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    VPS52 VPS52 subunit of GARP complex [ Homo sapiens (human) ]

    Gene ID: 6293, updated on 3-Apr-2024

    Summary

    Official Symbol
    VPS52provided by HGNC
    Official Full Name
    VPS52 subunit of GARP complexprovided by HGNC
    Primary source
    HGNC:HGNC:10518
    See related
    Ensembl:ENSG00000223501 MIM:603443; AllianceGenome:HGNC:10518
    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
    ARE1; SAC2; SACM2L; dJ1033B10.5
    Summary
    This gene encodes a protein that is similar to the yeast suppressor of actin mutations 2 gene. The yeast protein forms a subunit of the tetrameric Golgi-associated retrograde protein complex that is involved in vesicle trafficking from from both early and late endosomes, back to the trans-Golgi network. This gene is located on chromosome 6 in a head-to-head orientation with the gene encoding ribosomal protein S18. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]
    Expression
    Ubiquitous expression in thyroid (RPKM 15.7), testis (RPKM 14.8) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See VPS52 in Genome Data Viewer
    Location:
    6p21.32
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (33250272..33271965, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (33071634..33093327, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (33218049..33239742, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene zinc finger protein 70 pseudogene 1 Neighboring gene uncharacterized LOC105375022 Neighboring gene HLA complex group 25 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33244298-33245030 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33245765-33246496 Neighboring gene ribosomal protein S18 Neighboring gene beta-1,3-galactosyltransferase 4

    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?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • RP5-1033B10, DKFZp547I194

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables syntaxin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables syntaxin binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in Golgi to vacuole transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in ectodermal cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in embryonic ectodermal digestive tract development IEA
    Inferred from Electronic Annotation
    more info
     
    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 IDA
    Inferred from Direct Assay
    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 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 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 endosome membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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

    Preferred Names
    vacuolar protein sorting-associated protein 52 homolog
    Names
    SAC2 suppressor of actin mutations 2-like protein
    VPS52, GARP complex subunit
    vacuolar protein sorting 52 homolog

    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_001289174.2NP_001276103.1  vacuolar protein sorting-associated protein 52 homolog isoform 2

      See identical proteins and their annotated locations for NP_001276103.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, initiates translation at an alternate start codon and lacks an alternate exon in the 5' coding region, compared to variant 1. It encodes isoform 2, which is shorter and has a distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AK093057, AK299563, BQ022405
      UniProtKB/TrEMBL
      B4DS44
      Conserved Domains (1) summary
      pfam04129
      Location:27534
      Vps52; Vps52 / Sac2 family
    2. NM_001289175.1NP_001276104.1  vacuolar protein sorting-associated protein 52 homolog isoform 3

      See identical proteins and their annotated locations for NP_001276104.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. It encodes isoform 3, which is shorter at the N-terminus, compared to isoform 1.
      Source sequence(s)
      AK001725, AK093057, AK297935, AK299563, BQ022405, DC395438
      UniProtKB/TrEMBL
      A0A1U9X8S4, B3KMF7
      Conserved Domains (1) summary
      pfam04129
      Location:1476
      Vps52; Vps52 / Sac2 family
    3. NM_001289176.1NP_001276105.1  vacuolar protein sorting-associated protein 52 homolog isoform 4

      See identical proteins and their annotated locations for NP_001276105.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. It encodes isoform 4, which is shorter than isoform 1.
      Source sequence(s)
      AK001725, AK093057, AK299563, BQ022405, DC395438
      UniProtKB/TrEMBL
      B3KMF7
      Related
      ENST00000478934.5
      Conserved Domains (1) summary
      cl19950
      Location:1412
      Sec3_C; Exocyst complex component Sec3
    4. NM_022553.6NP_072047.4  vacuolar protein sorting-associated protein 52 homolog isoform 1

      See identical proteins and their annotated locations for NP_072047.4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AK001725, BC040114, DC400338
      Consensus CDS
      CCDS4770.2
      UniProtKB/Swiss-Prot
      A2BF38, B0UZZ4, B4DNI9, Q53GR4, Q5JPA0, Q5SQW1, Q8IUN6, Q8N1B4, Q9NPT5
      UniProtKB/TrEMBL
      B4DS44, Q4VXZ2
      Related
      ENSP00000409952.2, ENST00000445902.3
      Conserved Domains (1) summary
      pfam04129
      Location:94601
      Vps52; Vps52 / Sac2 family

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      33250272..33271965 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011514799.2XP_011513101.1  vacuolar protein sorting-associated protein 52 homolog isoform X2

