VPS54 Gene (Protein Coding)

VPS54 Subunit Of GARP Complex

GC02M063892
GIFtS:
38
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 isofo... See more...

Aliases for VPS54 Gene

Aliases for VPS54 Gene

  • VPS54 Subunit Of GARP Complex 2 3 5
  • HCC8 2 3 4
  • Vacuolar Protein Sorting-Associated Protein 54 3 4
  • Protein Phosphatase 1, Regulatory Subunit 164 2 3
  • Hepatocellular Carcinoma Protein 8 3 4
  • VPS54, GARP Complex Subunit 2 3
  • Tumor Antigen HOM-HCC-8 3 4
  • Tumor Antigen SLP-8p 3 4
  • PPP1R164 2 3
  • Vacuolar Protein Sorting 54 Homolog (S. Cerevisiae) 2
  • Vacuolar Protein Sorting 54 (Yeast) 2
  • Vacuolar Protein Sorting 54 Homolog 3
  • HVps54L 3
  • SLP-8p 3
  • VPS54L 3
  • VPS54 5
  • 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 Subunit Of GARP Complex) is a Protein Coding gene. Diseases associated with VPS54 include Frontotemporal Dementia And/Or Amyotrophic Lateral Sclerosis 3 and Frontotemporal Dementia And/Or Amyotrophic Lateral Sclerosis 4. 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 Summary 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 , Rfam classification and piRNA Summary for VPS54 Gene

Genomics for VPS54 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
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
GH02J064017 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 250.7 +0.4 418 3.6 ZBTB10 NR2C1 IKZF1 SMAD5 POLR2A NONO HOMEZ THAP11 ZNF395 REST HSALNG0015445 VPS54 WDPCP ENSG00000225889 UGP2
GH02J063975 Promoter 0.6 EPDnew 250.3 +43.8 43808 0.1 ZNF316 NFE2 ZBTB5 EMSY VPS54 piR-58790-002 piR-37663-029 UGP2
GH02J063839 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 60.8 +174.0 173971 12.1 CHD2 TBP MXD4 ZBTB10 SP1 FEZF1 CEBPA MNT BRCA1 SMAD5 UGP2 VPS54 AFTPH SERTAD2 MDH1 WDPCP ENSG00000225889 HSALNG0015441 lnc-VPS54-7 piR-41245-127
GH02J064090 Promoter 0.4 EPDnew 250.2 -71.0 -71030 0.1 RBM22 HSALNG0015447 lnc-UGP2-3-001 lnc-UGP2-3-002 VPS54 HSALNG0015451 PELI1
GH02J064635 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 39.8 -628.6 -628570 24.5 CHD2 TBP ZBTB10 SP1 MXD4 BCL11A FEZF1 CEBPA SIX5 NR2C1 SERTAD2 VPS54 AFTPH LINC02576 ENSG00000251775 LOC105374775 ENSG00000226756 RPS10P9
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VPS54 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for VPS54

Top Transcription factor binding sites by QIAGEN in the VPS54 gene promoter:
  • aMEF-2
  • FOXO1
  • FOXO1a
  • MEF-2A
  • USF-1
  • USF-1:USF-2
  • USF1
  • USF2

Genomic Locations for VPS54 Gene

Latest Assembly
chr2:63,892,146-64,019,428
(GRCh38/hg38)
Size:
127,283 bases
Orientation:
Minus strand

Previous Assembly
chr2:64,119,284-64,246,562
(GRCh37/hg19 by Entrez Gene)
Size:
127,279 bases
Orientation:
Minus strand

chr2:64,119,280-64,246,206
(GRCh37/hg19 by Ensembl)
Size:
126,927 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 Structure • Gene Density

RefSeq DNA sequence for VPS54 Gene

Proteins for VPS54 Gene

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  1. Antibodies for research
  2. Protein products for research
  3. Assay products for research

  • 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 (PubMed:15878329, PubMed:25799061, PubMed:27440922). EIPR1 interacts with GARP complex and mediates its recruitment to the trans-Golgi network (PubMed:27440922). Interacts with VPS51 in an EIPR1-independent manner (PubMed:31721635).
    SequenceCaution:
    • Sequence=BAA92134.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for VPS54 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VPS54 Gene

Protein Expression for VPS54 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for VPS54 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for VPS54 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibodies for research

  • Abcam antibodies for VPS54
  • Santa Cruz Biotechnology (SCBT) Antibodies for VPS54

No data available for DME Specific Peptides for VPS54 Gene

Domains & Families for VPS54 Gene

Gene Families for VPS54 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for VPS54 Gene

InterPro:
Blocks:
  • Vps54-like
ProtoNet:

Suggested Antigen Peptide Sequences for VPS54 Gene

GenScript: Design optimal peptide antigens:
  • Tumor antigen SLP-8p (VPS54_HUMAN)

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

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  1. Animal Models for research
  2. CRISPR products for research
  3. miRNA products for research
  4. Inhibitory RNAs for research
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  6. Cell Lines for research

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 3172165
GO:0019905 syntaxin binding IBA 21873635
genes like me logo Genes that share ontologies with VPS54: view
genes like me logo Genes that share phenotypes with VPS54: view

Animal Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VPS54

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. Membrane. Note=Associates with membranes in an EIPR1-independent manner. {ECO:0000250 UniProtKB:Q9JMK8}.

