ZFYVE28
Chr 4zinc finger FYVE-type containing 28
Also known as: LST2, LYST2, lst-2
The protein binds phosphatidylinositol-3-phosphate and negatively regulates epidermal growth factor receptor signaling by promoting receptor degradation in endosomes. Mutations cause spastic tetraplegia with thin corpus callosum and progressive microcephaly, inherited in an autosomal recessive pattern. This gene is highly constrained against loss-of-function variants, suggesting that complete loss of protein function is poorly tolerated.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
More LoF-intolerant than ~75% of genes
Tolerant to missense variation
This gene has evidence for multiple mechanisms of pathogenicity (gain-of-function and dominant-negative). Both the Badonyi & Marsh prediction and the broader genomic evidence point to gain-of-function as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.
Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.
ClinVar Variant Classifications
361 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 0 | 0 | 129 | 0 | 129 |
Likely Pathogenic | 0 | 0 | 6 | 0 | 6 |
VUS | 0 | 174 | 13 | 0 | 187 |
Likely Benign | 0 | 15 | 1 | 2 | 18 |
Benign | 0 | 2 | 0 | 2 | 4 |
| Total | 0 | 191 | 149 | 4 | 344 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
ZFYVE28 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →External Resources
Links to major genomics databases and tools