      See identical proteins and their annotated locations for XP_011513101.1

      UniProtKB/TrEMBL
      B4DS44
      Conserved Domains (1) summary
      pfam04129
      Location:27534
      Vps52; Vps52 / Sac2 family
    2. XM_011514798.3XP_011513100.1  vacuolar protein sorting-associated protein 52 homolog isoform X2

      See identical proteins and their annotated locations for XP_011513100.1

      UniProtKB/TrEMBL
      B4DS44
      Conserved Domains (1) summary
      pfam04129
      Location:27534
      Vps52; Vps52 / Sac2 family
    3. XM_011514797.2XP_011513099.1  vacuolar protein sorting-associated protein 52 homolog isoform X2

      See identical proteins and their annotated locations for XP_011513099.1

      UniProtKB/TrEMBL
      B4DS44
      Conserved Domains (1) summary
      pfam04129
      Location:27534
      Vps52; Vps52 / Sac2 family
    4. XM_017011179.3XP_016866668.1  vacuolar protein sorting-associated protein 52 homolog isoform X1

    Reference GRCh38.p14 ALT_REF_LOCI_2

    Genomic

    1. NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

      Range
      4661769..4683446 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054329851.1XP_054185826.1  vacuolar protein sorting-associated protein 52 homolog isoform X2

    2. XM_054329849.1XP_054185824.1  vacuolar protein sorting-associated protein 52 homolog isoform X2

    3. XM_054329850.1XP_054185825.1  vacuolar protein sorting-associated protein 52 homolog isoform X2

    4. XM_054329852.1XP_054185827.1  vacuolar protein sorting-associated protein 52 homolog isoform X1

    Reference GRCh38.p14 ALT_REF_LOCI_3

    Genomic

    1. NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

      Range
      4493784..4515479 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054330334.1XP_054186309.1  vacuolar protein sorting-associated protein 52 homolog isoform X2

    2. XM_054330332.1XP_054186307.1  vacuolar protein sorting-associated protein 52 homolog isoform X2

    3. XM_054330333.1XP_054186308.1  vacuolar protein sorting-associated protein 52 homolog isoform X2

    4. XM_054330335.1XP_054186310.1  vacuolar protein sorting-associated protein 52 homolog isoform X1

    Reference GRCh38.p14 ALT_REF_LOCI_4

    Genomic

    1. NT_167246.2 Reference GRCh38.p14 ALT_REF_LOCI_4

      Range
      4669733..4671435 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_5

    Genomic

    1. NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

      Range
      4686254..4707927 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054330849.1XP_054186824.1  vacuolar protein sorting-associated protein 52 homolog isoform X2

    2. XM_054330848.1XP_054186823.1  vacuolar protein sorting-associated protein 52 homolog isoform X2

    3. XM_054330850.1XP_054186825.1  vacuolar protein sorting-associated protein 52 homolog isoform X2

    4. XM_054330851.1XP_054186826.1  vacuolar protein sorting-associated protein 52 homolog isoform X1

    Reference GRCh38.p14 ALT_REF_LOCI_6

    Genomic

    1. NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

      Range
      4444672..4466382 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054331111.1XP_054187086.1  vacuolar protein sorting-associated protein 52 homolog isoform X2

    2. XM_054331110.1XP_054187085.1  vacuolar protein sorting-associated protein 52 homolog isoform X2

    3. XM_054331112.1XP_054187087.1  vacuolar protein sorting-associated protein 52 homolog isoform X2

    4. XM_054331113.1XP_054187088.1  vacuolar protein sorting-associated protein 52 homolog isoform X1

    Reference GRCh38.p14 ALT_REF_LOCI_7

    Genomic

    1. NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

      Range
      4698976..4720646 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054331372.1XP_054187347.1  vacuolar protein sorting-associated protein 52 homolog isoform X2

    2. XM_054331371.1XP_054187346.1  vacuolar protein sorting-associated protein 52 homolog isoform X2

    3. XM_054331373.1XP_054187348.1  vacuolar protein sorting-associated protein 52 homolog isoform X2

    4. XM_054331374.1XP_054187349.1  vacuolar protein sorting-associated protein 52 homolog isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      33071634..33093327 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054356196.1XP_054212171.1  vacuolar protein sorting-associated protein 52 homolog isoform X2

    2. XM_054356195.1XP_054212170.1  vacuolar protein sorting-associated protein 52 homolog isoform X2

    3. XM_054356197.1XP_054212172.1  vacuolar protein sorting-associated protein 52 homolog isoform X2

    4. XM_054356198.1XP_054212173.1  vacuolar protein sorting-associated protein 52 homolog isoform X1