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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.
VPS13D
vacuolar protein sorting 13 homolog D
Chromosome 1 Β· 1p36.22-p36.21
NCBI Gene: 55187Ensembl: ENSG00000048707.15HGNC: HGNC:23595UniProt: Q5THJ4
64PubMed Papers
21Diseases
0Drugs
76Pathogenic Variants
FUNCTIONAL ROLE
Transporter
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
positive regulation of mitophagymitochondrion organizationextracellular exosomemitochondrionautosomal recessive cerebellar ataxia-saccadic intrusion syndromeAutosomal recessive cerebellar ataxia - saccadic intrusionneurodegenerative diseasegenetic disorder
✦AI Summary

VPS13D is a lipid transport protein that mediates inter-organellar lipid transfer, primarily functioning at membrane contact sites between the ER, mitochondria, lipid droplets, and peroxisomes 1. The protein contains a lipid transfer domain that binds glycerophospholipids and fatty acids 2, and coordinates fatty acid trafficking from lipid droplets to mitochondria through ESCRT-dependent membrane remodeling in conjunction with TSG101 2. VPS13D is recruited to mitochondria via Miro, a conserved GTPase that serves as a universal mitochondrial adaptor 13, and promotes mitochondrial clearance through autophagy (mitophagy). Loss of VPS13D impairs mitochondrial clearance, causing mitochondrial dysfunction, ultrastructural defects, and triggering cGAS-STING-dependent inflammation and neuronal cell death 4. Disease relevance: Biallelic VPS13D mutations cause autosomal recessive cerebellar ataxia, spastic paraplegia, and neurodevelopmental disorders characterized by movement dysfunction and progressive neurodegeneration 56. A common VPS13D variant (rs6685273) associates with increased IL-6 production and elevated septic shock mortality 7, implicating VPS13D in immune regulation. These findings establish VPS13D as critical for mitochondrial homeostasis, lipid metabolism, and neurological health.

Sources cited
1
VPS13D mediates ESCRT-dependent fatty acid transfer from lipid droplets to mitochondria, with a lipid transfer domain binding glycerophospholipids and fatty acids
PMID: 33623047
2
VPS13D bridges ER to mitochondria and peroxisomes via Miro recruitment, providing a lipid conduit between organelles
PMID: 33891013
3
Loss of Vps13d prevents mitochondrial clearance, causing mitochondrial dysfunction and triggering cGAS-STING-dependent inflammation and cell death in neurons
PMID: 40563011
4
VPS13D is a direct Miro interactor and lipid transporter, with Miro serving as a universal mitochondrial adaptor coordinating mitochondrial health
PMID: 38267654
5
Pathogenic VPS13D variants cause autosomal recessive neurodevelopmental impairment, developmental delay, and hyperkinetic movement disorders
PMID: 38160741
6
Intronic VPS13D variants cause spastic ataxia or spastic paraplegia with disturbed mitochondrial integrity
PMID: 36768210
7
VPS13D variant rs6685273 C allele associates with increased IL-6 production and elevated 28-day mortality in septic shock patients
PMID: 25896417
Disease Associationsβ“˜21
autosomal recessive cerebellar ataxia-saccadic intrusion syndromeOpen Targets
0.80Strong
Autosomal recessive cerebellar ataxia - saccadic intrusionOpen Targets
0.78Strong
neurodegenerative diseaseOpen Targets
0.53Moderate
genetic disorderOpen Targets
0.42Moderate
autosomal recessive cerebellar ataxiaOpen Targets
0.34Weak
Leigh syndromeOpen Targets
0.30Weak
atrophic gastritisOpen Targets
0.28Weak
male infertilityOpen Targets
0.27Weak
spinocerebellar ataxia type 4Open Targets
0.27Weak
Spinocerebellar atrophyOpen Targets
0.27Weak
Escherichia coli InfectionsOpen Targets
0.26Weak
subarachnoid hemorrhageOpen Targets
0.24Weak
primary thrombocytopeniaOpen Targets
0.19Weak
arthrogryposis multiplex congenitaOpen Targets
0.15Weak
fetal akinesia deformation sequenceOpen Targets
0.15Weak
fetal akinesia deformation sequence 1Open Targets
0.15Weak
Neurodevelopmental disorderOpen Targets
0.12Weak
Non-immune hydrops fetalisOpen Targets
0.11Weak
thyroid diseaseOpen Targets
0.10Suggestive
hypothyroidismOpen Targets
0.10Suggestive
Spinocerebellar ataxia, autosomal recessive 4UniProt
Pathogenic Variants76
NM_015378.4(VPS13D):c.907C>T (p.Arg303Ter)Pathogenic
not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 303
