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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
VPS13A
vacuolar protein sorting 13 homolog A
Chromosome 9 Β· 9q21.2
NCBI Gene: 23230Ensembl: ENSG00000197969.14HGNC: HGNC:1908UniProt: Q96RL7
106PubMed Papers
21Diseases
0Drugs
496Pathogenic Variants
FUNCTIONAL ROLE
Transporter
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
lysosomal protein catabolic processmitochondrial outer membranemitochondrial membraneendosome membraneChoreoacanthocytosischorea-acanthocytosisneurodegenerative diseasegenetic disorder
✦AI Summary

VPS13A is a lipid transport protein that mediates transfer of lipids between organelle membranes at contact sites 1. The protein contains an N-terminal tubular domain with a hydrophobic cavity capable of solubilizing and transporting glycerolipids 1. VPS13A localizes to the ER, mitochondria, and lipid droplets, where it interacts with ER-resident protein VAP-A via its FFAT domain and with mitochondria through its C-terminal domain 2. VPS13A is required for establishing and maintaining ER-mitochondria contact sites that enable lipid transfer, regulates mitochondrial morphology, and negatively controls lipid droplet size and motility 2. The protein is also essential for efficient lysosomal protein degradation and autophagy 3. Mutations in VPS13A cause chorea-acanthocytosis, an autosomal recessive neurodegenerative disorder 4. VPS13A deficiency impairs autophagy in skeletal muscle, resulting in cellular energy depletion, defective myofibril stability, and premature muscle senescence characterized by accumulation of senescence markers and activation of pro-inflammatory pathways 3. The clinical heterogeneity observed in VPS13A disease may reflect additional mutations in genes encoding VPS13A-interacting partners 5. Rapamycin treatment can rescue autophagy and senescence markers, suggesting therapeutic potential 3.

Sources cited
1
VPS13A contains an N-terminal tubular domain with hydrophobic cavity for lipid transport; tethers ER to mitochondria and lipid droplets
PMID: 30093493
2
VPS13A localizes at ER-mitochondria contact sites via VAP-A interaction; required for maintaining contact sites; regulates mitochondrial morphology and lipid droplet motility
PMID: 30741634
3
VPS13A deficiency impairs autophagy in muscle; causes metabolic remodeling, energy depletion, myofibril dysfunction, and premature senescence; rapamycin rescues autophagy markers
PMID: 40275365
4
VPS13A mutations cause chorea-acanthocytosis with neurological symptoms and brain atrophy
PMID: 38290845
5
VPS13A mutations show clinical heterogeneity; co-mutations in interacting partners may contribute to disease phenotype variation
PMID: 37209156
Disease Associationsβ“˜21
ChoreoacanthocytosisOpen Targets
0.84Strong
chorea-acanthocytosisOpen Targets
0.72Strong
neurodegenerative diseaseOpen Targets
0.54Moderate
genetic disorderOpen Targets
0.42Moderate
cervical carcinomaOpen Targets
0.31Weak
open-angle glaucomaOpen Targets
0.30Weak
cholelithiasisOpen Targets
0.29Weak
diabetes mellitusOpen Targets
0.28Weak
Abnormality of the nervous systemOpen Targets
0.27Weak
ocular hypotensionOpen Targets
0.26Weak
acute tonsillitisOpen Targets
0.25Weak
bone fractureOpen Targets
0.25Weak
Loss of consciousnessOpen Targets
0.25Weak
benign chondrogenic neoplasmOpen Targets
0.24Weak
Genu valgumOpen Targets
0.24Weak
Genu varumOpen Targets
0.24Weak
mixed connective tissue diseaseOpen Targets
0.23Weak
vascular dementiaOpen Targets
0.11Weak
azoospermiaOpen Targets
0.10Weak
neoplasmOpen Targets
0.08Suggestive
ChoreoacanthocytosisUniProt
Pathogenic Variants496
NM_033305.3(VPS13A):c.7736_7739del (p.Arg2579fs)Pathogenic
not provided|VPS13A-related neurodegenerative disease|VPS13A-related disorder
β˜…β˜…β˜†β˜†2026β†’ Residue 2579
NM_033305.3(VPS13A):c.3556_3557dup (p.Val1187fs)Pathogenic
not provided|VPS13A-related neurodegenerative disease
β˜…β˜…β˜†β˜†2026β†’ Residue 1187
NM_033305.3(VPS13A):c.4411C>T (p.Arg1471Ter)Pathogenic