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
lysosome 2
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 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 IEA,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:0006896 Golgi to vacuole transport IBA 21873635
GO:0007041 lysosomal transport IMP 25799061
GO:0015031 protein transport IEA --
GO:0040008 regulation of growth IEA --
GO:0042147 retrograde transport, endosome to Golgi IEA,IMP 25799061
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

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  1. Drug products for research
No Compound Related Data Available

Transcripts for VPS54 Gene

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mRNA/cDNA for VPS54 Gene

2 REFSEQ mRNAs :
15 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VPS54

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

Expression for VPS54 Gene

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  1. Primer products for research
  2. Gene Expression Assays for research

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for VPS54 Gene

mRNA expression in normal human tissues for VPS54 Gene
mRNA expression by GTEx for VPS54 GenemRNA expression by BioGPS 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, MaxQB, and MOPED for VPS54 Gene



Protein tissue co-expression partners for VPS54 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for VPS54

SOURCE GeneReport for Unigene cluster for VPS54 Gene:

Hs.48499

Evidence on tissue expression from TISSUES for VPS54 Gene

  • Skin(4.4)
  • Nervous system(2.7)
genes like me logo Genes that share expression patterns with VPS54: view

Primer products for research

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 30 31
  • 99.83 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia VPS54 30 31
  • 95.7 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia VPS54 30 31
  • 95.56 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Vps54 30 17 31
  • 91.3 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia VPS54 31
  • 91 (a)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia VPS54 31
  • 91 (a)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Vps54 30
  • 89.08 (n)
Chicken
(Gallus gallus)
 Aves VPS54 30 31
  • 82.34 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia VPS54 31
  • 86 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia vps54 30
  • 74.14 (n)
Str.19681 30
Zebrafish
(Danio rerio)
 Actinopterygii vps54 30 31
  • 63.92 (n)
 OneToOne
Fruit Fly
(Drosophila melanogaster)
 Insecta scat 30 31
  • 49.5 (n)
 OneToOne
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP008353 30
  • 47.28 (n)
Worm
(Caenorhabditis elegans)
 Secernentea vps-54 30 31
  • 46.31 (n)
 OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes VPS54 33
Thale Cress
(Arabidopsis thaliana)
 eudicotyledons VPS54 30
  • 45.97 (n)
Rice
(Oryza sativa)
 Liliopsida Os04g0212100 30
  • 42.98 (n)
Sea Squirt
(Ciona savignyi)
 Ascidiacea CSA.1333 31
  • 39 (a)
 OneToOne
Species where no ortholog for VPS54 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for VPS54: view image

Paralogs for VPS54 Gene

No data available for Paralogs for VPS54 Gene

Variants for VPS54 Gene

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  1. SNP Genotyping and Copy Number Assays for research

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for VPS54 Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
rs1200103911 Uncertain Significance: not provided 63,920,551(-) G/C
NM_016516.3(VPS54):c.1946C>G (p.Thr649Ser) 		MISSENSE
rs139082064 Uncertain Significance: not provided 63,949,117(-) T/C
NM_016516.3(VPS54):c.1057A>G (p.Met353Val) 		MISSENSE
rs1422204880 Uncertain Significance: not provided 63,933,691(-) G/C
NM_016516.3(VPS54):c.1721C>G (p.Pro574Arg) 		MISSENSE
rs1575966808 Uncertain Significance: Reduced number of teeth 63,965,958(-) C/G
NM_016516.3(VPS54):c.501G>C (p.Met167Ile) 		MISSENSE
rs193225211 Benign: not provided 63,899,588(-) G/A
NM_016516.3(VPS54):c.2626-7C>T 		INTRON

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for VPS54 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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)

Additional Variant Information for VPS54 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
VPS54

SNP Genotyping and Copy Number Assays for research

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

Disorders for VPS54 Gene

MalaCards: The human disease database

(7) MalaCards diseases for VPS54 Gene - From: COP

- 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
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
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
  2. TSSC1 is novel component of the endosomal retrieval machinery. (PMID: 27440922) Gershlick DC … Bonifacino JS (Molecular biology of the cell 2016) 3 4
  3. EARP is a multisubunit tethering complex involved in endocytic recycling. (PMID: 25799061) Schindler C … Bonifacino JS (Nature cell biology 2015) 3 4
  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
  5. 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 41

ExternalLinks

View latest publications for VPS54 gene in Mastermind

Products for VPS54 Gene

Sources for VPS54 Gene