VPS13D

Chr 1

vacuolar protein sorting 13 homolog D

Also known as: BLTP5D, SCA24, SCAR4, SCASI

NCBI Gene: 55187ENSG00000048707UniProt: Q5THJ4

This gene encodes a protein belonging to the vacuolar-protein-sorting-13 gene family. In yeast, vacuolar-protein-sorting-13 proteins are involved in trafficking of membrane proteins between the trans-Golgi network and the prevacuolar compartment. While several transcript variants may exist for this gene, the full-length natures of only two have been described to date. These two represent the major variants of this gene and encode distinct isoforms. [provided by RefSeq, Jul 2008]

ResearchGenerating clinical summary…
LOEUF 0.33
Clinical Summary— VPS13D
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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.
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Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint?
0.33LOEUF
pLI 0.000
Z-score 9.80
OE 0.27 (0.21–0.33)
Highly constrained

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

Missense Constraint?
2.50Z-score
OE missense 0.86 (0.82–0.89)
2029 obs / 2371.0 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?
LoF OE?0.27 (0.21–0.33)
0≤0.351.4
Missense OE?0.86 (0.82–0.89)
0≤0.61.4
Synonymous OE?1.00
0≤1.21.6
LoF obs/exp: 55 / 207.3Missense obs/exp: 2029 / 2371.0Syn Z: 0.09

ClinVar Variant Classifications

0 submitted variants in ClinVar

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.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

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External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients