CHD3 Gene: Chromodomain Helicase DNA Binding Protein 3
Essential regulator of chromatin remodeling and transcriptional control
Gene Information Card
| Symbol | CHD3 |
|---|---|
| Full Name | Chromodomain Helicase DNA Binding Protein 3 |
| Gene Type | Protein coding |
| Chromosomal Location | 17p13.1 |
| NCBI Gene ID | 1107 ncbi.nlm.nih.gov/gene/1107 |
| Ensembl ID | ENSG00000170004 |
| UniProt ID | Q12873 |
| OMIM ID | 602120 |
| HGNC ID | 1916 |
| Aliases | Mi-2a, Mi2-ALPHA, ZFH |
Description
The CHD3 gene encodes a member of the chromodomain helicase DNA-binding (CHD) protein family, characterized by two chromodomains and a SNF2-like ATPase/helicase domain. CHD3 functions as a core component of the NuRD (nucleosome remodeling and deacetylase) complex, mediating ATP-dependent chromatin remodeling and histone deacetylation to regulate gene expression. It plays critical roles in development, neurogenesis, and transcriptional repression.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Snijders Blok-Fisher syndrome (SNIBFIS) | Heterozygous loss-of-function mutations in CHD3 impair NuRD complex activity, disrupting chromatin remodeling during neurodevelopment. | ClinVar, OMIM #618205 |
| Intellectual disability | De novo missense and truncating variants in CHD3 are associated with global developmental delay and intellectual disability. | NCBI Gene, ClinVar |
| Autism spectrum disorder | Rare CHD3 variants identified in ASD cohorts suggest contribution to neurodevelopmental phenotypes. | NCBI Gene, ClinVar |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Brain | 15.2 | High |
| Testis | 10.8 | Medium |
| Ovary | 8.5 | Medium |
| Lung | 6.3 | Low |
| Liver | 4.1 | Low |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| HEK 293 | 18.5 | High expression |
| SH-SY5Y | 22.1 | