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]

GeneReviewsResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtSpinocerebellar ataxia, autosomal recessive 4

Clinical highlights

Gene-disease validity (ClinGen)
Leigh syndrome · ARLimitednot for standalone diagnostic reporting
Interpreting a novel variant
This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.
0
Active trials
11
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.33
LOEUF· LoF intol.
—
Mechanism
📖
GeneReview available — VPS13D
Authoritative clinical overview · Recommended first read
Open GeneReview ↗
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.

Search ClinicalTrials.gov →

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