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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
VPS53
VPS53 subunit of GARP complex
Chromosome 17 Β· 17p13.3
NCBI Gene: 55275Ensembl: ENSG00000141252.21HGNC: HGNC:25608UniProt: B3KS06
62PubMed Papers
21Diseases
0Drugs
16Pathogenic Variants
FUNCTIONAL ROLE
Transporter
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
endocytic recyclingmembraneperinuclear region of cytoplasmrecycling endosomepontocerebellar hypoplasia type 2Eprostate carcinomaneurodegenerative diseaseprogressive cerebello-cerebral atrophy
✦AI Summary

VPS53 encodes a critical subunit of the GARP (Golgi-associated retrograde protein) complex that mediates retrograde transport from endosomes to the trans-Golgi network (TGN) 1. The protein functions in maintaining mannose 6-phosphate receptor cycling between the TGN and endosomes, which is essential for proper lysosomal sorting of acid hydrolases 2. VPS53 also participates in the EARP complex, promoting endocytic recycling by associating with Rab4-positive endosomes to facilitate transferrin receptor recycling to the plasma membrane 2. Loss-of-function mutations in VPS53 cause severe neurological disorders, including progressive cerebello-cerebral atrophy type 2 (PCCA2) characterized by profound mental retardation, progressive microcephaly, spasticity, and early-onset epilepsy 1. The gene has also been associated with complicated hereditary spastic paraparesis, expanding its disease phenotype beyond PCCA2 3. Mechanistically, VPS53 dysfunction disrupts intracellular cholesterol transport and sphingolipid homeostasis in lysosomes, leading to neurodegeneration 3. In cellular studies, VPS53 demonstrates tumor suppressor properties in colorectal cancer by inducing autophagy signaling pathways 4. The protein's essential role in membrane trafficking makes it crucial for cellular homeostasis and survival.

Sources cited
1
VPS53 encodes a GARP complex subunit and mutations cause progressive cerebello-cerebral atrophy type 2
PMID: 24577744
2
VPS53 functions in GARP complex for retrograde transport and EARP complex for endocytic recycling
PMID: 27440922
3
VPS53 mutations cause complicated hereditary spastic paraparesis and disrupt cholesterol transport
PMID: 31418091
4
VPS53 acts as tumor suppressor in colorectal cancer by inducing autophagy
PMID: 33116643
⚠Limited data available β€” This gene has 4 indexed publications. Summary and analysis may be incomplete.
Disease Associationsβ“˜21
pontocerebellar hypoplasia type 2EOpen Targets
0.75Strong
prostate carcinomaOpen Targets
0.54Moderate
neurodegenerative diseaseOpen Targets
0.53Moderate
progressive cerebello-cerebral atrophyOpen Targets
0.50Moderate
prostate cancerOpen Targets
0.50Moderate
pontocerebellar hypoplasiaOpen Targets
0.46Moderate
Non-syndromic pontocerebellar hypoplasiaOpen Targets
0.41Moderate
type 2 diabetes mellitusOpen Targets
0.38Weak
Intellectual disabilityOpen Targets
0.37Weak
developmental disabilityOpen Targets
0.37Weak
developmental dysplasia of the hipOpen Targets
0.33Weak
alcohol drinkingOpen Targets
0.31Weak
dislocationOpen Targets
0.27Weak
ArthropathyOpen Targets
0.26Weak
Abnormality of the skeletal systemOpen Targets
0.26Weak
self-injurious ideationOpen Targets
0.25Weak
color vision disorderOpen Targets
0.23Weak
diabetes mellitusOpen Targets
0.22Weak
non-alcoholic fatty liver diseaseOpen Targets
0.21Weak
genetic disorderOpen Targets
0.19Weak
Pontocerebellar hypoplasia 2EUniProt
Pathogenic Variants16
NM_001128159.3(VPS53):c.300_301dup (p.Gln101fs)Likely pathogenic
