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Vps54 Gene Detail
Summary
  • Symbol
    Vps54
  • Name
    VPS54 GARP complex subunit
  • Synonyms
    5330404P15Rik, mSLP8, Vps54l, wr
  • Feature Type
    protein coding gene
  • IDs
    MGI:2178798
    NCBI Gene: 245944
  • Alliance
    gene page
  • Transcription Start Sites
    8 TSS
Location &
Maps
more
  • Sequence Map
    Chr11:21239281-21321136 bp, + strand
  • From Ensembl annotation of GRCm38

    View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 11, 13.89 cM, cytoband A3
  • Mapping Data
    14 experiments
Strain
Comparison
more
  • SNPs within 2kb
    258 from dbSNP Build 142
  • Strain Annotations
    18
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_2178798
 protein coding gene Chr11:21239032-21321136 (+)
129S1/SvImJ MGP_129S1SvImJ_G0018071
 protein coding gene Chr11:18833648-18919831 (+)
A/J MGP_AJ_G0018044
 protein coding gene Chr11:18165442-18248985 (+)
AKR/J MGP_AKRJ_G0018008
 protein coding gene Chr11:18808356-18893918 (+)
BALB/cJ MGP_BALBcJ_G0018012
 protein coding gene Chr11:18280637-18363870 (+)
C3H/HeJ MGP_C3HHeJ_G0017826
 protein coding gene Chr11:18695462-18782349 (+)
C57BL/6NJ MGP_C57BL6NJ_G0018464
 protein coding gene Chr11:19670615-19760583 (+)
CAROLI/EiJ MGP_CAROLIEiJ_G0016122
 protein coding gene Chr11:17119609-17199886 (+)
CAST/EiJ MGP_CASTEiJ_G0017387
 protein coding gene Chr11:18684339-18776204 (+)
CBA/J MGP_CBAJ_G0017800
 protein coding gene Chr11:20516875-20609617 (+)
DBA/2J MGP_DBA2J_G0017910
 protein coding gene Chr11:18111385-18193640 (+)
FVB/NJ MGP_FVBNJ_G0017902
 protein coding gene Chr11:17873507-17957207 (+)
LP/J MGP_LPJ_G0017981
 protein coding gene Chr11:18983206-19069976 (+)
NOD/ShiLtJ MGP_NODShiLtJ_G0017928
 protein coding gene Chr11:20931383-21020468 (+)
NZO/HlLtJ MGP_NZOHlLtJ_G0018505
 protein coding gene Chr11:18893538-18977226 (+)
PWK/PhJ MGP_PWKPhJ_G0017168
 protein coding gene Chr11:18123810-18208879 (+)
SPRET/EiJ MGP_SPRETEiJ_G0016965
 protein coding gene Chr11:18609033-18701261 (+)
WSB/EiJ MGP_WSBEiJ_G0017441
 protein coding gene Chr11:18541058-18628784 (+)



Homology
more
  • Human Ortholog
    VPS54, VPS54 subunit of GARP complex
  • Vertebrate Orthologs
    10
  • Human Ortholog
    VPS54, VPS54 subunit of GARP complex
    Orthology source: HomoloGene, HGNC
  • Synonyms
    HCC8, hVps54L, PPP1R164, SLP-8p, VPS54L, WR
  • Links
    NCBI Gene ID: 51542
    neXtProt AC: NX_Q9P1Q0
    UniProt: Q9P1Q0

  • Chr Location
    2p15-p14; chr2:63892149-64019421 (-)  GRCh38.p7
  • HomoloGene
    Vertebrate Homology Class 5605
    1 human;1 mouse;1 rat;1 chimpanzee;1 cattle;1 dog;1 chicken;1 zebrafish;1 frog, western clawed;1 macaque, rhesus
  • HCOP
    human homology predictions: VPS54
  • Gene Tree
    Vps54
Human Diseases
more
  • Diseases
    2 with Vps54 mouse models

Human Disease Mouse Models
      
IDs
 View 1 model
IDs
 View 1 model
Click on a disease name to see all genes associated with that disease.

