HDAC10

Chr 22

histone deacetylase 10

Also known as: HD10

NCBI Gene: 83933ENSG00000100429UniProt: Q969S8OMIM: 608544

The protein functions primarily as a polyamine deacetylase that acts preferentially on N(8)-acetylspermidine and may play roles in autophagy and DNA repair processes. Mutations in this gene have not been definitively associated with human disease based on the available data. The gene shows very low constraint against loss-of-function variants (pLI near 0), suggesting that complete loss of function may be well tolerated.

OMIMResearchSummary from RefSeq, UniProt
DNmechanismLOEUF 1.51
Clinical Summary— HDAC10
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
143 unique Pathogenic / Likely Pathogenic· 121 VUS of 310 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.51LOEUF
pLI 0.000
Z-score -0.95
OE 1.17 (0.92–1.51)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
-0.45Z-score
OE missense 1.06 (0.98–1.15)
423 obs / 397.7 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE1.17 (0.92–1.51)
0≤0.351.4
Missense OE1.06 (0.98–1.15)
0≤0.61.4
Synonymous OE1.15
0≤1.21.6
LoF obs/exp: 43 / 36.8Missense obs/exp: 423 / 397.7Syn Z: -1.64
DN
0.6259th %ile
GOF
0.4973th %ile
LOF
0.3844th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

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

310 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic140
Likely Pathogenic3
VUS121
Likely Benign8
Benign1
140
Pathogenic
3
Likely Pathogenic
121
VUS
8
Likely Benign
1
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
140
0
140
Likely Pathogenic
0
0
3
0
3
VUS
0
110
11
0
121
Likely Benign
0
6
2
0
8
Benign
0
0
1
0
1
Total01161570273

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

HDAC10 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Macrophage HDAC10 deficiency ameliorates PM2.5-induced lung inflammation by suppressing Beclin1 deacetylation-dependent autophagy.
Huang J et al.·J Hazard Mater
2026
Unraveling the Catalytic Mechanism and Substrate Selectivity of HDAC10: A Dual-Filter Approach for Polyamine Deacetylation.
Cai S et al.·JACS Au
2025Open AccessFunctional
Periplocin Targets HDAC10 to Inhibit NF-κB Signaling and Induce Apoptosis in Myeloid Leukemia Cells.
Li W et al.·J Cancer
2025Open Access
Discovery of a Novel Selective PAK1/HDAC6/HDAC10 Inhibitor ZMF-25 that Induces Mitochondrial Metabolic Breakdown and Autophagy-Related Cell Death in Triple-Negative Breast Cancer.
Zhang J et al.·Research (Wash D C)
2025Open Access
The protein deacetylase HDAC10 controls DNA replication in malignant lymphoid cells.
Mieland AO et al.·Leukemia
2025Open Access
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients