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    VPS26C VPS26 endosomal protein sorting factor C [ Homo sapiens (human) ]

    Gene ID: 10311, updated on 27-Nov-2024

    Summary

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    Official Symbol
    VPS26Cprovided by HGNC
    Official Full Name
    VPS26 endosomal protein sorting factor Cprovided by HGNC
    Primary source
    HGNC:HGNC:3044
    See related
    Ensembl:ENSG00000157538 MIM:605298; AllianceGenome:HGNC:3044
    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
    DCRA; DSCR3; DSCRA
    Summary
    The region of chromosome 21 between genes CBR and ERG (CBR-ERG region), which spans 2.5 Mb on 21q22.2, has been defined by analysis of patients with partial trisomy 21. It contributes significantly to the pathogenesis of many characteristics of Down syndrome, including morphological features, hypotonia, and cognitive disability. The DSCR3 (Down syndrome critical region gene 3) gene is found in this region and is predictated to contain eight exons. DSCR3 is expressed in most tissues examined. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in kidney (RPKM 11.4), duodenum (RPKM 10.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See VPS26C in Genome Data Viewer
    Location:
    21q22.13
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (37223420..37268108, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (35605645..35650315, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (38595721..38640409, complement)

    Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene tetratricopeptide repeat domain 3 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr21:38567734-38568933 Neighboring gene TTC3 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:38579468-38580304 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18444 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18445 Neighboring gene RNA, 7SL, cytoplasmic 678, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18446 Neighboring gene Down syndrome critical region 9 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18447 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:38629775-38630367 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:38630368-38630960 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13299 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18449 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13300 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:38655347-38656273 Neighboring gene uncharacterized LOC124905018 Neighboring gene uncharacterized LOC124905019

    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
    • 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. The arrestin fold: variations on a theme. Aubry L, et al. Curr Genomics, 2009 Apr. PMID 19794886, Free PMC Article
    2. VPS26C homozygous nonsense variant in two cousins with neurodevelopmental deficits, growth failure, skeletal abnormalities, and distinctive facial features. Beetz C, et al. Clin Genet, 2020 Apr. PMID 31845315
    3. Isolation of a novel human gene from the Down syndrome critical region of chromosome 21q22.2. Nakamura A, et al. J Biochem, 1997 Oct. PMID 9399594
    4. Vacuolar Protein Sorting 26C encodes an evolutionarily conserved large retromer subunit in eukaryotes that is important for root hair growth in Arabidopsis thaliana. Jha SG, et al. Plant J, 2018 May. PMID 29495075
    5. Evolutionary reconstruction of the retromer complex and its function in Trypanosoma brucei. Koumandou VL, et al. J Cell Sci, 2011 May 1. PMID 21502137, Free PMC Article

    See all (33) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. VPS26C homozygous nonsense variant in two cousins with neurodevelopmental deficits, growth failure, skeletal abnormalities, and distinctive facial features.
      Title: VPS26C homozygous nonsense variant in two cousins with neurodevelopmental deficits, growth failure, skeletal abnormalities, and distinctive facial features.
    2. These studies illustrate that GFP-HsDSCR3 is able to complement the vps26c root hair phenotype in Arabidopsis, indicating a deep conservation of cellular function for this large retromer subunit across plant and animal kingdoms.
      Title: Vacuolar Protein Sorting 26C encodes an evolutionarily conserved large retromer subunit in eukaryotes that is important for root hair growth in Arabidopsis thaliana.
    3. Heterotrimer composed of DSCR3, C16orf62 and VPS29 orchestrates endosomal cargo retrieval and recycling.
      Title: Retriever is a multiprotein complex for retromer-independent endosomal cargo recycling.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    No evidence available (Last evaluated 2012-04-24)

    ClinGen Genome Curation Page
    Triplosensitivity

    No evidence available (Last evaluated 2012-04-24)

    ClinGen Genome Curation Page

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC117385

    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
    		  
    Component Evidence Code Pubs
    is_active_in endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus HDA PubMed 

    General protein information

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    Preferred Names
    vacuolar protein sorting-associated protein 26C
    Names
    DSCR3 arrestin fold containing
    Down syndrome critical region 3
    Down syndrome critical region gene 3
    Down syndrome critical region protein 3
    Down syndrome critical region protein A

    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.

    Genomic

    1. NG_009410.2 RefSeqGene

      Range
      5774..49686
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001331018.1 → NP_001317947.1  vacuolar protein sorting-associated protein 26C isoform 2

      Status: REVIEWED

      Source sequence(s)
      AK303624, AP001412, BX648191, D87343, DA311783, DB286372
      Consensus CDS
      CCDS82671.1
      UniProtKB/TrEMBL
      A8MY26
      Related
      ENSP00000381967.1, ENST00000399001.5
      Conserved Domains (1) summary
      cl22903
      Location:31 → 158
      Arrestin_N; Arrestin (or S-antigen), N-terminal domain

    2. NM_001331021.1 → NP_001317950.1  vacuolar protein sorting-associated protein 26C isoform 3

      Status: REVIEWED

      Source sequence(s)
      AK303624, AP001412, AP001432, BX648191
      Consensus CDS
      CCDS82672.1
      UniProtKB/TrEMBL
      A8MTY9
      Related
      ENSP00000381964.1, ENST00000398998.1
      Conserved Domains (1) summary
      cl22903
      Location:7 → 235
      Arrestin_N; Arrestin (or S-antigen), N-terminal domain

    3. NM_001331022.1 → NP_001317951.1  vacuolar protein sorting-associated protein 26C isoform 4

      Status: REVIEWED

      Source sequence(s)
      AK300024, AK303624, AP001412, BX648191, D87343, DA311783, DB286372
      Consensus CDS
      CCDS82673.1
      UniProtKB/TrEMBL
      B7Z606
      Related
      ENSP00000419496.1, ENST00000476950.5
      Conserved Domains (1) summary
      cl22903
      Location:1 → 256
      Arrestin_N; Arrestin (or S-antigen), N-terminal domain

    4. NM_006052.2 → NP_006043.1  vacuolar protein sorting-associated protein 26C isoform 1

      See identical proteins and their annotated locations for NP_006043.1

      Status: REVIEWED

      Source sequence(s)
      AP001412, AP001432
      Consensus CDS
      CCDS33553.1
      UniProtKB/Swiss-Prot
      B2R6T8, B7Z6B1, D3DSH4, O14972, Q2TAY6
      Related
      ENSP00000311399.6, ENST00000309117.11
      Conserved Domains (1) summary
      cl22903
      Location:1 → 283
      Arrestin_N; Arrestin (or S-antigen), N-terminal domain

    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_000021.9 Reference GRCh38.p14 Primary Assembly

      Range
      37223420..37268108 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047440658.1 → XP_047296614.1  vacuolar protein sorting-associated protein 26C isoform X1

    RNA

    1. XR_007067776.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060945.1 Alternate T2T-CHM13v2.0

      Range
      35605645..35650315 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054324301.1 → XP_054180276.1  vacuolar protein sorting-associated protein 26C isoform X1

    RNA

    1. XR_008485322.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O14972.1 GenPept UniProtKB/Swiss-Prot:O14972

    Gene LinkOut

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

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