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    VPS53 VPS53 subunit of GARP complex [ Homo sapiens (human) ]

    Gene ID: 55275, updated on 2-Nov-2024

    Summary

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    Official Symbol
    VPS53provided by HGNC
    Official Full Name
    VPS53 subunit of GARP complexprovided by HGNC
    Primary source
    HGNC:HGNC:25608
    See related
    Ensembl:ENSG00000141252 MIM:615850; AllianceGenome:HGNC:25608
    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
    HCCS1; PCH2E; hVps53L; pp13624
    Summary
    Involved in endocytic recycling and retrograde transport, endosome to Golgi. Acts upstream of or within lysosomal transport. Located in several cellular components, including Golgi apparatus; perinuclear region of cytoplasm; and recycling endosome. Part of EARP complex and GARP complex. Implicated in pontocerebellar hypoplasia type 2E. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in thyroid (RPKM 6.1), brain (RPKM 5.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See VPS53 in Genome Data Viewer
    Location:
    17p13.3
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (508668..714839, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (391960..599311, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (411908..618079, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371430 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7938 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11437 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr17:276928-277621 Neighboring gene ligand of ATE1 Neighboring gene refilin B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7939 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:423721-424222 Neighboring gene uncharacterized LOC124903890 Neighboring gene uncharacterized LOC124903891 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:463241-464440 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7940 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:475469-476353 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:487351-487501 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:504328-505527 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:560426-561625 Neighboring gene Sharpr-MPRA regulatory region 8461 Neighboring gene ribosomal protein S4X pseudogene 17 Neighboring gene Sharpr-MPRA regulatory region 15051 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:610400-610605 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11438 Neighboring gene uncharacterized LOC124903893 Neighboring gene Sharpr-MPRA regulatory region 11717 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7941 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7942 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7943 Neighboring gene TLC domain containing 3A

    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 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 minimum LOH region defined on chromosome 17p13.3 in human hepatocellular carcinoma with gene content analysis. Zhao X, et al. Cancer Lett, 2003 Feb 20. PMID 12565177
    2. Hepatocellular carcinoma suppressor 1 promoter hypermethylation in serum. A diagnostic and prognostic study in hepatitis B. Tian MM, et al. Clin Res Hepatol Gastroenterol, 2017 Mar. PMID 28189396
    3. HCCS1 inhibits the stemness of human pancreatic cancer stem-like cells. Xie XH, et al. Eur Rev Med Pharmacol Sci, 2019 Mar. PMID 30915757
    4. VPS53 gene is associated with a new phenotype of complicated hereditary spastic paraparesis. Hausman-Kedem M, et al. Neurogenetics, 2019 Oct. PMID 31418091
    5. Transcription of the putative tumor suppressor gene HCCS1 requires binding of ETS-2 to its consensus near the transcription start site. Zhu JD, et al. Cell Res, 2006 Sep. PMID 16953216

    See all (55) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. VPS53 gene is associated with a new phenotype of complicated hereditary spastic paraparesis.
      Title: VPS53 gene is associated with a new phenotype of complicated hereditary spastic paraparesis.
    2. HCCS1 inhibits the stemness of human pancreatic cancer stem-like cells.
      Title: HCCS1 inhibits the stemness of human pancreatic cancer stem-like cells.
    3. Novel and deleterious variants in VPS53, GLB1, and MLC1, genes previously associated with variable neurodevelopmental anomalies, were found to segregate with intellectual disabilities in the three families.
      Title: Novel variants underlying autosomal recessive intellectual disability in Pakistani consanguineous families.
    4. sensitivity of serum Hepatocellular carcinoma suppressor 1 (HCCS1) promoter methylation for discriminating patients with hepatocellular carcinoma from chronic hepatitis B was 62.5%
      Title: Hepatocellular carcinoma suppressor 1 promoter hypermethylation in serum. A diagnostic and prognostic study in hepatitis B.
    5. Golgi-associated retrograde protein orchestrates retrograde transport from endosomes to the trans-Golgi network by promoting vesicle tethering and assembly of SNARE complexes in consecutive, independent steps.[Golgi associated retrograde protein]
      Title: Dual roles of the mammalian GARP complex in tethering and SNARE complex assembly at the trans-golgi network.
    6. Missorting of cathepsin D in GARP-depleted cells results from accumulation of recycling MPRs in a population of light, small vesicles downstream of endosomes.
      Title: Requirement of the human GARP complex for mannose 6-phosphate-receptor-dependent sorting of cathepsin D to lysosomes.
    7. Data show that transcription of the putative tumor suppressor gene HCCS1 requires binding of ETS-2 to its consensus near the transcription start site; observations provide insight into the mechanistic aspects of HCCS1 transcription regulation
      Title: Transcription of the putative tumor suppressor gene HCCS1 requires binding of ETS-2 to its consensus near the transcription start site.
    8. Amphipathic tail-anchoring peptide (ATAP) targets specifically to mitochondria, and induces caspase-dependent apoptosis that does not require Bax or Bak.
      Title: The tail-anchoring domain of Bfl1 and HCCS1 targets mitochondrial membrane permeability to induce apoptosis.
    9. Golgi associated retrograde protein complex, consisting of the Vps52, Vps53, and Vps54 proteins, shows significant conservation between various species but diversification and specialization result in important differences in human cells.
      Title: Characterization of the human GARP (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 2E
    MedGen: C4014488 OMIM: 615851 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
    EBI GWAS Catalog

    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

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of vacuolar protein sorting 53 homolog (VPS53) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

    Go to the HIV-1, Human Interaction Database

    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

    • FLJ10979, FLJ41112, FLJ61757, MGC39512

    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 endocytic recycling NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    acts_upstream_of_or_within lysosomal transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein targeting to lysosome 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 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 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 IDA
    Inferred from Direct Assay
    more info
    		  
    located_in endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    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

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    Preferred Names
    vacuolar protein sorting-associated protein 53 homolog
    Names
    VPS53, GARP complex subunit
    hepatocellular carcinoma suppressor 1

    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_034190.1 RefSeqGene

      Range
      5018..211189
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001128159.3 → NP_001121631.1  vacuolar protein sorting-associated protein 53 homolog isoform 1

      See identical proteins and their annotated locations for NP_001121631.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and it encodes the longer protein (isoform 1).
      Source sequence(s)
      AC015853, AK001841, AK092532, AL701573, EU021218
      Consensus CDS
      CCDS45558.1
      UniProtKB/Swiss-Prot
      A8K2S8, B3FH42, Q5VIR6, Q8WYW3, Q9BRR2, Q9BY02, Q9NV25
      UniProtKB/TrEMBL
      A0A7P0Z400
      Related
      ENSP00000401435.2, ENST00000437048.7
      Conserved Domains (1) summary
      pfam04100
      Location:39 → 453
      Vps53_N; Vps53-like, N-terminal

    2. NM_001366253.2 → NP_001353182.1  vacuolar protein sorting-associated protein 53 homolog isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC015853, AC027455
      Consensus CDS
      CCDS92214.1
      UniProtKB/TrEMBL
      B1AA17
      Related
      ENSP00000459312.1, ENST00000571805.6
      Conserved Domains (1) summary
      pfam04100
      Location:39 → 453
      Vps53_N; Vps53-like, N-terminal

    3. NM_001366254.2 → NP_001353183.1  vacuolar protein sorting-associated protein 53 homolog isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC015853, AC027455
      UniProtKB/TrEMBL
      B3KS06
      Related
      ENSP00000506052.1, ENST00000681096.1
      Conserved Domains (1) summary
      pfam04100
      Location:6 → 255
      Vps53_N; Vps53-like, N-terminal

    4. NM_018289.4 → NP_060759.2  vacuolar protein sorting-associated protein 53 homolog isoform 2

      See identical proteins and their annotated locations for NP_060759.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) has multiple differences in the coding region and uses a different segment for its 3' UTR but maintains the reading frame, compared to variant 1. The resulting protein (isoform 2) has a shorter and distinct C-terminus when it is compared to isoform 2.
      Source sequence(s)
      AC015853, AK001841, AK092532, AK290343
      Consensus CDS
      CCDS10995.1
      UniProtKB/TrEMBL
      B1AA17
      Related
      ENSP00000291074.5, ENST00000291074.10
      Conserved Domains (1) summary
      pfam04100
      Location:39 → 424
      Vps53_N; Vps53-like, N-terminal

