U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from MedGen

    • Showing Current items.

    VPS4A vacuolar protein sorting 4 homolog A [ Homo sapiens (human) ]

    Gene ID: 27183, updated on 5-May-2024

    Summary

    Official Symbol
    VPS4Aprovided by HGNC
    Official Full Name
    vacuolar protein sorting 4 homolog Aprovided by HGNC
    Primary source
    HGNC:HGNC:13488
    See related
    Ensembl:ENSG00000132612 MIM:609982; AllianceGenome:HGNC:13488
    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
    SKD1; SKD2; VPS4; SKD1A; CIMDAG; VPS4-1
    Summary
    The protein encoded by this gene is a member of the AAA protein family (ATPases associated with diverse cellular activities), and is the homolog of the yeast Vps4 protein. In humans, two paralogs of the yeast protein have been identified. The former share a high degree of aa sequence similarity with each other, and also with yeast Vps4 and mouse Skd1 proteins. The mouse Skd1 (suppressor of K+ transport defect 1) has been shown to be really an yeast Vps4 ortholog. Functional studies indicate that both human paralogs associate with the endosomal compartments, and are involved in intracellular protein trafficking, similar to Vps4 protein in yeast. The gene encoding this paralog has been mapped to chromosome 16; the gene for the other resides on chromosome 18. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in brain (RPKM 45.1), fat (RPKM 36.4) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See VPS4A in Genome Data Viewer
    Location:
    16q22.1
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (69311350..69326939)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (75113104..75128634)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (69345253..69360842)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 22, pseudogene Neighboring gene syntrophin beta 2 Neighboring gene zinc finger CCHC-type and RNA binding motif containing 1 pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:69344125-69345075 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:69345076-69346025 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:69349279-69350478 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:69363857-69364504 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7657 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:69365153-69365800 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7658 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7659 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11036 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11037 Neighboring gene component of oligomeric golgi complex 8 Neighboring gene peptide deformylase, mitochondrial Neighboring gene nucleolar pre-rRNA processing protein NIP7 Neighboring gene transmembrane p24 trafficking protein 6

    Genomic regions, transcripts, and products

    Expression

    • Project title: 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    HIV-1 incorporates VPS4A and CHMP4b into virions PubMed
    HIV-1 replication requires VPS4A function as expression of a dominant negative VPS4A (DE228Q) decreased Gag VLP production PubMed
    HIV-1 replication is inhibited by overexpression of VPS4A in HEK293T cells PubMed
    Knockdown of vacuolar protein sorting 4 homolog A (VPS4A) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Nef nef HIV-1 Nef targets CD4 to CD63-containing lysosomes for Nef-induced degradation of CD4, which requires the VPS4-mediated ESCRT machinery PubMed
    Pr55(Gag) gag Expressing a dominant negative mutant of VSP4A E228Q or silencing VSP4A by siRNA upregulate the amount of HIV-1 Gag on the plasma membrane and downregulate release of Gag virus-like particles PubMed
    gag CHMP4B and VPS4A are recruited to the site of HIV-1 Gag assembly, in which VPS4A remains associated with the Gag assembly site twice longer than CHMP4B PubMed
    gag VPS4A/B proteins are recruited to assist with membrane fission after full assembly of HIV-1 Gag into the VLP PubMed
    gag ALIX, CHMP2A/B, CHMP4A/B, and VPS4A/B proteins are required for the budding of HIV-1 Gag and the HIV-1 infectivity PubMed
    gag VPS4A increases co-localization of HIV-1 Gag with the ESCRT proteins Chmp1b, Chmp4b, and Chmp4c at sites of HIV-1 assembly PubMed
    gag Replacing the NC-p1-p6 region of HIV-1 Gag with the leucine zipper domain of yeast GCN4 overcomes inhibition of HIV-1 particle budding by dominant-negative ESCRT proteins such as CHMP3 and Vps4A PubMed
    gag ISG15 inhibits budding of HIV-1 by disrupting the association between Vps4 and the Gag budding complex PubMed
    gag VPS4A is co-localized with nascent HIV-1 Gag molecules at the host cell plasma membrane by using live-cell imaging PubMed
    Vpu vpu The v-ATPase VPS4 is required for Vpu-induced cell surface downregulation of BST-2. VPS4 E223/Q mutant impairs the ability of Vpu to downregulate BST-2 from the cell surface PubMed
    p1 gag The budding defect of p6-deficient HIV-1 Gag is caused primarily by C-terminal exposure of p1, which activates a cis-acting inhibitory budding signal (IBS) and impairs an exosomes and microvesicles (EMV) cargo-VPS4 interaction PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ22197