not provided|Pontocerebellar hypoplasia type 2E
β˜…β˜…β˜†β˜†2024β†’ Residue 101
NM_001128159.3(VPS53):c.2084A>G (p.Gln695Arg)Pathogenic
Pontocerebellar hypoplasia type 2E|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 695
NM_001128159.3(VPS53):c.1556+5G>APathogenic
Pontocerebellar hypoplasia type 2E|Pontoneocerebellar hypoplasia|not provided
β˜…β˜…β˜†β˜†2023
NM_001128159.3(VPS53):c.137A>G (p.Glu46Gly)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 46
NM_001128159.3(VPS53):c.1642G>T (p.Glu548Ter)Likely pathogenic
Pontocerebellar hypoplasia type 2E
β˜…β˜†β˜†β˜†2024β†’ Residue 548
NM_001128159.3(VPS53):c.1915del (p.Thr639fs)Likely pathogenic
Pontocerebellar hypoplasia type 2E
β˜…β˜†β˜†β˜†2024β†’ Residue 639
NM_001128159.3(VPS53):c.238C>T (p.Arg80Ter)Likely pathogenic
Pontocerebellar hypoplasia type 2E
β˜…β˜†β˜†β˜†2024β†’ Residue 80
NM_001128159.3(VPS53):c.609-1G>TLikely pathogenic
Pontocerebellar hypoplasia type 2E|Melanoma
β˜…β˜†β˜†β˜†2024
NM_001128159.3(VPS53):c.168+2T>GLikely pathogenic
Pontocerebellar hypoplasia type 2E
β˜…β˜†β˜†β˜†2024
NM_001128159.3(VPS53):c.800_801del (p.Glu267fs)Likely pathogenic
Pontocerebellar hypoplasia type 2E
β˜…β˜†β˜†β˜†2024β†’ Residue 267
NM_001128159.3(VPS53):c.687+1G>ALikely pathogenic
Pontocerebellar hypoplasia type 2E
β˜…β˜†β˜†β˜†2024
NM_001128159.3(VPS53):c.1972del (p.Ser658fs)Likely pathogenic
Pontocerebellar hypoplasia type 2E
β˜…β˜†β˜†β˜†2024β†’ Residue 658
NM_001128159.3(VPS53):c.840G>A (p.Trp280Ter)Likely pathogenic
Pontocerebellar hypoplasia type 2E
β˜…β˜†β˜†β˜†2024β†’ Residue 280
NM_001128159.3(VPS53):c.88-2A>GLikely pathogenic
not provided
β˜…β˜†β˜†β˜†2017
NM_001128159.3(VPS53):c.692C>T (p.Pro231Leu)Likely pathogenic
Pontocerebellar hypoplasia type 2E
β˜†β˜†β˜†β˜†2019β†’ Residue 231
NM_001128159.3(VPS53):c.1516C>T (p.Arg506Ter)Likely pathogenic
Pontocerebellar hypoplasia type 2E
β˜†β˜†β˜†β˜†2018β†’ Residue 506
View on ClinVar β†—
Related Genes
EIPR1Protein interaction100%VTI1AProtein interaction100%ARFRP1Protein interaction94%RAB6AProtein interaction93%STX10Protein interaction93%COG1Protein interaction93%
Tissue Expression6 tissues
Brain
100%
Bone Marrow
85%
Lung
60%
Liver
51%
Ovary
50%
Heart
45%
Gene Interaction Network
Click a node to explore
VPS53EIPR1VTI1AARFRP1RAB6ASTX10COG1
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q5VIR6
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.77LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.63 [0.52–0.77]
RankingsWhere VPS53 stands among ~20K protein-coding genes
  • #7,522of 20,598
    Most Researched62
  • #2,411of 5,498
    Most Pathogenic Variants16
  • #6,272of 17,882
    Most Constrained (LOEUF)0.77
Genes detectedVPS53
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Extensive germline-somatic interplay contributes to prostate cancer progression through HNF1B co-option of TMPRSS2-ERG.
PMID: 36443337
Nat Commun Β· 2022
1.00
2
VPS53 gene is associated with a new phenotype of complicated hereditary spastic paraparesis.
PMID: 31418091
Neurogenetics Β· 2019
0.90
3
VPS53 Suppresses Malignant Properties in Colorectal Cancer by Inducing the Autophagy Signaling Pathway.
PMID: 33116643
Onco Targets Ther Β· 2020
0.80
4
Clinical and molecular characteristics of paediatric mature B-cell acute lymphocytic leukaemia and non-Hodgkin lymphoma with bone marrow involvement: A joint study between the CCCG leukaemia and lymphoma groups.
PMID: 39962993
Br J Haematol Β· 2025
0.70
5
TSSC1 is novel component of the endosomal retrieval machinery.
PMID: 27440922
Mol Biol Cell Β· 2016
0.60