HDAC5

Chr 17

histone deacetylase 5

The protein deacetylates lysine residues on core histones and represses transcription of genes including myocyte enhancer factor MEF2C, playing a critical role in muscle maturation and epigenetic regulation. Pathogenic variants cause a neurodevelopmental disorder with intellectual disability, developmental delay, and distinctive facial features through an autosomal dominant inheritance pattern. The mechanism of pathogenicity is loss of function, as the gene is extremely intolerant to loss-of-function variants.

Summary from RefSeq, UniProt, Mechanism
Research Assistant →
0
Active trials
66
Pubs (1 yr)
0
P/LP submissions
P/LP missense
0.14
LOEUF· LoF intol.
LOF
Mechanism· predicted
Clinical SummaryHDAC5
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.
Some data sources returned errors (1)

ncbi: Error: NCBI fetch failed: 429 https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Dual constrained — LoF & missense intolerant
LoF Constraint
0.14LOEUF
pLI 1.000
Z-score 6.49
OE 0.05 (0.020.14)
Highly constrained

Among the most LoF-intolerant genes (~top 3%)

Missense Constraint
3.32Z-score
OE missense 0.63 (0.580.68)
402 obs / 638.0 exp
Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios
LoF OE0.05 (0.020.14)
00.351.4
Missense OE0.63 (0.580.68)
00.61.4
Synonymous OE0.99
01.21.6
LoF obs/exp: 3 / 54.9Missense obs/exp: 402 / 638.0Syn Z: 0.18
DN
0.3992th %ile
GOF
0.4480th %ile
LOF
0.72top 10%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · LOEUF 0.14

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

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

HDAC5 · 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 →
Clinical Literature
Open Research Assistant →