Vps54 VPS54 GARP complex subunit [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Vps54provided by MGI
Official Full Name: VPS54 GARP complex subunitprovided by MGI
Primary source: MGI:MGI:2178798
See related: Ensembl:ENSMUSG00000020128 AllianceGenome:MGI:2178798
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: wr; Hcc8; mSLP8; Vps54l
Summary: Predicted to enable syntaxin binding activity. Acts upstream of or within several processes, including homeostasis of number of cells within a tissue; musculoskeletal movement; and neurofilament cytoskeleton organization. Predicted to be located in several cellular components, including nucleoplasm; perinuclear region of cytoplasm; and trans-Golgi network. Predicted to be part of GARP complex. Used to study Werdnig-Hoffmann disease and amyotrophic lateral sclerosis type 1. Orthologous to human VPS54 (VPS54 subunit of GARP complex). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in CNS E11.5 (RPKM 6.9), bladder adult (RPKM 5.9) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 11 A3.1; 11 13.89 cM

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	11	NC_000077.7 (21189032..21271133)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	11	NC_000077.6 (21239032..21321133)

Chromosome 11 - NC_000077.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

UBPy-sorted cargo to acrosome biogenesis and effects of its derailment in a mouse model of globozoospermia, the infertile Vps54 (L967Q) mutant, are reported.
Title: Dynamic of contribution of UBPy-sorted cargo to acrosome biogenesis: effects of its derailment in a mouse model of globozoospermia, the infertile Vps54 (L967Q) mutant.
This study demonstrated that the cerebellum is affected by neurodegenerative and inflammatory processes in the Wobbler mouse model of ALS.
Title: The Spatiotemporal Pattern of Degeneration in the Cerebellum of the Wobbler Mouse.
Investigation of cells derived from wobbler and Vps54 null mutant embryos demonstrates impaired retrograde transport of the Cholera-toxin B subunit to the trans-Golgi network and mis-sorting of mannose-6-phosphate receptors and cargo proteins.
Title: Loss of vps54 function leads to vesicle traffic impairment, protein mis-sorting and embryonic lethality.
We conclude that a missense mutation in VPS54, an essential component of the Golgi-associated retrograde protein complex, not only prevents the formation of an acrosome but also initiates a cascade of metabolic abnormalities and a stress reaction.
Title: Pathoproteomics of testicular tissue deficient in the GARP component VPS54: the wobbler mouse model of globozoospermia.
Severely reduced levels of mutant Vps54 and, consequently, of the whole GARP complex underlie the phenotype of the wobbler mouse.
Title: Structural basis for the wobbler mouse neurodegenerative disorder caused by mutation in the Vps54 subunit of the GARP complex.
Mutation of Vps54 causes motor neuron disease and defective spermiogenesis in the wobbler mouse
Title: Mutation of Vps54 causes motor neuron disease and defective spermiogenesis in the wobbler mouse.

