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Vps41 VPS41 HOPS complex subunit [ Mus musculus (house mouse) ]

Gene ID: 218035, updated on 11-Apr-2024

Summary

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Official Symbol
Vps41provided by MGI
Official Full Name
VPS41 HOPS complex subunitprovided by MGI
Primary source
MGI:MGI:1929215
See related
Ensembl:ENSMUSG00000041236 AllianceGenome:MGI:1929215
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
Vam2; mVam2
Summary
Enables microtubule binding activity. Predicted to be involved in several processes, including endosomal vesicle fusion; lysosomal transport; and protein targeting to vacuole. Predicted to act upstream of or within autophagy and protein transport. Located in early endosome; late endosome; and microtubule cytoskeleton. Human ortholog(s) of this gene implicated in autosomal recessive cerebellar ataxia. Orthologous to human VPS41 (VPS41 subunit of HOPS complex). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in frontal lobe adult (RPKM 8.5), cortex adult (RPKM 8.2) and 28 other tissues See more
Orthologs
human all
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Genomic context

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Location:
13 A2; 13 6.75 cM
Exon count:
30
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 13 NC_000079.7 (18901462..19050981)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 13 NC_000079.6 (18717292..18866811)

Chromosome 13 - NC_000079.7Genomic Context describing neighboring genes Neighboring gene POU domain, class 6, transcription factor 2 Neighboring gene predicted gene, 31832 Neighboring gene predicted gene, 46402 Neighboring gene STARR-seq mESC enhancer starr_33769 Neighboring gene STARR-seq mESC enhancer starr_33770 Neighboring gene STARR-seq mESC enhancer starr_33771 Neighboring gene STARR-seq mESC enhancer starr_33773 Neighboring gene STARR-seq mESC enhancer starr_33776 Neighboring gene STARR-seq mESC enhancer starr_33777 Neighboring gene STARR-seq mESC enhancer starr_33781 Neighboring gene STARR-seq mESC enhancer starr_33782 Neighboring gene STARR-seq mESC enhancer starr_33784 Neighboring gene predicted gene, 26172 Neighboring gene predicted gene, 53776

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Simple and straightforward construction of a mouse gene targeting vector using in vitro transposition reactions. Aoyama M, et al. Nucleic Acids Res, 2005 Mar 22. PMID 15784610, Free PMC Article
  2. Pancreatic β-Cell-Specific Deletion of VPS41 Causes Diabetes Due to Defects in Insulin Secretion. Burns CH, et al. Diabetes, 2021 Feb. PMID 33168621, Free PMC Article
  3. Impaired stimulation of p38α-MAPK/Vps41-HOPS by LPS from pathogenic Coxiella burnetii prevents trafficking to microbicidal phagolysosomes. Barry AO, et al. Cell Host Microbe, 2012 Dec 13. PMID 23245320
  4. Isolation of differentially expressed genes from wild-type and Twist mutant mouse limb buds. Loebel DA, et al. Genesis, 2002 Jul. PMID 12124942
  5. Spatial restriction of bone morphogenetic protein signaling in mouse gastrula through the mVam2-dependent endocytic pathway. Aoyama M, et al. Dev Cell, 2012 Jun 12. PMID 22698281

See all (28) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. VPS41-mediated incomplete autophagy aggravates cadmium-induced apoptosis in mouse hepatocytes.
    Title: VPS41-mediated incomplete autophagy aggravates cadmium-induced apoptosis in mouse hepatocytes.
  2. Pancreatic beta-Cell-Specific Deletion of VPS41 Causes Diabetes Due to Defects in Insulin Secretion.
    Title: Pancreatic β-Cell-Specific Deletion of VPS41 Causes Diabetes Due to Defects in Insulin Secretion.
  3. Lack of Coxiella burnetii targeting to degradative compartments involves an antagonistic engagement of TLR4 by lipopolysaccharides, lack of p38alpha-MAPK-driven phosphorylation, and block in recruitment of the Vps41 to lipopolysaccharide-containing vesicles.
    Title: Impaired stimulation of p38α-MAPK/Vps41-HOPS by LPS from pathogenic Coxiella burnetii prevents trafficking to microbicidal phagolysosomes.
  4. It was found that Vam2, which interacts with BMP type I receptor, is required for the spatiotemporal modulation of BMP signaling, via sequestration of the receptor complex in the late stages of the endocytic pathway.
    Title: Spatial restriction of bone morphogenetic protein signaling in mouse gastrula through the mVam2-dependent endocytic pathway.
Submit: New GeneRIF Correction

