
(Arabidopsis thaliana)
eudicotyledons VPS54 34
  • 45.97 (n)
rice
(Oryza sativa)
Liliopsida Os04g0212100 34
  • 42.98 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.1333 35
  • 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 Sequence Context AA Info Type
rs1000004378 -- 63,970,695(+) TTTTA(A/G)GGTGC intron-variant
rs1000035797 -- 63,995,674(+) AGACA(A/G)TCTGT intron-variant
rs1000047525 -- 63,902,352(+) AGCCT(A/G)CTACT intron-variant
rs1000052236 -- 64,014,397(+) ACAAG(A/G)TAATC intron-variant
rs1000105195 -- 64,010,106(+) CAAAG(C/T)GCTGG intron-variant

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

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

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

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 and GeneCards

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 64
  2. EARP is a multisubunit tethering complex involved in endocytic recycling. (PMID: 25799061) Schindler C. … Bonifacino J.S. (Nat. Cell Biol. 2015) 3 4 64
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  4. Ang2/fat-free is a conserved subunit of the Golgi-associated retrograde protein complex. (PMID: 20685960) Perez-Victoria F.J. … Bonifacino J.S. (Mol. Biol. Cell 2010) 3 4 64
  5. 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 22 64

Products for VPS54 Gene

Sources for VPS54 Gene

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