not provided|VPS13A-related neurodegenerative disease
β˜…β˜…β˜†β˜†2026β†’ Residue 1471
NM_033305.3(VPS13A):c.754+1G>ALikely pathogenic
not provided|VPS13A-related neurodegenerative disease
β˜…β˜…β˜†β˜†2026
NM_033305.3(VPS13A):c.9094G>T (p.Glu3032Ter)Pathogenic
not provided|VPS13A-related neurodegenerative disease
β˜…β˜…β˜†β˜†2026β†’ Residue 3032
NM_033305.3(VPS13A):c.883-1_892delLikely pathogenic
not provided|VPS13A-related neurodegenerative disease
β˜…β˜…β˜†β˜†2026
NM_033305.3(VPS13A):c.6094C>T (p.Arg2032Ter)Pathogenic
not provided|VPS13A-related disorder|VPS13A-related neurodegenerative disease
β˜…β˜…β˜†β˜†2026β†’ Residue 2032
NM_033305.3(VPS13A):c.2716del (p.Val905_Val906insTer)Pathogenic
not provided|VPS13A-related neurodegenerative disease
β˜…β˜…β˜†β˜†2026β†’ Residue 905
NM_033305.3(VPS13A):c.3338del (p.Lys1113fs)Pathogenic
not provided|VPS13A-related neurodegenerative disease
β˜…β˜…β˜†β˜†2026β†’ Residue 1113
NM_033305.3(VPS13A):c.9431_9432del (p.Glu3144fs)Pathogenic
not provided|VPS13A-related neurodegenerative disease
β˜…β˜…β˜†β˜†2026β†’ Residue 3144
NM_033305.3(VPS13A):c.6059del (p.Pro2020fs)Pathogenic
not provided|VPS13A-related neurodegenerative disease
β˜…β˜…β˜†β˜†2026β†’ Residue 2020
NM_033305.3(VPS13A):c.1596-1G>CPathogenic
not provided|VPS13A-related neurodegenerative disease
β˜…β˜…β˜†β˜†2025
NM_033305.3(VPS13A):c.7156-2A>TPathogenic
not provided|VPS13A-related neurodegenerative disease
β˜…β˜…β˜†β˜†2025
NM_033305.3(VPS13A):c.3889C>T (p.Arg1297Ter)Pathogenic
not provided|VPS13A-related neurodegenerative disease|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 1297
NM_033305.3(VPS13A):c.3817C>T (p.Arg1273Ter)Pathogenic
not provided|VPS13A-related neurodegenerative disease
β˜…β˜…β˜†β˜†2025β†’ Residue 1273
NM_033305.3(VPS13A):c.799C>T (p.Arg267Ter)Pathogenic
not provided|VPS13A-related neurodegenerative disease
β˜…β˜…β˜†β˜†2025β†’ Residue 267
NM_033305.3(VPS13A):c.5881C>T (p.Arg1961Ter)Pathogenic
not provided|VPS13A-related neurodegenerative disease
β˜…β˜…β˜†β˜†2025β†’ Residue 1961
NM_033305.3(VPS13A):c.4326T>A (p.Tyr1442Ter)Pathogenic
not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 1442
NM_033305.3(VPS13A):c.1400_1401del (p.Leu466_Tyr467insTer)Pathogenic
not provided|VPS13A-related neurodegenerative disease
β˜…β˜…β˜†β˜†2025β†’ Residue 466
NM_033305.3(VPS13A):c.6404dup (p.Ser2136fs)Pathogenic
VPS13A-related neurodegenerative disease|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 2136
View on ClinVar β†—
Related Genes
JPH3Protein interaction83%VAPAProtein interaction80%KELProtein interaction73%XKProtein interaction73%ADD2Protein interaction71%VPS13CShared pathway63%
Tissue Expression6 tissues
Bone Marrow
100%
Heart
77%
Brain
41%
Lung
40%
Liver
37%
Ovary
23%
Gene Interaction Network
Click a node to explore
VPS13AJPH3VAPAKELXKADD2VPS13C
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q96RL7
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.70LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.62 [0.55–0.70]
RankingsWhere VPS13A stands among ~20K protein-coding genes
  • #4,506of 20,598
    Most Researched106 Β· top quartile
  • #107of 5,498
    Most Pathogenic Variants496 Β· top 5%
  • #5,276of 17,882
    Most Constrained (LOEUF)0.70
Genes detectedVPS13A
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
VPS13A and VPS13C are lipid transport proteins differentially localized at ER contact sites.
PMID: 30093493
J Cell Biol Β· 2018
1.00
2
Chorea-acanthocytosis.
PMID: 38290845
Pract Neurol Β· 2024
0.90
3
Human VPS13A is associated with multiple organelles and influences mitochondrial morphology and lipid droplet motility.
PMID: 30741634
Elife Β· 2019
0.80
4
Premature skeletal muscle aging in VPS13A deficiency relates to impaired autophagy.
PMID: 40275365
Acta Neuropathol Commun Β· 2025
0.70
5
Exome sequencing of choreoacanthocytosis reveals novel mutations in VPS13A and co-mutation in modifier gene(s).
PMID: 37209156
Mol Genet Genomics Β· 2023
0.60