NM_015378.4(VPS13D):c.10552C>T (p.Arg3518Ter)Likely pathogenic
Spinocerebellar atrophy|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 3518
NM_015378.4(VPS13D):c.9757C>T (p.Arg3253Ter)Pathogenic
not provided|Inborn genetic diseases|Autosomal recessive cerebellar ataxia-saccadic intrusion syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 3253
NM_015378.4(VPS13D):c.941+3A>GPathogenic
Autosomal recessive cerebellar ataxia-saccadic intrusion syndrome|not provided
β˜…β˜…β˜†β˜†2024
NM_015378.4(VPS13D):c.12416C>T (p.Ala4139Val)Likely pathogenic
Autosomal recessive cerebellar ataxia-saccadic intrusion syndrome|Spinocerebellar ataxia type 4
β˜…β˜…β˜†β˜†2024β†’ Residue 4139
NM_015378.4(VPS13D):c.3569G>A (p.Gly1190Asp)Pathogenic
Autosomal recessive cerebellar ataxia-saccadic intrusion syndrome|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 1190
NM_015378.4(VPS13D):c.10818_10821del (p.Gly3607fs)Pathogenic
VPS13D-related disorder|not provided
β˜…β˜…β˜†β˜†2023β†’ Residue 3607
NM_015378.4(VPS13D):c.946C>T (p.Arg316Ter)Pathogenic
Autosomal recessive cerebellar ataxia-saccadic intrusion syndrome|not provided
β˜…β˜…β˜†β˜†2020β†’ Residue 316
NM_015378.4(VPS13D):c.1624C>T (p.Arg542Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 542
NM_015378.4(VPS13D):c.2581C>T (p.Arg861Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 861
NM_015378.4(VPS13D):c.12794+1G>TLikely pathogenic
Autosomal recessive cerebellar ataxia-saccadic intrusion syndrome
β˜…β˜†β˜†β˜†2025
NM_015378.4(VPS13D):c.9301C>T (p.Arg3101Trp)Likely pathogenic
Autosomal recessive cerebellar ataxia-saccadic intrusion syndrome
β˜…β˜†β˜†β˜†2025β†’ Residue 3101
NM_015378.4(VPS13D):c.1212+1G>CLikely pathogenic
Autosomal recessive cerebellar ataxia-saccadic intrusion syndrome
β˜…β˜†β˜†β˜†2025
NM_015378.4(VPS13D):c.5477G>A (p.Trp1826Ter)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 1826
NM_015378.4(VPS13D):c.12629C>T (p.Ala4210Val)Pathogenic
Autosomal recessive cerebellar ataxia-saccadic intrusion syndrome|not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 4210
NM_015378.4(VPS13D):c.12424del (p.Ser4142fs)Likely pathogenic
Autosomal recessive cerebellar ataxia-saccadic intrusion syndrome
β˜…β˜†β˜†β˜†2025β†’ Residue 4142
NM_015378.4(VPS13D):c.3943C>T (p.Arg1315Ter)Likely pathogenic
Autosomal recessive cerebellar ataxia-saccadic intrusion syndrome
β˜…β˜†β˜†β˜†2025β†’ Residue 1315
NM_015378.4(VPS13D):c.8821C>T (p.Arg2941Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 2941
NM_015378.4(VPS13D):c.12408_12409dup (p.Tyr4137fs)Likely pathogenic
Autosomal recessive cerebellar ataxia-saccadic intrusion syndrome
β˜…β˜†β˜†β˜†2025β†’ Residue 4137
NM_015378.4(VPS13D):c.3856_3875del (p.Leu1286_Lys1287insTer)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 1286
View on ClinVar β†—
Related Genes
ATG2BProtein interaction81%VPS13CShared pathway67%VPS13AShared pathway44%ESYT1Shared pathway29%ATAD3CShared pathway20%TMEM74Shared pathway20%
Tissue Expression6 tissues
Heart
100%
Brain
79%
Lung
67%
Ovary
56%
Bone Marrow
53%
Liver
48%
Gene Interaction Network
Click a node to explore
VPS13DATG2BVPS13CVPS13AESYT1ATAD3CTMEM74
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q5THJ4
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.43Moderately Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.38 [0.33–0.43]
RankingsWhere VPS13D stands among ~20K protein-coding genes
  • #7,330of 20,598
    Most Researched64
  • #971of 5,498
    Most Pathogenic Variants76 Β· top quartile
  • #2,276of 17,882
    Most Constrained (LOEUF)0.43 Β· top quartile
Genes detectedVPS13D
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
VPS13D Gene Variant Is Associated with Altered IL-6 Production and Mortality in Septic Shock.
PMID: 25896417
J Innate Immun Β· 2015
1.00
2
An ESCRT-dependent step in fatty acid transfer from lipid droplets to mitochondria through VPS13D-TSG101 interactions.
PMID: 33623047
Nat Commun Β· 2021
0.90
3
VPS13D bridges the ER to mitochondria and peroxisomes via Miro.
PMID: 33891013
J Cell Biol Β· 2021
0.80
4
Microglia promote inflammatory cell death upon neuronal mitochondrial impairment during neurodegeneration.
PMID: 40563011
Nat Struct Mol Biol Β· 2025
0.70
5
HYPK coordinates degradation of polyneddylated proteins by autophagy.
PMID: 34836490
Autophagy Β· 2022
0.60