JADE3
Chr Xjade family PHD finger 3
Also known as: JADE-3, PHF16
The protein functions as a scaffold subunit of HBO1 complexes that acetylate histone H4, playing a direct role in chromatin modification and gene regulation. Mutations cause autosomal dominant intellectual disability with developmental delay and variable additional features. This gene is highly constrained against loss-of-function variants (pLI 0.999, LOEUF 0.124), indicating that even heterozygous disruption can cause disease.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Among the most LoF-intolerant genes (~top 3%)
Mild missense constraint
The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.
ClinVar Variant Classifications
130 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 | 54 | 0 | 54 |
Likely Pathogenic | 0 | 0 | 1 | 0 | 1 |
VUS | 0 | 62 | 6 | 0 | 68 |
Likely Benign | 0 | 6 | 0 | 1 | 7 |
Benign | 0 | 0 | 0 | 0 | 0 |
| Total | 0 | 68 | 61 | 1 | 130 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
JADE3 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
3D Protein StructureAlphaFold
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