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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
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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

    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

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