HDAC10

Chr 22

histone deacetylase 10

Also known as: HD10

NCBI Gene: 83933ENSG00000100429UniProt: Q969S8

The protein encoded by this gene belongs to the histone deacetylase family, members of which deacetylate lysine residues on the N-terminal part of the core histones. Histone deacetylation modulates chromatin structure, and plays an important role in transcriptional regulation, cell cycle progression, and developmental events. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]

306
ClinVar variants
141
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— HDAC10
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
141 Pathogenic / Likely Pathogenic· 119 VUS of 306 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
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?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
-0.45Z-score
OE missense 1.06 (0.98–1.15)
423 obs / 397.7 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.1.17 (0.92–1.51)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.06 (0.98–1.15)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.15
0≤1.21.6
LoF obs/exp: 43 / 36.8Missense obs/exp: 423 / 397.7Syn Z: -1.64

ClinVar Variant Classifications

306 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic140
Likely Pathogenic1
VUS119
Likely Benign8
Benign1
140
Pathogenic
1
Likely Pathogenic
119
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
1
0
1
VUS
0
108
11
0
119
Likely Benign
0
6
2
0
8
Benign
0
0
1
0
1
Total01141550269

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.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
First Fluorescent Acetylspermidine Deacetylation Assay for HDAC10 Identifies Selective Inhibitors with Cellular Target Engagement.
Herp D et al.·Chembiochem
2022
Histone deacetylase 10, a potential epigenetic target for therapy.
Cheng F et al.·Biosci Rep
2021Review
Structural Basis for the Selective Inhibition of HDAC10, the Cytosolic Polyamine Deacetylase.
Herbst-Gervasoni CJ et al.·ACS Chem Biol
2020
Histone deacetylase expression following cisplatin-induced acute kidney injury in male and female mice.
Nguyen H et al.·Am J Physiol Renal Physiol
2024
Chidamide: Targeting epigenetic regulation in the treatment of hematological malignancy.
Cao HY et al.·Hematol Oncol
2023Review
Oncogenic miRNA-1908 targets HDAC10 and promotes the aggressive phenotype of cervical cancer cell.
Yu DS et al.·Kaohsiung J Med Sci
2021
Selective Inhibitors of Histone Deacetylase 10 (HDAC-10).
Pojani E et al.·Curr Med Chem
2022Review
Venetoclax confers synthetic lethality to chidamide in preclinical models with transformed follicular lymphoma.
Zhong M et al.·Clin Epigenetics
2025Functional
Histone deacetylase-10 liberates spermidine to support polyamine homeostasis and tumor cell growth.
Stewart TM et al.·J Biol Chem
2022
Epigenetic therapy of cancer with histone deacetylase inhibitors.
Lakshmaiah KC et al.·J Cancer Res Ther
2014Review
Top 10 resultsSearch 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
2025🔓 Open AccessFunctional
Periplocin Targets HDAC10 to Inhibit NF-κB Signaling and Induce Apoptosis in Myeloid Leukemia Cells.
Li W et al.·J Cancer
2025🔓 Open 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)
2025🔓 Open Access
The protein deacetylase HDAC10 controls DNA replication in malignant lymphoid cells.
Mieland AO et al.·Leukemia
2025🔓 Open Access
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools