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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
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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.
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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
not available

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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