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VPS54 VPS54 subunit of GARP complex [ Homo sapiens (human) ]

Gene ID: 51542, updated on 22-Sep-2022

Summary

Official Symbol
VPS54provided by HGNC
Official Full Name
VPS54 subunit of GARP complexprovided by HGNC
Primary source
HGNC:HGNC:18652
See related
Ensembl:ENSG00000143952 MIM:614633; AllianceGenome:HGNC:18652
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
WR; HCC8; SLP-8p; VPS54L; hVps54L; PPP1R164
Summary
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]
Expression
Ubiquitous expression in thyroid (RPKM 11.2), prostate (RPKM 10.0) and 25 other tissues See more
Orthologs
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Genomic context

See VPS54 in Genome Data Viewer
Location:
2p15-p14
Exon count:
29
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (63892150..64019428, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (63899706..64027065, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (64119284..64246562, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene WD repeat containing planar cell polarity effector Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 66 Neighboring gene Sharpr-MPRA regulatory region 3928 Neighboring gene Sharpr-MPRA regulatory region 742 Neighboring gene UDP-glucose pyrophosphorylase 2 Neighboring gene uncharacterized LOC124907774 Neighboring gene pellino E3 ubiquitin protein ligase 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables syntaxin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
involved_in Golgi to vacuole transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in L-glutamate import IEA
Inferred from Electronic Annotation
more info
 
involved_in apoptotic DNA fragmentation IEA
Inferred from Electronic Annotation
more info
 
involved_in astrocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in cellular calcium ion homeostasis IEA
Inferred from Electronic Annotation
more info
 
involved_in cellular response to progesterone stimulus IEA
Inferred from Electronic Annotation
more info
 
involved_in gene expression IEA
Inferred from Electronic Annotation
more info
 
involved_in homeostasis of number of cells within a tissue IEA
Inferred from Electronic Annotation
more info
 
involved_in in utero embryonic development IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within lysosomal transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in microglia differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in mitochondrion organization IEA
Inferred from Electronic Annotation
more info
 
involved_in motor behavior IEA
Inferred from Electronic Annotation
more info
 
involved_in motor neuron apoptotic process IEA
Inferred from Electronic Annotation
more info
 
involved_in musculoskeletal movement IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of motor neuron apoptotic process IEA
Inferred from Electronic Annotation
more info
 
involved_in neural tissue regeneration IEA
Inferred from Electronic Annotation
more info
 
involved_in neurofilament cytoskeleton organization IEA
Inferred from Electronic Annotation
more info
 
involved_in neuroinflammatory response IEA
Inferred from Electronic Annotation
more info
 
involved_in neuromuscular synaptic transmission IEA
Inferred from Electronic Annotation
more info
 
involved_in neuron projection morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in post-embryonic forelimb morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in protein localization to cell surface IEA
Inferred from Electronic Annotation
more info
 
involved_in protein targeting to ER IEA
Inferred from Electronic Annotation
more info
 
involved_in protein targeting to lysosome IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of growth IEA
Inferred from Electronic Annotation
more info
 
involved_in respiratory electron transport chain IEA
Inferred from Electronic Annotation
more info
 
involved_in response to antibiotic IEA
Inferred from Electronic Annotation
more info
 
involved_in response to calcium ion IEA
Inferred from Electronic Annotation
more info
 
involved_in retrograde transport, endosome to Golgi IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in retrograde transport, endosome to Golgi IC
Inferred by Curator
more info
PubMed 
acts_upstream_of_or_within retrograde transport, endosome to Golgi IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in skeletal muscle tissue growth IEA
Inferred from Electronic Annotation
more info
 
involved_in spermatid differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in sphingolipid catabolic process IEA
Inferred from Electronic Annotation
more info
 
involved_in striated muscle contraction IEA
Inferred from Electronic Annotation
more info
 
involved_in synaptic transmission, GABAergic IEA
Inferred from Electronic Annotation
more info
 
involved_in synaptic transmission, glutamatergic IEA
Inferred from Electronic Annotation
more info
 
involved_in thrombin-activated receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
involved_in ubiquitin recycling IEA
Inferred from Electronic Annotation
more info
 
involved_in vacuole organization IEA
Inferred from Electronic Annotation
more info
 
involved_in vesicle-mediated cholesterol transport IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
part_of GARP complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
part_of GARP complex IC
Inferred by Curator
more info
PubMed 
part_of GARP complex IDA
Inferred from Direct Assay
more info
PubMed 
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytosol IEA
Inferred from Electronic Annotation
more info
 
located_in membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in mitochondrion IEA
Inferred from Electronic Annotation
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
located_in synapse IEA
Inferred from Electronic Annotation
more info
 
located_in trans-Golgi network IDA
Inferred from Direct Assay
more info
PubMed 
located_in trans-Golgi network IMP
Inferred from Mutant Phenotype
more info
PubMed 
located_in trans-Golgi network membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
vacuolar protein sorting-associated protein 54
Names
VPS54, GARP complex subunit
hepatocellular carcinoma protein 8
protein phosphatase 1, regulatory subunit 164
tumor antigen HOM-HCC-8
tumor antigen SLP-8p
vacuolar protein sorting 54 homolog

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_042277.1 RefSeqGene

    Range
    4653..131931
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001005739.2NP_001005739.1  vacuolar protein sorting-associated protein 54 isoform 2

    See identical proteins and their annotated locations for NP_001005739.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in one of the 5' coding exons compared to transcript variant 1, resulting in a shorter isoform (2) compared to isoform 1.
    Source sequence(s)
    AC092588, AK002205, AL514510, AW452246, BC030275, BC041868
    Consensus CDS
    CCDS46302.1
    UniProtKB/Swiss-Prot
    Q9P1Q0
    Related
    ENSP00000386980.3, ENST00000409558.8
    Conserved Domains (1) summary
    pfam07928
    Location:725855
    Vps54; Vps54-like protein
  2. NM_016516.3NP_057600.2  vacuolar protein sorting-associated protein 54 isoform 1

    See identical proteins and their annotated locations for NP_057600.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AC092588, AF102177, AK002205, AL514510, AW452246, BC030275, BC041868
    Consensus CDS
    CCDS33208.1
    UniProtKB/Swiss-Prot
    Q9NUJ0, Q9P1Q0
    Related
    ENSP00000272322.4, ENST00000272322.9
    Conserved Domains (1) summary
    pfam07928
    Location:737867
    Vps54; Vps54-like protein

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    63892150..64019428 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017004316.2XP_016859805.1  vacuolar protein sorting-associated protein 54 isoform X3

    Related
    ENSP00000346499.3, ENST00000354504.7
  2. XM_047444728.1XP_047300684.1  vacuolar protein sorting-associated protein 54 isoform X1

    UniProtKB/Swiss-Prot
    Q9NUJ0
  3. XM_047444730.1XP_047300686.1  vacuolar protein sorting-associated protein 54 isoform X3

  4. XM_047444727.1XP_047300683.1  vacuolar protein sorting-associated protein 54 isoform X1

    UniProtKB/Swiss-Prot
    Q9NUJ0
  5. XM_047444729.1XP_047300685.1  vacuolar protein sorting-associated protein 54 isoform X2

  6. XM_047444731.1XP_047300687.1  vacuolar protein sorting-associated protein 54 isoform X4

  7. XM_047444732.1XP_047300688.1  vacuolar protein sorting-associated protein 54 isoform X5

RNA

  1. XR_007076389.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    63899706..64027065 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)