Vps53 VPS53 GARP complex subunit [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Vps53provided by MGI
Official Full Name: VPS53 GARP complex subunitprovided by MGI
Primary source: MGI:MGI:1915549
See related: Ensembl:ENSMUSG00000017288 AllianceGenome:MGI:1915549
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: Hccs1; 2010002A08Rik; 2310040I21Rik; 3100002B05Rik
Summary: Involved in protein targeting to lysosome and vesicle-mediated cholesterol transport. Predicted to be located in several cellular components, including perinuclear region of cytoplasm; recycling endosome; and trans-Golgi network. Predicted to be part of EARP complex and GARP complex. Human ortholog(s) of this gene implicated in pontocerebellar hypoplasia type 2E. Orthologous to human VPS53 (VPS53 subunit of GARP complex). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in CNS E18 (RPKM 8.3), cerebellum adult (RPKM 8.2) and 28 other tissues See more
Orthologs: human all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 11 B5; 11 45.92 cM

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	11	NC_000077.7 (75937052..76070464, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	11	NC_000077.6 (76046226..76179638, complement)

Chromosome 11 - NC_000077.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Disruption of HCCS1 in mice leads to embryonic lethality, accompanied by abnormal labyrinth architecture resulting from the excessive proliferation of trophoblast cells in the placenta.
Title: HCCS1 overexpression induces apoptosis via cathepsin D and intracellular calcium, and HCCS1 disruption in mice causes placental abnormality.

Submit: New GeneRIF Correction

Variation

Go to the top of the page Help

Alleles

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

Endonuclease-mediated (2)
Gene trapped (1)
Targeted (3) 1 citation

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

36.MMHAP4FRD12.seq (e-PCR)
- UniSTS:124183

BB162755 (e-PCR)
- UniSTS:185897

D11Bhm25 (e-PCR), detects polymorphism
- UniSTS:141624

D11Bhm26 (e-PCR), detects polymorphism
- UniSTS:141625

D11Bhm27 (e-PCR), detects polymorphism
- UniSTS:141626

D10Chm174 (e-PCR)
- UniSTS:518202

D11Bhm28 (e-PCR), detects polymorphism
- UniSTS:141627

D11Mit321 (e-PCR), detects polymorphism
- UniSTS:126534

D11Mit7 (e-PCR), detects polymorphism
- UniSTS:126617

Gene Ontology Provided by MGI

Process	Evidence Code	Pubs
involved_in endocytic recycling	ISO Inferred from Sequence Orthology more info
involved_in endocytic recycling	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within lysosomal transport	ISO Inferred from Sequence Orthology more info	PubMed
involved_in protein targeting to lysosome	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in retrograde transport, endosome to Golgi	IBA Inferred from Biological aspect of Ancestor more info
involved_in retrograde transport, endosome to Golgi	ISO Inferred from Sequence Orthology more info
involved_in retrograde transport, endosome to Golgi	ISS Inferred from Sequence or Structural Similarity more info
involved_in vesicle-mediated cholesterol transport	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of EARP complex	ISO Inferred from Sequence Orthology more info	PubMed
part_of EARP complex	ISS Inferred from Sequence or Structural Similarity more info
part_of GARP complex	IBA Inferred from Biological aspect of Ancestor more info
part_of GARP complex	ISO Inferred from Sequence Orthology more info	PubMed
located_in Golgi apparatus	ISO Inferred from Sequence Orthology more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in endosome membrane	IEA Inferred from Electronic Annotation more info
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
located_in membrane	ISO Inferred from Sequence Orthology more info	PubMed
located_in perinuclear region of cytoplasm	IEA Inferred from Electronic Annotation more info
located_in perinuclear region of cytoplasm	ISO Inferred from Sequence Orthology more info
located_in recycling endosome	ISO Inferred from Sequence Orthology more info	PubMed
located_in recycling endosome	ISS Inferred from Sequence or Structural Similarity more info
located_in trans-Golgi network	ISO Inferred from Sequence Orthology more info	PubMed

General protein information

Go to the top of the page Help

Preferred Names: vacuolar protein sorting-associated protein 53 homolog

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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.