VPS50

Chr 7AR

VPS50 subunit of EARP/GARPII complex

Also known as: CCDC132, NEDMSC, VPS54L

Enables SNARE binding activity. Acts upstream of or within endocytic recycling. Located in recycling endosome. Part of EARP complex. [provided by Alliance of Genome Resources, Jul 2025]

OMIMResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

Neurodevelopmental disorder with microcephaly, seizures, and neonatal cholestasisMIM #619685
AR

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
0
Pubs (1 yr)
P/LP submissions
P/LP missense
0.33
LOEUF· LoF intol.
DN
Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

LoF intolerant — likely haploinsufficient
LoF Constraint?
0.33LOEUF
pLI 0.814
Z-score 5.63
OE 0.21 (0.130.33)
Highly constrained

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

Missense Constraint?
2.50Z-score
OE missense 0.68 (0.620.74)
325 obs / 479.1 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?
LoF OE?0.21 (0.130.33)
00.351.4
Missense OE?0.68 (0.620.74)
00.61.4
Synonymous OE?1.02
01.21.6
LoF obs/exp: 12 / 58.4Missense obs/exp: 325 / 479.1Syn Z: -0.25

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

VPS50 · 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

No active trials found for this gene.

Search ClinicalTrials.gov →