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    VPS26A VPS26 retromer complex component A [ Homo sapiens (human) ]

    Gene ID: 9559, updated on 3-Dec-2024

    Summary

    Official Symbol
    VPS26Aprovided by HGNC
    Official Full Name
    VPS26 retromer complex component Aprovided by HGNC
    Primary source
    HGNC:HGNC:12711
    See related
    Ensembl:ENSG00000122958 MIM:605506; AllianceGenome:HGNC:12711
    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
    HB58; PEP8A; VPS26; Hbeta58
    Summary
    This gene belongs to a group of vacuolar protein sorting (VPS) genes. The encoded protein is a component of a large multimeric complex, termed the retromer complex, involved in retrograde transport of proteins from endosomes to the trans-Golgi network. The close structural similarity between the yeast and human proteins that make up this complex suggests a similarity in function. Expression studies in yeast and mammalian cells indicate that this protein interacts directly with VPS35, which serves as the core of the retromer complex. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in testis (RPKM 20.4), esophagus (RPKM 15.7) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See VPS26A in Genome Data Viewer
    Location:
    10q22.1
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (69124178..69174412)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (69991871..70042751)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (70883934..70934168)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378342 Neighboring gene Sharpr-MPRA regulatory region 5024 Neighboring gene MPRA-validated peak1005 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3475 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3476 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3477 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:70812477-70812978 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:70812979-70813478 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3478 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2426 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3480 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3479 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3481 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3482 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3483 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3484 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16959 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:70828777-70829328 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16968 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr10:70847990-70849189 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2427 Neighboring gene serglycin Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3485 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2428 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:70884392-70884898 Neighboring gene ribosomal protein S12 pseudogene 17 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3486 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:70949649-70949852 Neighboring gene Suv3 like RNA helicase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2429 Neighboring gene uncharacterized LOC101928994 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16991 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16994 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16995 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3487 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3488 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr10:70991590-70992789 Neighboring gene hexokinase domain containing 1

    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?

    Phenotypes

    EBI GWAS Catalog

    Description
    Genome-wide analysis of polymorphisms associated with cytokine responses in smallpox vaccine recipients.
    EBI GWAS Catalog
    Genome-wide association study in individuals of South Asian ancestry identifies six new type 2 diabetes susceptibility loci.
    EBI GWAS Catalog
    Identification of HKDC1 and BACE2 as genes influencing glycemic traits during pregnancy through genome-wide association studies.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env Depletion of VPS26 by siRNA increases plasma membrane expression of HIV-1 gp120/gp41 and incorporation into viral particles, indicating that VPS26 regulates gp120/gp41 trafficking in cells PubMed
    Envelope transmembrane glycoprotein gp41 env The gp41 cytoplasmic tail binds directly to retromer components VPS26 and VPS35 in HIV-1-infected cells PubMed
    env Depletion of VPS26 by siRNA increases plasma membrane expression of HIV-1 gp120/gp41 and incorporation into viral particles, indicating that VPS26 regulates gp120/gp41 trafficking in cells PubMed
    env The gp41 cytoplasmic tail determines sensitivity to VPS26 depletion in HIV-1-infected cells, and the cytoplasmic tail alone is sufficient for trafficking of Env through the retromer-containing compartment 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

    • FLJ12930

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in endocytic recycling IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in intracellular protein transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of macroautophagy TAS
    Traceable Author Statement
    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 IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in retrograde transport, endosome to Golgi NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in early endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endosome membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in lysosome IDA
    Inferred from Direct Assay
    more info
     
    part_of retromer complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of retromer complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of retromer complex NAS
    Non-traceable Author Statement
    more info
    PubMed 
    part_of retromer, cargo-selective complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of retromer, cargo-selective complex NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in tubular endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in vesicle IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    vacuolar protein sorting-associated protein 26A
    Names
    VPS26 retromer complex comonent A
    vacuolar protein sorting 26 homolog A
    vesicle protein sorting 26A

    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_001035260.3NP_001030337.1  vacuolar protein sorting-associated protein 26A isoform 2

      See identical proteins and their annotated locations for NP_001030337.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an exon in the 3' coding region which results in a frameshift and early translation termination, compared to variant 1. The encoded isoform (2) has a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AF054179, AL596223, BQ068008, BX647725, DA498726
      Consensus CDS
      CCDS41536.1
      UniProtKB/TrEMBL
      S4R3Q6
      Related
      ENSP00000378532.1, ENST00000395098.5
      Conserved Domains (1) summary
      pfam03643
      Location:8243
      Vps26; Vacuolar protein sorting-associated protein 26
    2. NM_001318944.2NP_001305873.1  vacuolar protein sorting-associated protein 26A isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) includes an additional exon in the 5' region, and it thus differs in its 5' UTR and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (3) has a shorter and distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AK309021, AL596223, BX647725, DA498726
      UniProtKB/TrEMBL
      B4DLT1
      Conserved Domains (1) summary
      pfam03643
      Location:45276
      Vps26; Vacuolar protein sorting-associated protein 26
    3. NM_001318945.2NP_001305874.1  vacuolar protein sorting-associated protein 26A isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) includes an additional exon in the 5' region, and it thus differs in its 5' UTR and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (4) has a shorter and distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AK297142, AL596223, BX647725, DA498726
      UniProtKB/TrEMBL
      B4DLT1
      Conserved Domains (1) summary
      pfam03643
      Location:34266
      Vps26; Vacuolar protein sorting-associated protein 26
    4. NM_001318946.2NP_001305875.1  vacuolar protein sorting-associated protein 26A isoform 5

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks an alternate exon in the 5' region, and it thus differs in its 5' UTR and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (5) is shorter at the N-terminus, compared to isoform 1.
      Source sequence(s)
      AF054179, AL596223, BX647725, DA498726
      UniProtKB/TrEMBL
      A8K3C1
      Conserved Domains (1) summary
      pfam03643
      Location:2172
      Vps26; Vacuolar protein sorting-associated protein 26
    5. NM_004896.5NP_004887.2  vacuolar protein sorting-associated protein 26A isoform 1

      See identical proteins and their annotated locations for NP_004887.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AF054179, AL596223, BX647725, DA498726
      Consensus CDS
      CCDS7286.1
      UniProtKB/Swiss-Prot
      A8MZ56, B2RDD3, O75436, Q8TBH4, Q9H982
      UniProtKB/TrEMBL
      B4DLT1
      Related
      ENSP00000263559.6, ENST00000263559.11
      Conserved Domains (1) summary
      pfam03643
      Location:8283
      Vps26; Vacuolar protein sorting-associated protein 26

    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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      69124178..69174412
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      69991871..70042751
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054367220.1XP_054223195.1  vacuolar protein sorting-associated protein 26A isoform X1

      UniProtKB/Swiss-Prot
      A8MZ56, B2RDD3, O75436, Q8TBH4, Q9H982
      UniProtKB/TrEMBL
      B4DLT1