VPS13D

Chr 1AR

vacuolar protein sorting 13 homolog D

The protein belongs to the vacuolar-protein-sorting-13 family and functions in trafficking membrane proteins between the trans-Golgi network and prevacuolar compartment. Biallelic mutations cause spinocerebellar ataxia, autosomal recessive 4, following an autosomal recessive inheritance pattern. The gene is highly intolerant to loss-of-function variants, suggesting pathogenicity occurs through disrupted intracellular membrane protein trafficking.

OMIMResearchSummary from RefSeq, OMIM
ARLOEUF 0.331 OMIM phenotype
Clinical SummaryVPS13D
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Gene-Disease Validity (ClinGen)
Leigh syndrome · ARLimited

Limited evidence — not for standalone diagnostic reporting

Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.27) despite low pLI — interpret in context.
Some data sources returned errors (1)

ncbi: Error: NCBI fetch failed: 429 https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

LoF intolerant — likely haploinsufficient
LoF Constraint
0.33LOEUF
pLI 0.000
Z-score 9.80
OE 0.27 (0.210.33)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint
2.50Z-score
OE missense 0.86 (0.820.89)
2029 obs / 2371.0 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios
LoF OE0.27 (0.210.33)
00.351.4
Missense OE0.86 (0.820.89)
00.61.4
Synonymous OE1.00
01.21.6
LoF obs/exp: 55 / 207.3Missense obs/exp: 2029 / 2371.0Syn Z: 0.09

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

VPS13D · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