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      508668..714839 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047436345.1 → XP_047292301.1  vacuolar protein sorting-associated protein 53 homolog isoform X2

    2. XM_047436344.1 → XP_047292300.1  vacuolar protein sorting-associated protein 53 homolog isoform X1

      UniProtKB/Swiss-Prot
      A8K2S8, B3FH42, Q5VIR6, Q8WYW3, Q9BRR2, Q9BY02, Q9NV25
      Related
      ENSP00000505997.1, ENST00000680465.1

    3. XM_047436346.1 → XP_047292302.1  vacuolar protein sorting-associated protein 53 homolog isoform X3

      Related
      ENSP00000505594.1, ENST00000681510.1

    4. XM_047436347.1 → XP_047292303.1  vacuolar protein sorting-associated protein 53 homolog isoform X4

    5. XM_047436348.1 → XP_047292304.1  vacuolar protein sorting-associated protein 53 homolog isoform X5

    6. XM_047436349.1 → XP_047292305.1  vacuolar protein sorting-associated protein 53 homolog isoform X6

    7. XM_047436351.1 → XP_047292307.1  vacuolar protein sorting-associated protein 53 homolog isoform X8

      Related
      ENSP00000506475.1, ENST00000681133.1

    8. XM_047436350.1 → XP_047292306.1  vacuolar protein sorting-associated protein 53 homolog isoform X7

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_017363817.1 Reference GRCh38.p14 PATCHES

      Range
      68145..274316 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054332081.1 → XP_054188056.1  vacuolar protein sorting-associated protein 53 homolog isoform X2

    2. XM_054332080.1 → XP_054188055.1  vacuolar protein sorting-associated protein 53 homolog isoform X1

      UniProtKB/Swiss-Prot
      A8K2S8, B3FH42, Q5VIR6, Q8WYW3, Q9BRR2, Q9BY02, Q9NV25

    3. XM_054332082.1 → XP_054188057.1  vacuolar protein sorting-associated protein 53 homolog isoform X3

    4. XM_054332083.1 → XP_054188058.1  vacuolar protein sorting-associated protein 53 homolog isoform X4

    5. XM_054332084.1 → XP_054188059.1  vacuolar protein sorting-associated protein 53 homolog isoform X5

    6. XM_054332085.1 → XP_054188060.1  vacuolar protein sorting-associated protein 53 homolog isoform X6

    7. XM_054332087.1 → XP_054188062.1  vacuolar protein sorting-associated protein 53 homolog isoform X8

    8. XM_054332086.1 → XP_054188061.1  vacuolar protein sorting-associated protein 53 homolog isoform X7

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      391960..599311 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054316606.1 → XP_054172581.1  vacuolar protein sorting-associated protein 53 homolog isoform X2

    2. XM_054316605.1 → XP_054172580.1  vacuolar protein sorting-associated protein 53 homolog isoform X1

      UniProtKB/Swiss-Prot
      A8K2S8, B3FH42, Q5VIR6, Q8WYW3, Q9BRR2, Q9BY02, Q9NV25

    3. XM_054316607.1 → XP_054172582.1  vacuolar protein sorting-associated protein 53 homolog isoform X3

    4. XM_054316608.1 → XP_054172583.1  vacuolar protein sorting-associated protein 53 homolog isoform X4

    5. XM_054316609.1 → XP_054172584.1  vacuolar protein sorting-associated protein 53 homolog isoform X5

    6. XM_054316610.1 → XP_054172585.1  vacuolar protein sorting-associated protein 53 homolog isoform X6

    7. XM_054316612.1 → XP_054172587.1  vacuolar protein sorting-associated protein 53 homolog isoform X8

    8. XM_054316611.1 → XP_054172586.1  vacuolar protein sorting-associated protein 53 homolog isoform X7

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5VIR6.2 GenPept UniProtKB/Swiss-Prot:Q5VIR6

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