  • Mutations/Alleles
    1 with disease annotations
  • References
    3 with disease annotations
Mutations,
Alleles, and
Phenotypes
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  • Phenotype Summary
    51 phenotypes from 2 alleles in 3 genetic backgrounds
    123 phenotype references
Phenotype Overview

adipose tissue
behavior/neurological
cardiovascular system
cellular
craniofacial
digestive/alimentary system
embryo
endocrine/exocrine glands
growth/size/body
hearing/vestibular/ear
hematopoietic system
homeostasis/metabolism
immune system
integument
limbs/digits/tail
liver/biliary system
mortality/aging
muscle
neoplasm
nervous system
pigmentation
renal/urinary system
reproductive system
respiratory system
skeleton
taste/olfaction
vision/eye

Click cells to view annotations.
Homozygous mutants show progressive ataxia, tremors, and limb paralysis with degeneration of motor nerve cells of brainstem and spinal cord and atrophy of skeletal muscle beginning about 3-weeks of age. Mutants are sterile and most die by 3-months of age.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    18
  • GO References
    8
Molecular Function

carbohydrate derivative binding
cytoskeletal protein binding
DNA binding
enzyme regulator
hydrolase
ligase
lipid binding
oxidoreductase
RNA binding
signaling receptor activity
signaling receptor binding
transcription
transferase
transporter
Biological Process

carbohydrate derivative metabolism
cell death
cell differentiation
cell population proliferation
cellular component organization
establishment of localization
homeostatic process
immune system process
lipid metabolic process
nucleic acid-templated transcription
protein metabolic process
response to stimulus
signaling
system development
Cellular Component

cell projection
cytoplasmic vesicle
cytoskeleton
cytosol
endoplasmic reticulum
endosome
extracellular region
Golgi apparatus
mitochondrion
non-membrane-bounded organelle
nucleus
organelle envelope
organelle lumen
plasma membrane
synapse
vacuole
Click cells to view annotations.
Expression
less
Expression Overview

early conceptus
embryo ectoderm
embryo endoderm
embryo mesoderm
embryo mesenchyme
extraembryonic component
alimentary system
auditory system
branchial arches
cardiovascular system
connective tissue
endocrine system
exocrine system
hemolymphoid system
integumental system
limbs
liver and biliary system
musculoskeletal system
nervous system
olfactory system
reproductive system
respiratory system
urinary system
visual system
Click cells to view annotations.


  • Assay Results
    631
  • cDNA Data
    104
  • Comparison Matrix
    Gene Expression + Phenotype
    • Interactions
    less
    Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic ENSMUSG00000020128 Ensembl Gene Model | MGI Sequence Detail 81856 C57BL/6J ±  kb
    transcript ENSMUST00000006221 Ensembl | MGI Sequence Detail 4323 Not Applicable  
    polypeptide ENSMUSP00000006221 Ensembl | MGI Sequence Detail 977 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    • UniProt
      5 Sequences
    • Protein Ontology
      PR:000017346 vacuolar protein sorting-associated protein 54
      (term hierarchy)
    • PDB
      3N1B, 3N1E
    • InterPro Domains
      IPR039745 Vacuolar protein sorting-associated protein 54
      IPR012501 Vacuolar protein sorting-associated protein 54, C-terminal
      IPR019515 Vacuolar protein sorting-associated protein 54, N-terminal
    Molecular
    Reagents
    less
    • All nucleic 108
      Genomic 1
      cDNA 107

      Microarray probesets 7
    Other
    Accession IDs
    less
    MGD-MRK-15459, MGI:2443077, MGI:98964
    References
    more
    • Summaries
      All 164
      Diseases 3
      Gene Ontology 8
      Phenotypes 123
    • Earliest
      J:5102 Duchen LW, et al., An hereditary motor neurone disease with progressive denervation of muscle in the mouse: the mutant 'wobbler'. J Neurol Neurosurg Psychiatry. 1968 Dec;31(6):535-42
    • Latest
      J:289825 Petit CS, et al., Inhibition of sphingolipid synthesis improves outcomes and survival in GARP mutant wobbler mice, a model of motor neuron degeneration. Proc Natl Acad Sci U S A. 2020 May 12;117(19):10565-10574
    Contributing Projects:
    Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB), Gene Ontology (GO)
    Citing These Resources
    Funding Information
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    Send questions and comments to User Support.     		last database update
    02/16/2021
    MGI 6.16     		The Jackson Laboratory