Submit: New GeneRIF Correction

Phenotypes

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Associated conditions

Description	Tests
wobbler GeneReviews: Not available

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Spontaneous (1)
Gene trapped (1) 1 citation
Endonuclease-mediated (2)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables syntaxin binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in Golgi to vacuole transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in L-glutamate import	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in apoptotic DNA fragmentation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in astrocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to progesterone stimulus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in homeostasis of number of cells	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within homeostasis of number of cells within a tissue	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in homeostasis of number of cells within a tissue	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in in utero embryonic development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in intracellular calcium ion homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in limb development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in limb morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within lysosomal transport	ISO Inferred from Sequence Orthology more info	PubMed
involved_in microglia differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mitochondrion organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in motor behavior	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in motor neuron apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within musculoskeletal movement	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of motor neuron apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neural tissue regeneration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neurofilament cytoskeleton organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuroinflammatory response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuromuscular synaptic transmission	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuron apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuron projection morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in post-embryonic forelimb morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein localization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein localization to cell surface	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein targeting to ER	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein targeting to lysosome	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein targeting to vacuole	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within protein transport	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of growth	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in respiratory electron transport chain	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to antibiotic	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to calcium ion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in retrograde transport, endosome to Golgi	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within retrograde transport, endosome to Golgi	ISO Inferred from Sequence Orthology more info	PubMed
involved_in skeletal muscle tissue development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in skeletal muscle tissue growth	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in spermatid differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sphingolipid catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in striated muscle contraction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in synaptic transmission, GABAergic	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in synaptic transmission, glutamatergic	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in thrombin-activated receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ubiquitin recycling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in vacuole organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in vesicle-mediated cholesterol transport	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of GARP complex	IBA Inferred from Biological aspect of Ancestor more info
part_of GARP complex	IDA Inferred from Direct Assay more info	PubMed
part_of GARP complex	ISO Inferred from Sequence Orthology more info	PubMed
located_in Golgi apparatus	ISO Inferred from Sequence Orthology more info
is_active_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	ISO Inferred from Sequence Orthology more info
is_active_in mitochondrion	IMP Inferred from Mutant Phenotype more info	PubMed
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in perinuclear region of cytoplasm	ISO Inferred from Sequence Orthology more info
located_in trans-Golgi network	ISO Inferred from Sequence Orthology more info	PubMed

General protein information

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Preferred Names: vacuolar protein sorting-associated protein 54

Names: tumor antigen SLP-8p homolog; vacuolar protein sorting 54

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.

mRNA and Protein(s)

NM_001290628.1 → NP_001277557.1 vacuolar protein sorting-associated protein 54 isoform 2

See identical proteins and their annotated locations for NP_001277557.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate splice site in the 5' coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.

Source sequence(s)

AF424699, AK036667, AL669979, CJ134863

Consensus CDS

CCDS70147.1

UniProtKB/TrEMBL

Q91ZJ4

Related

ENSMUSP00000105206.2, ENSMUST00000109578.8

Conserved Domains (1) summary

pfam07928
Location:727 → 855

Vps54; Vps54-like protein
NM_139061.5 → NP_620692.3 vacuolar protein sorting-associated protein 54 isoform 1

See identical proteins and their annotated locations for NP_620692.3

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AF424699, AK036667, AL669979, CJ134863

Consensus CDS

CCDS24463.1

UniProtKB/Swiss-Prot

Q5SPW0, Q8BPB3, Q8CFZ7, Q8CHL5, Q8R3R4, Q8R3X1

UniProtKB/TrEMBL

Q91ZJ4

Related

ENSMUSP00000006221.8, ENSMUST00000006221.14

Conserved Domains (1) summary

pfam07928
Location:739 → 867

Vps54; Vps54-like protein

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000077.7 Reference GRCm39 C57BL/6J

Range

21189032..21271133

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011243720.2 → XP_011242022.1 vacuolar protein sorting-associated protein 54 isoform X1

See identical proteins and their annotated locations for XP_011242022.1

UniProtKB/Swiss-Prot

Q5SPW0, Q8BPB3, Q8CFZ7, Q8CHL5, Q8R3R4, Q8R3X1

UniProtKB/TrEMBL

Q91ZJ4

Conserved Domains (1) summary

pfam07928
Location:739 → 867

Vps54; Vps54-like protein
XM_030246004.2 → XP_030101864.1 vacuolar protein sorting-associated protein 54 isoform X2

UniProtKB/TrEMBL

Q91ZJ4

Conserved Domains (1) summary

pfam07928
Location:727 → 855

Vps54; Vps54-like protein
XM_006514699.5 → XP_006514762.1 vacuolar protein sorting-associated protein 54 isoform X3

UniProtKB/TrEMBL

Q5SRW8

Related

ENSMUSP00000116739.2, ENSMUST00000132017.2

Conserved Domains (1) summary

pfam07928
Location:573 → 701

Vps54; Vps54-like protein