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Tbio
VPS53
Vacuolar protein sorting-associated protein 53 homolog

Protein Summary
Description
Acts as component of the GARP complex that is involved in retrograde transport from early and late endosomes to the trans-Golgi network (TGN). The GARP complex is required for the maintenance of the cycling of mannose 6-phosphate receptors between the TGN and endosomes, this cycling is necessary for proper lysosomal sorting of acid hydrolases such as CTSD (PubMed:15878329, PubMed:18367545). Acts as component of the EARP complex that is involved in endocytic recycling. The EARP complex associates with Rab4-positive endosomes and promotes recycling of internalized transferrin receptor (TFRC) to the plasma membrane (PubMed:25799061). 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]
Uniprot Accession IDs
Gene Name
Ensembl ID
  • ENST00000291074
  • ENSP00000291074
  • ENSG00000141252
  • ENST00000437048
  • ENSP00000401435
  • ENST00000571805
  • ENSP00000459312
  • ENST00000638350
  • ENSP00000492070
  • ENSG00000283883
  • ENST00000639801
  • ENSP00000492761
  • ENST00000639896
  • ENSP00000492119

Symbol
  • HCCS1
  • PCH2E
  • hVps53L
  • pp13624
Illumination Graph
Knowledge Table
Most Knowledge About
Knowledge Value (0 to 1 scale)
kinase perturbation
0.99
microRNA
0.9
histone modification site profile
0.89
transcription factor perturbation
0.84
disease perturbation
0.79


Protein Classes
No PANTHER Classes or DTO Classes found
IDG Development Level Summary
Tdark

These are targets about which virtually nothing is known. They do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 14.83   (req: < 5)
Gene RIFs: 7   (req: <= 3)
Antibodies: 120   (req: <= 50)
Tbio

These targets do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 14.83   (req: >= 5)
Gene RIFs: 7   (req: > 3)
Antibodies: 120   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 4
Tchem

Target has at least one ChEMBL compound with an activity cutoff of < 30 nM - AND - satisfies the preceding conditions

Active Ligand: 0
Tclin

Target has at least one approved drug - AND - satisfies the preceding conditions

Active Drug: 0
Expression Data (0 Tissues)
No expression data found
Protein Sequence and Structure
Residue Counts
Protein Sequence
ProtVista Viewer
Related Tools (4)
Target Illumination GWAS Analytics (TIGA)
Thumbnail image for Target Illumination GWAS Analytics (TIGA)
TIGA scores and ranks GWAS discovered associations according to the quantity and quality of the evidence supporting the association.
GENEVA
Thumbnail image for GENEVA
GENEVA (GENe Expression Variance Analysis) allows you to identify RNA-sequencing datasets from the Gene Expression Omnibus (GEO) that contain conditions modulating a gene or a gene signature.
GlyGen
Thumbnail image for GlyGen
GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data.
ARCHS4
Thumbnail image for ARCHS4
ARCHS4 provides access to gene-function predictions based on RNA-seq co-expression, and gene expression levels across cell and tissues.
Approved Drugs (0)
No approved drugs found
Active Ligands (0)
No active ligands found
Protein-Protein Interactions (140)
VPS50
Tbio
Novelty:  0.17236696
p_int:  1
Score:  0.999
Data Source:  BioPlex,STRINGDB
VPS54
Tbio
Novelty:  0.04428383
p_int:  0.999999961
p_ni:  3.7e-8
p_wrong:  2e-9
Score:  0.999
Data Source:  BioPlex,Reactome,STRINGDB
EIPR1
Tbio
Novelty:  0.08803081
p_int:  0.999999186
p_ni:  8.14e-7
Score:  0.855
Data Source:  BioPlex,STRINGDB
GINS2
Tbio
Novelty:  0.0078966
p_int:  0.999999145
p_ni:  8.55e-7
Data Source:  BioPlex
CCDC40
Tbio
Novelty:  0.06726469
p_int:  0.999959586
p_ni:  0.000040414
Data Source:  BioPlex
DTNBP1
Tbio
Novelty:  0.00341619
p_int:  0.999904415
p_ni:  0.000095585
Score:  0.24
Data Source:  BioPlex,STRINGDB
EXOC1
Tbio
Novelty:  0.01073858
p_int:  0.99970381
p_ni:  0.00029619
Score:  0.726
Data Source:  BioPlex,STRINGDB
PSMD7
Tbio
Family:  Enzyme
Novelty:  0.03090292
p_int:  0.998270389
p_ni:  0.001729611
Score:  0.206
Data Source:  BioPlex,STRINGDB
SNAP29
Tbio
Novelty:  0.02009206
p_int:  0.996481164
p_ni:  0.003518836
Score:  0.687
Data Source:  BioPlex,STRINGDB
ENTHD1
Tdark
Novelty:  5.29427978
p_int:  0.995580146
p_ni:  0.004419798
p_wrong:  5.7e-8
Data Source:  BioPlex
Nearest Tclin Targets
Nearest Tclin calculations are only available for targets with KEGG Pathway annotations.
Pathways (4)
Intra-Golgi and retrograde Golgi-to-ER traffic (R-HSA-6811442)

