HDAC2
Chr 6histone deacetylase 2
Also known as: HD2, KDAC2, RPD3, YAF1
HDAC2 encodes a histone deacetylase that removes acetyl groups from core histones H2A, H2B, H3, and H4, leading to transcriptional repression and regulation of cell cycle progression and developmental events. Heterozygous loss-of-function mutations cause a neurodevelopmental disorder with intellectual disability and developmental delay through an autosomal dominant inheritance pattern. The pathogenic mechanism involves haploinsufficiency, as HDAC2 is highly intolerant to loss-of-function variants.
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Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Among the most LoF-intolerant genes (~top 3%)
Highly missense-constrained (top ~0.1%)
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
83 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 | 19 | 0 | 19 |
Likely Pathogenic | 0 | 0 | 3 | 0 | 3 |
VUS | 1 | 25 | 3 | 0 | 29 |
Likely Benign | 0 | 0 | 3 | 2 | 5 |
Benign | 0 | 0 | 2 | 1 | 3 |
| Total | 1 | 25 | 30 | 3 | 59 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
HDAC2 · 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
External Resources
Links to major genomics databases and tools