HDAC9
Histone Deacetylase 9: Epigenetic Regulator in Development and Disease
Gene Information Card
| Symbol | HDAC9 |
|---|---|
| Full Name | Histone Deacetylase 9 |
| Gene Type | Protein coding |
| Chromosomal Location | 7p21.1 |
| NCBI Gene ID | 9734 ncbi.nlm.nih.gov/gene/9734 |
| Ensembl ID | ENSG00000048052 |
| UniProt ID | Q9UKV0 |
| OMIM ID | 606543 |
| HGNC ID | 14063 |
| Aliases | HDAC7B, HDAC9B, HDAC9FL, HDRP, MITR |
Description
HDAC9 encodes a member of the class II histone deacetylase family. This protein regulates transcription by deacetylating lysine residues on histone and non-histone proteins, thereby modulating chromatin structure and gene expression. HDAC9 is involved in muscle development, neuronal function, and immune regulation. Alternative splicing generates multiple isoforms with distinct functions.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Large artery stroke | HDAC9 variants increase risk via altered vascular gene expression | GWAS (PMID: 22544366) |
| Cardiac hypertrophy | HDAC9 represses anti-hypertrophic genes in cardiomyocytes | Mouse models (PMID: 15016915) |
| Schizophrenia | HDAC9 dysregulation affects synaptic plasticity genes | Postmortem brain studies (PMID: 25664887) |
| Huntington disease | HDAC9 interacts with huntingtin protein, modulating toxicity | Cell and animal models (PMID: 16936731) |
| Cancer (various) | HDAC9 overexpression promotes proliferation and metastasis in solid tumors | Expression profiling and functional assays (PMID: 26030138) |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Skeletal muscle | 12.5 | Medium |
| Heart | 9.8 | Medium |
| Brain (cortex) | 6.2 | Low |
| Lung | 4.1 | Low |
| Liver | 1.3 | Not detected |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| HeLa | 8.5 | Cervical cancer cell line |
| K562 | 6.0 | Leukemia cell line |
| HUVEC | 5.2 | Endothelial cells |
| SH-SY5Y | 7.8 | Neuroblastoma cell line |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| rs2107595 | SNP (intergenic) | Risk allele frequency ~0.15 in Europeans | Associated with large artery stroke |
| c.1960C>T (p.Arg654*) | Nonsense | Rare | Loss of function, linked to intellectual disability |
| c.1123G>A (p.Gly375Arg) | Missense | Rare | Altered deacetylase activity, reported in autism spectrum disorder |
Mutation functional classification
Loss of Function (LOF)
Nonsense and frameshift mutations that truncate the protein or disrupt the catalytic domain lead to loss of deacetylase activity.
Gain of Function (GOF)
Not well characterized; some missense variants may enhance HDAC9 activity but evidence is limited.
Dominant Negative (DN)
Isoforms lacking the catalytic domain can act as dominant-negative repressors by competing with full-length HDAC9 for binding partners.
View complete mutation data：
Gene Ontology (GO)
| • histone deacetylase activity (GO:0004407) | • nucleus (GO:0005634) |
| • negative regulation of transcription by RNA polymerase II (GO:0000122) | • histone deacetylation (GO:0016575) |
| • negative regulation of transcription (GO:0045892) | • cytoplasm (GO:0005737) |
Pathways
• Notch signaling pathway (Reactome: R-HSA-157118)
• Chromatin modifying enzymes (Reactome: R-HSA-3247509)
• Class II HDACs (Reactome: R-HSA-3214815)
Protein Summary
HDAC9 is a class IIa histone deacetylase that removes acetyl groups from lysine residues on histones and transcription factors. It shuttles between the nucleus and cytoplasm in response to cellular signals. HDAC9 interacts with MEF2, FOXP3, and other transcription factors to regulate gene programs in muscle, immune, and neuronal cells. Its expression is dynamically regulated during development and in disease states.
Related Services
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| HDAC9 Knockout HEK293 Cell Line | EDJ-KQ3111 | Human | 9734 | Details Get a Quote |
| HDAC9 Knockout HCT 116 Cell Line | EDJ-KQ23074 | Human | 9734 | Details Get a Quote |
| HDAC9 Knockout HeLa Cell Line | EDJ-KQ55241 | Human | 9734 | Details Get a Quote |
| HDAC9 Knockout A-549 Cell Line | EDJ-KQ63720 | Human | 9734 | Details Get a Quote |
