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VPS51 VPS51 subunit of GARP complex [ Homo sapiens (human) ]

Gene ID: 738, updated on 5-Mar-2024

Summary

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Official Symbol
VPS51provided by HGNC
Official Full Name
VPS51 subunit of GARP complexprovided by HGNC
Primary source
HGNC:HGNC:1172
See related
Ensembl:ENSG00000149823 MIM:615738; AllianceGenome:HGNC:1172
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
FFR; ANG2; ANG3; PCH13; C11orf2; C11orf3
Summary
This gene encodes a member of the vacuolar protein sorting-associated protein 51 family. The encoded protein is a component of the Golgi-associated retrograde protein complex which acts as a tethering factor for carriers in retrograde transport from the early and late endosomes to the trans-Golgi network. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2012]
Expression
Ubiquitous expression in ovary (RPKM 41.5), colon (RPKM 30.6) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
11q13.1
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (65096214..65111862)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (65089493..65105141)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (64863686..64879334)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene N-acetylated alpha-linked acidic dipeptidase like 1 Neighboring gene Sharpr-MPRA regulatory region 288 Neighboring gene cell division cycle associated 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64846103-64846604 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4939 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4940 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64852413-64852997 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:64857368-64857540 Neighboring gene zinc finger protein like 1 Neighboring gene transmembrane protein 262 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64863491-64864285 Neighboring gene Sharpr-MPRA regulatory region 6888 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64877599-64878526 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64878527-64879452 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4942 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3509 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64882956-64883501 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64883502-64884046 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64884593-64885136 Neighboring gene Sharpr-MPRA regulatory region 3974 Neighboring gene transmembrane 7 superfamily member 2 Neighboring gene zinc finger HIT-type containing 2

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. VPS51 biallelic variants cause microcephaly with brain malformations: A confirmatory report. Uwineza A, et al. Eur J Med Genet, 2019 Aug. PMID 31207318
  2. A neurodevelopmental disorder caused by mutations in the VPS51 subunit of the GARP and EARP complexes. Gershlick DC, et al. Hum Mol Genet, 2019 May 1. PMID 30624672, Free PMC Article
  3. Soluble fms-like tyrosine kinase-1 and angiotensin2 target calcitonin gene-related peptide family peptides in maternal vascular smooth muscle cells in pregnancy†. Chauhan M, et al. Biol Reprod, 2021 May 7. PMID 33624744, Free PMC Article
  4. Construction of a 1.2-Mb sequence-ready contig of chromosome 11q13 encompassing the multiple endocrine neoplasia type 1 (MEN1) gene. The European Consortium on MEN1. Lemmens I, et al. Genomics, 1997 Aug 15. PMID 9286704
  5. Structural basis for the interaction of the Golgi-Associated Retrograde Protein Complex with the t-SNARE Syntaxin 6. Abascal-Palacios G, et al. Structure, 2013 Sep 3. PMID 23932592, Free PMC Article

See all (52) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Soluble fms-like tyrosine kinase-1 and angiotensin2 target calcitonin gene-related peptide family peptides in maternal vascular smooth muscle cells in pregnancydagger.
    Title: Soluble fms-like tyrosine kinase-1 and angiotensin2 target calcitonin gene-related peptide family peptides in maternal vascular smooth muscle cells in pregnancy†.
  2. This observation supports a pathogenic effect of VPS51 variants, which has only been reported previously once, in a single child with microcephaly. It confirms the key role of membrane trafficking in normal brain development and homeostasis.
    Title: VPS51 biallelic variants cause microcephaly with brain malformations: A confirmatory report.
  3. A dityrosine motif of Ang2 interacts with a highly conserved groove in Syntaxin 6.
    Title: Structural basis for the interaction of the Golgi-Associated Retrograde Protein Complex with the t-SNARE Syntaxin 6.
  4. Ang2 is the missing component of the Golgi-associated retrograde protein complex in most eukaryotes.
    Title: Ang2/fat-free is a conserved subunit of the Golgi-associated retrograde protein complex.
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

Associated conditions

Description Tests
Pontocerebellar hypoplasia, type 13
MedGen: C5231425 OMIM: 618606 GeneReviews: Not available
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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

Clone Names

  • FLJ13879, FLJ36472

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables molecular_function ND
No biological Data available
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in Golgi organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in Golgi vesicle transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in autophagy IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in brain morphogenesis IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in endocytic recycling IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in endocytic recycling IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in endocytic recycling NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in lysosomal transport IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within lysosomal transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein targeting IEA
Inferred from Electronic Annotation
more info
  
involved_in protein transport IEA
Inferred from Electronic Annotation
more info
  
involved_in retrograde transport, endosome to Golgi IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in retrograde transport, endosome to Golgi IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of_or_within 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 
involved_in vesicle-mediated cholesterol transport IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of EARP complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of EARP complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of EARP complex IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of GARP complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of GARP complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of GARP complex NAS
Non-traceable Author Statement
more info
 PubMed 
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IEA
Inferred from Electronic Annotation
more info
  
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
  
is_active_in membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in membrane TAS
Traceable Author Statement
more info
  
located_in nucleolus IDA
Inferred from Direct Assay
more info
  
located_in recycling endosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in recycling endosome NAS
Non-traceable Author Statement
more info
 PubMed 
located_in trans-Golgi network membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
vacuolar protein sorting-associated protein 51 homolog
Names
VPS51, GARP complex subunit
another new gene 2 protein
protein fat-free homolog
vacuolar protein sorting 51 homolog

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.

mRNA and Protein(s)

  1. NM_013265.4 → NP_037397.2  vacuolar protein sorting-associated protein 51 homolog

    See identical proteins and their annotated locations for NP_037397.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the shorter transcript and encodes the functional protein.
    Source sequence(s)
    AF024631, AP003068, AW007399, HY270070
    Consensus CDS
    CCDS8093.1
    UniProtKB/Swiss-Prot
    Q6PJV5, Q7L8A6, Q8WZ35, Q96DF4, Q96GR3, Q9UID3
    Related
    ENSP00000279281.3, ENST00000279281.8
    Conserved Domains (2) summary
    pfam08700
    Location:63 → 147
    Vps51; Vps51/Vps67
    cl19297
    Location:101 → 262
    Dor1; Dor1-like family

RNA

  1. NR_073519.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AP003068, AW007399, BC007198, BG391473, BI752026, CD388131, HY270070

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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    65096214..65111862
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    65089493..65105141
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UID3.2 GenPept UniProtKB/Swiss-Prot:Q9UID3

Gene LinkOut

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