Click on a row in the table to change the structure displayed.

Find Similar Targets
Items per page:
1 – 4 of 4
Data Source
Name
Explore in Pharos
Explore in Source
Reactome
Intra-Golgi and retrograde Golgi-to-ER traffic
Reactome
Membrane Trafficking
Reactome
Retrograde transport at the Trans-Golgi-Network
Reactome
Vesicle-mediated transport
Name
Explore in Pharos
Explore in Source
Intra-Golgi and retrograde Golgi-to-ER traffic
Membrane Trafficking
Retrograde transport at the Trans-Golgi-Network
Vesicle-mediated transport
Viral Interactions (0)
No viral interactions found
Gene Ontology Terms (13)
Find Similar Targets
Items per page:
10
1 – 9 of 9
GO Term
Evidence
Assigned by
Inferred from Direct Assay (IDA)
HPA
Inferred from Direct Assay (IDA)
UniProtKB
Inferred from Direct Assay (IDA)
MGI
Inferred from Direct Assay (IDA)
UniProtKB
Inferred from Direct Assay (IDA)
MGI
Inferred from Direct Assay (IDA)
UniProtKB
Inferred from Direct Assay (IDA)
UniProtKB
Traceable Author Statement (TAS)
Reactome
Inferred from Electronic Annotation (IEA)
UniProtKB-SubCell
Disease Associations (null)
No disease associations found
GWAS Traits (16)
Items per page:
1 – 5 of 16
GWAS Trait
EFO ID
ENSG ID
Study Count
SNP Count
Beta Count
Odds Ratio
Evidence (Mean Rank Score)
Provenance
hip circumference
2
30
31
96.7
hip circumference
2
30
31
96.7
BMI-adjusted hip circumference
3
29
30
95.2
BMI-adjusted hip circumference
3
29
30
95.2
4
1
0
1.1
76.1
Items per page:
1 – 5 of 16
GWAS Trait
EFO ID
Beta Count
Odds Ratio
Evidence (Mean Rank Score)
Provenance
hip circumference
31
96.7
hip circumference
31
96.7
BMI-adjusted hip circumference
30
95.2
BMI-adjusted hip circumference
30
95.2
0
1.1
76.1
Find similar targets by:
IDG Resources
No IDG generated resources found
Orthologs (15)
1 – 5 of 15
Species
Name
Source ID
Gene ID
OMA
EggNOG
Inparanoid
Chimp
VPS53, GARP complex subunit
VGNC:9781
454402
Macaque
VPS53, GARP complex subunit
699470
Mouse
MGI:1915549
68299
Rat
RGD:1311391
287535
Dog
VPS53, GARP complex subunit
VGNC:48297
491188
Species
Name
OMA
EggNOG
Inparanoid
Chimp
VPS53, GARP complex subunit
Macaque
VPS53, GARP complex subunit
Mouse
Rat
Dog
VPS53, GARP complex subunit
Publication Statistics
PubMed Score 14.83
PubMed score by year
PubTator Score 5.01
PubTator score by year
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Related Publications
Items per page:
0 of 0
PMID
Year
Title