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    VPS41 VPS41 subunit of HOPS complex [ Homo sapiens (human) ]

    Gene ID: 27072, updated on 14-Nov-2024

    Summary

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    Official Symbol
    VPS41provided by HGNC
    Official Full Name
    VPS41 subunit of HOPS complexprovided by HGNC
    Primary source
    HGNC:HGNC:12713
    See related
    Ensembl:ENSG00000006715 MIM:605485; AllianceGenome:HGNC:12713
    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
    HVPS41; HVSP41; SCAR29; hVps41p
    Summary
    Vesicle mediated protein sorting plays an important role in segregation of intracellular molecules into distinct organelles. Genetic studies in yeast have identified more than 40 vacuolar protein sorting (VPS) genes involved in vesicle transport to vacuoles. This gene encodes the human ortholog of yeast Vps41 protein which is also conserved in Drosophila, tomato, and Arabidopsis. Expression studies in yeast and human indicate that this protein may be involved in the formation and fusion of transport vesicles from the Golgi. Several transcript variants encoding different isoforms have been described for this gene, however, the full-length nature of not all is known. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in brain (RPKM 18.7), gall bladder (RPKM 13.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See VPS41 in Genome Data Viewer
    Location:
    7p14.1
    Exon count:
    31
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (38722974..38909191, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (38880029..39066224, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (38762574..38948791, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene keratin 8 pseudogene 20 Neighboring gene CFAP144 pseudogene 1 Neighboring gene MPRA-validated peak6495 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:38925534-38926050 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:38926051-38926567 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25874 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:38989846-38991045 Neighboring gene POU6F2 antisense RNA 2 Neighboring gene MPRA-validated peak6496 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr7:39082046-39082670 Neighboring gene POU class 6 homeobox 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:39298804-39299337 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:39310732-39311232 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:39311233-39311733 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:39349937-39350440 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:39350441-39350942 Neighboring gene uncharacterized LOC105375239 Neighboring gene small nucleolar RNA, H/ACA box 20B

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

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    Related articles in PubMed

    1. VPS41, a protein involved in lysosomal trafficking, is protective in Caenorhabditis elegans and mammalian cellular models of Parkinson's disease. Ruan Q, et al. Neurobiol Dis, 2010 Feb. PMID 19850127, Free PMC Article
    2. hVPS41 is expressed in multiple isoforms and can associate with vesicles through a RING-H2 finger motif. McVey Ward D, et al. Exp Cell Res, 2001 Jul 1. PMID 11412045
    3. hVps41 and VAMP7 function in direct TGN to late endosome transport of lysosomal membrane proteins. Pols MS, et al. Nat Commun, 2013. PMID 23322049
    4. Loss-of-Function Variants in HOPS Complex Genes VPS16 and VPS41 Cause Early Onset Dystonia Associated with Lysosomal Abnormalities. Steel D, et al. Ann Neurol, 2020 Nov. PMID 32808683
    5. Neurodegenerative VPS41 variants inhibit HOPS function and mTORC1-dependent TFEB/TFE3 regulation. van der Welle REN, et al. EMBO Mol Med, 2021 May 7. PMID 33851776, Free PMC Article

    See all (63) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Neurodegenerative VPS41 variants inhibit HOPS function and mTORC1-dependent TFEB/TFE3 regulation.
      Title: Neurodegenerative VPS41 variants inhibit HOPS function and mTORC1-dependent TFEB/TFE3 regulation.
    2. Bi-allelic variants in HOPS complex subunit VPS41 cause cerebellar ataxia and abnormal membrane trafficking.
      Title: Bi-allelic variants in HOPS complex subunit VPS41 cause cerebellar ataxia and abnormal membrane trafficking.
    3. Loss-of-Function Variants in HOPS Complex Genes VPS16 and VPS41 Cause Early Onset Dystonia Associated with Lysosomal Abnormalities.
      Title: Loss-of-Function Variants in HOPS Complex Genes VPS16 and VPS41 Cause Early Onset Dystonia Associated with Lysosomal Abnormalities.
    4. Here, the authors show that Vps8 overexpression inhibits homotypic fusion and vacuole protein sorting (HOPS)-dependent trafficking routes including late endosome maturation, autophagosome-lysosome fusion, crinophagy and lysosome-related organelle formation. Mechanistically, Vps8 overexpression abolishes the late endosomal localization of HOPS-specific Vps41/Lt and prevents HOPS assembly.
      Title: Vps8 overexpression inhibits HOPS-dependent trafficking routes by outcompeting Vps41/Lt.
    5. Our results indicate that an ARF-like GTPase gene product, ARL-8, mitigates endocytic Ab neurodegeneration in a VPS-41-dependent manner, rather than through RAB-7 and AP3 as with alpha-synuclein..we demonstrate that the LC3 orthologue, LGG-2, plays a critical role in Ab toxicity with ARL-8.
      Title: Distinct functional roles of Vps41-mediated neuroprotection in Alzheimer's and Parkinson's disease models of neurodegeneration.
    6. VPS18 recruits VPS41 to the human HOPS complex via a RING-RING interaction
      Title: VPS18 recruits VPS41 to the human HOPS complex via a RING-RING interaction.
    7. VPS41 subunit of HOPS complex was defined to be the major partner for interacting with RILP.
      Title: RILP interacts with HOPS complex via VPS41 subunit to regulate endocytic trafficking.
    8. hVps41 and VAMP7 are specifically involved in the fusion of trans-Golgi network-derived lysosome-associated membrane protein carriers with late endosomes.
      Title: hVps41 and VAMP7 function in direct TGN to late endosome transport of lysosomal membrane proteins.
    9. Vps41 knockdown impairs late endosome fusion and fusion between late endosomes and lysosomes.
      Title: The HOPS proteins hVps41 and hVps39 are required for homotypic and heterotypic late endosome fusion.
    10. Both a functional heterotetrameric adaptor protein complex and a homotypic fusion and vacuole protein sorting-tethering complex are required for VPS41 to elicit neuroprotection in a transgenic model of Parkinson's disease.
      Title: Functional analysis of VPS41-mediated neuroprotection in Caenorhabditis elegans and mammalian models of Parkinson's disease.
    Submit: New GeneRIF Correction See all GeneRIFs (12)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Spinocerebellar ataxia, autosomal recessive 29
    MedGen: C5543595 OMIM: 619389 GeneReviews: Not available
    		not available

