VPS52

Chr 6

VPS52 subunit of GARP complex

Also known as: ARE1, SAC2, SACM2L, dJ1033B10.5

NCBI Gene: 6293ENSG00000223501UniProt: Q8N1B4

This gene encodes a protein that is similar to the yeast suppressor of actin mutations 2 gene. The yeast protein forms a subunit of the tetrameric Golgi-associated retrograde protein complex that is involved in vesicle trafficking from from both early and late endosomes, back to the trans-Golgi network. This gene is located on chromosome 6 in a head-to-head orientation with the gene encoding ribosomal protein S18. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]

ResearchGenerating clinical summary…

Clinical highlights

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
4
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.49
LOEUF
Multiple*
Mechanism· predicted
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint?
0.49LOEUF
pLI 0.000
Z-score 4.30
OE 0.32 (0.21–0.49)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?
2.50Z-score
OE missense 0.66 (0.60–0.73)
286 obs / 432.2 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?
LoF OE?0.32 (0.21–0.49)
0≤0.351.4
Missense OE?0.66 (0.60–0.73)
0≤0.61.4
Synonymous OE?0.84
0≤1.21.6
LoF obs/exp: 15 / 46.7Missense obs/exp: 286 / 432.2Syn Z: 1.60

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

VPS52 · 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