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IMP
    Inferred from Mutant Phenotype
    more info
     
    enables ATP hydrolysis activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables ATP hydrolysis activity IMP
    Inferred from Mutant Phenotype
    more info
     
    enables ATP hydrolysis activity TAS
    Traceable Author Statement
    more info
     
    enables ATP-dependent protein disaggregase activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein-containing complex binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in ESCRT III complex disassembly NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in ESCRT complex disassembly NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in abscission IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in actomyosin contractile ring contraction TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in autophagosome maturation NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in autophagy NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in cell division IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cytoskeleton-dependent cytokinesis TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in endosomal transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in endosomal transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in endosomal vesicle fusion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in intracellular cholesterol transport IMP
    Inferred from Mutant Phenotype
    more info
     
    involved_in late endosomal microautophagy ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in late endosome to lysosome transport via multivesicular body sorting pathway NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in macroautophagy NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in membrane fission NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in midbody abscission IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in midbody abscission NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in mitotic cytokinesis checkpoint signaling IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in mitotic metaphase chromosome alignment IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in mitotic nuclear membrane reassembly TAS
    Traceable Author Statement
    more info
     
    involved_in multivesicular body assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in multivesicular body assembly NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in multivesicular body sorting pathway NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in negative regulation of cytokinesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in nuclear envelope organization TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in nuclear membrane reassembly NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in nuclear membrane reassembly TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in nucleus organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in nucleus organization NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in plasma membrane repair NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in positive regulation of exosomal secretion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of viral budding via host ESCRT complex IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in protein targeting to lysosome IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of protein localization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of protein localization to plasma membrane IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in vacuole organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in vesicle budding from membrane IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in vesicle uncoating IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in vesicle-mediated transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in viral budding from plasma membrane IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in viral budding via host ESCRT complex IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in viral release from host cell IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of ATPase complex NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in Flemming body IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in centrosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in early endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endosome membrane IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in extracellular exosome HDA PubMed 
    located_in late endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in late endosome membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in lysosome IDA
    Inferred from Direct Assay
    more info
     
    located_in midbody IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in midbody NAS
    Non-traceable Author Statement
    more info
    PubMed 
    colocalizes_with midbody TAS
    Traceable Author Statement
    more info
    PubMed 
    part_of nuclear pore NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in spindle pole IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in vacuolar membrane IDA
    Inferred from Direct Assay
    more info
     

    General protein information

    Preferred Names
    vacuolar protein sorting-associated protein 4A
    Names
    SKD1-homolog
    hVPS4
    vacuolar protein sorting factor 4A
    vacuolar sorting protein 4
    NP_037377.1

    NCBI Reference Sequences (RefSeq)

    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_013245.3NP_037377.1  vacuolar protein sorting-associated protein 4A

      See identical proteins and their annotated locations for NP_037377.1

      Status: REVIEWED

      Source sequence(s)
      AC026464, AF255952
      Consensus CDS
      CCDS45517.1
      UniProtKB/Swiss-Prot
      B2RCB7, Q8TF07, Q9UI03, Q9UN37, Q9Y582
      UniProtKB/TrEMBL
      I3L4J1
      Related
      ENSP00000254950.11, ENST00000254950.13
      Conserved Domains (3) summary
      PTZ00454
      Location:4348
      PTZ00454; 26S protease regulatory subunit 6B-like protein; Provisional
      pfam09336
      Location:374434
      Vps4_C; Vps4 C terminal oligomerization domain
      cd19521
      Location:121291
      RecA-like_VPS4; ATPase domain of vacuolar protein sorting-associated protein 4

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      69311350..69326939
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      75113104..75128634
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)