Variation

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Alleles

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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC159002

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables identical protein binding ISO
Inferred from Sequence Orthology
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables microtubule binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in Golgi vesicle transport ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within autophagy IEA
Inferred from Electronic Annotation
more info
  
involved_in cellular response to starvation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in endosomal vesicle fusion IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in endosomal vesicle fusion ISO
Inferred from Sequence Orthology
more info
  
involved_in endosome to lysosome transport ISO
Inferred from Sequence Orthology
more info
  
involved_in intracellular protein transport IEA
Inferred from Electronic Annotation
more info
  
involved_in intracellular transport IEA
Inferred from Electronic Annotation
more info
  
involved_in late endosome to lysosome transport ISO
Inferred from Sequence Orthology
more info
  
involved_in macroautophagy IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein targeting to vacuole IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within protein transport IEA
Inferred from Electronic Annotation
more info
  
involved_in regulated exocytosis ISO
Inferred from Sequence Orthology
more info
  
involved_in vesicle-mediated transport ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
part_of AP-3 adaptor complex ISO
Inferred from Sequence Orthology
more info
  
located_in Golgi apparatus IEA
Inferred from Electronic Annotation
more info
  
located_in Golgi-associated vesicle ISO
Inferred from Sequence Orthology
more info
  
part_of HOPS complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of HOPS complex ISO
Inferred from Sequence Orthology
more info
  
part_of clathrin complex ISO
Inferred from Sequence Orthology
more info
  
located_in clathrin-coated vesicle ISO
Inferred from Sequence Orthology
more info
  
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasmic vesicle IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol ISO
Inferred from Sequence Orthology
more info
  
located_in early endosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endosome IEA
Inferred from Electronic Annotation
more info
  
located_in endosome membrane ISO
Inferred from Sequence Orthology
more info
  
is_active_in late endosome IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in late endosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in late endosome ISO
Inferred from Sequence Orthology
more info
  
located_in late endosome membrane ISO
Inferred from Sequence Orthology
more info
  
part_of lysosomal HOPS complex ISO
Inferred from Sequence Orthology
more info
  
located_in lysosomal membrane ISO
Inferred from Sequence Orthology
more info
  
located_in lysosome ISO
Inferred from Sequence Orthology
more info
  
located_in membrane ISO
Inferred from Sequence Orthology
more info
  
located_in microtubule cytoskeleton IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
vacuolar protein sorting-associated protein 41 homolog
Names
VAM2 homolog
vacuolar protein sorting 41

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)

  1. NM_172120.4 → NP_742118.3  vacuolar protein sorting-associated protein 41 homolog

    See identical proteins and their annotated locations for NP_742118.3

    Status: VALIDATED

    Source sequence(s)
    AB028843, AI851542
    Consensus CDS
    CCDS26257.1
    UniProtKB/Swiss-Prot
    Q05AE9, Q3TPS1, Q5KU39, Q80V99, Q8BKK6, Q8CG01, Q8CJC3
    Related
    ENSMUSP00000072729.5, ENSMUST00000072961.6
    Conserved Domains (3) summary
    smart00299
    Location:570 → 707
    CLH; Clathrin heavy chain repeat homology
    pfam00637
    Location:574 → 709
    Clathrin; Region in Clathrin and VPS
    sd00039
    Location:87 → 131
    7WD40; WD40 repeat [structural motif]

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

  1. NC_000079.7 Reference GRCm39 C57BL/6J

    Range
    18901462..19050981
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006516641.3 → XP_006516704.1  vacuolar protein sorting-associated protein 41 homolog isoform X1

    UniProtKB/TrEMBL
    Q3TS83
    Conserved Domains (2) summary
    smart00299
    Location:413 → 550
    CLH; Clathrin heavy chain repeat homology
    cd16690
    Location:629 → 683
    RING-H2_Vps41; RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 41 (Vps41) and similar proteins
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5KU39.1 GenPept UniProtKB/Swiss-Prot:Q5KU39

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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