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

Gene ID: 55275, updated on 7-Dec-2018

Summary

Official Symbol
VPS53provided by HGNC
Official Full Name
VPS53, GARP complex subunitprovided by HGNC
Primary source
HGNC:HGNC:25608
See related
Ensembl:ENSG00000141252 MIM:615850
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
This gene encodes a protein with sequence similarity to the yeast Vps53p protein. Vps53p is involved in retrograde vesicle trafficking in late Golgi. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in thyroid (RPKM 6.1), brain (RPKM 5.4) and 25 other tissues See more
Orthologs

Genomic context

See VPS53 in Genome Data Viewer
Location:
17p13.3
Exon count:
26
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 17 NC_000017.11 (508668..714856, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (411908..618096, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371430 Neighboring gene chromosome 17 open reading frame 97 Neighboring gene refilin B Neighboring gene ribosomal protein S4X pseudogene 17 Neighboring gene family with sequence similarity 57 member A Neighboring gene gem nuclear organelle associated protein 4 Neighboring gene diazepam binding inhibitor-like 5, pseudogene

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Pontocerebellar hypoplasia, type 2e
MedGen: C4014488 OMIM: 615851 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

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

HIV-1 interactions

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 BioSystems

  • Intra-Golgi and retrograde Golgi-to-ER traffic, organism-specific biosystem (from REACTOME)
    Intra-Golgi and retrograde Golgi-to-ER traffic, organism-specific biosystemThe mammalian Golgi complex, a central hub of both anterograde and retrograde trafficking, is a ribbon of stacked cisterna with biochemically distinct compartments (reviewed in Glick and Nakano, 2009...
  • Membrane Trafficking, organism-specific biosystem (from REACTOME)
    Membrane Trafficking, organism-specific biosystemThe secretory membrane system allows a cell to regulate delivery of newly synthesized proteins, carbohydrates, and lipids to the cell surface, a necessity for growth and homeostasis. The system is ma...
  • Retrograde transport at the Trans-Golgi-Network, organism-specific biosystem (from REACTOME)
    Retrograde transport at the Trans-Golgi-Network, organism-specific biosystemThe trans-Golgi network is the docking site for retrograde cargo from the endolysosomal system and the plasma membrane. Typical cargo includes recycling resident TGN proteins such as TGOLN2 (also kn...
  • Vesicle-mediated transport, organism-specific biosystem (from REACTOME)
    Vesicle-mediated transport, organism-specific biosystemThe transit of proteins and other cargo through the cell requires a cellular transport process in which transported substances are moved in membrane-bounded vesicles. Transported substances are enclo...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ10979, FLJ41112, FLJ61757, MGC39512

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
endocytic recycling IMP
Inferred from Mutant Phenotype
more info
PubMed 
lysosomal transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein transport IEA
Inferred from Electronic Annotation
more info
 
retrograde transport, endosome to Golgi IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
retrograde transport, endosome to Golgi IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
EARP complex IDA
Inferred from Direct Assay
more info
PubMed 
GARP complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
GARP complex IDA
Inferred from Direct Assay
more info
PubMed 
Golgi apparatus IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
endosome membrane IEA
Inferred from Electronic Annotation
more info
 
membrane IDA
Inferred from Direct Assay
more info
PubMed 
perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
recycling endosome IDA
Inferred from Direct Assay
more info
PubMed 
trans-Golgi network membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
vacuolar protein sorting-associated protein 53 homolog

NCBI Reference Sequences (RefSeq)

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
    5001..211189
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001128159.3NP_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
    Q5VIR6
    UniProtKB/TrEMBL
    B3KS06
    Related
    ENSP00000401435.2, ENST00000437048.6
    Conserved Domains (1) summary
    pfam04100
    Location:39453
    Vps53_N; Vps53-like, N-terminal
  2. NM_001366253.1NP_001353182.1  vacuolar protein sorting-associated protein 53 homolog isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC015853, AC027455
    Conserved Domains (1) summary
    pfam04100
    Location:39453
    Vps53_N; Vps53-like, N-terminal
  3. NM_001366254.1NP_001353183.1  vacuolar protein sorting-associated protein 53 homolog isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC015853, AC027455
    Conserved Domains (1) summary
    pfam04100
    Location:6255
    Vps53_N; Vps53-like, N-terminal
  4. NM_018289.3NP_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)
    AK001841, AK092532, AK290343
    Consensus CDS
    CCDS10995.1
    UniProtKB/Swiss-Prot
    Q5VIR6
    UniProtKB/TrEMBL
    B3KS06
    Related
    ENSP00000291074.5, ENST00000291074.9
    Conserved Domains (1) summary
    pfam04100
    Location:39424
    Vps53_N; Vps53-like, N-terminal

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p12 Primary Assembly

    Range
    508668..714856 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017024817.2XP_016880306.1  vacuolar protein sorting-associated protein 53 homolog isoform X1

  2. XM_017024818.1XP_016880307.1  vacuolar protein sorting-associated protein 53 homolog isoform X2

  3. XM_011523953.2XP_011522255.1  vacuolar protein sorting-associated protein 53 homolog isoform X3

    Conserved Domains (1) summary
    pfam04100
    Location:6255
    Vps53_N; Vps53-like, N-terminal

RNA

  1. XR_001752553.2 RNA Sequence

  2. XR_934061.3 RNA Sequence

  3. XR_934062.2 RNA Sequence

Reference GRCh38.p12 PATCHES

Genomic

  1. NW_017363817.1 Reference GRCh38.p12 PATCHES

    Range
    68145..274333 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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