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

    Gene ID: 738, updated on 27-Nov-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
    mouse all
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    Genomic context

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    See VPS51 in Genome Data Viewer
    Location:
    11q13.1
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (65096214..65111862)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (65089493..65105141)
    RS_2024_09 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 (59) 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
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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 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_2024_08

    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

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

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