    EBI GWAS Catalog

    Description
    A genome-wide study of common SNPs and CNVs in cognitive performance in the CANTAB.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables microtubule binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in Golgi vesicle transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in endosomal vesicle fusion NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in endosome to lysosome transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in late endosome to lysosome transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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
    		  
    involved_in regulation of SNARE complex assembly NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in vesicle-mediated transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of AP-3 adaptor complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in Golgi-associated vesicle IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    part_of HOPS complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of HOPS complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of HOPS complex IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    part_of HOPS complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of clathrin complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in clathrin-coated vesicle IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in early endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endosome membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endosome membrane TAS
    Traceable Author Statement
    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 membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of lysosomal HOPS complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in lysosomal membrane HDA PubMed 
    located_in lysosomal membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in lysosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in microtubule cytoskeleton IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    vacuolar protein sorting-associated protein 41 homolog
    Names
    S53
    VPS41, HOPS complex subunit
    vacuolar assembly protein 41
    vacuolar protein sorting 41 homolog

    NCBI Reference Sequences (RefSeq)

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    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.

    mRNA and Protein(s)

    1. NM_014396.4 → NP_055211.2  vacuolar protein sorting-associated protein 41 homolog isoform 1

      See identical proteins and their annotated locations for NP_055211.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the full-length isoform (1).
      Source sequence(s)
      AC004850, BC044851, U87309
      Consensus CDS
      CCDS5457.1
      UniProtKB/Swiss-Prot
      E9PF36, P49754, Q86TP8, Q99851, Q99852
      UniProtKB/TrEMBL
      B2RB94
      Related
      ENSP00000309457.4, ENST00000310301.9
      Conserved Domains (3) summary
      smart00299
      Location:571 → 708
      CLH; Clathrin heavy chain repeat homology
      sd00039
      Location:138 → 169
      7WD40; WD40 repeat [structural motif]
      cd16690
      Location:787 → 841
      RING-H2_Vps41; RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 41 (Vps41) and similar proteins

    2. NM_080631.4 → NP_542198.2  vacuolar protein sorting-associated protein 41 homolog isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) is missing a sequence segment in the coding region compared to transcript variant 1. However, it maintains the same reading frame and encodes an isoform (2) which is 25 aa shorter than isoform 1.
      Source sequence(s)
      AC004850, BC044851
      Consensus CDS
      CCDS5458.2
      UniProtKB/TrEMBL
      B2RB94
      Related
      ENSP00000379297.2, ENST00000395969.6
      Conserved Domains (2) summary
      smart00299
      Location:546 → 683
      CLH; Clathrin heavy chain repeat homology
      cd16690
      Location:762 → 816
      RING-H2_Vps41; RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 41 (Vps41) and similar proteins

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      38722974..38909191 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017011988.2 → XP_016867477.1  vacuolar protein sorting-associated protein 41 homolog isoform X1

    RNA

    1. XR_007060008.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      38880029..39066224 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054357904.1 → XP_054213879.1  vacuolar protein sorting-associated protein 41 homolog isoform X1

    RNA

    1. XR_008487564.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P49754.3 GenPept UniProtKB/Swiss-Prot:P49754

    Gene LinkOut

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

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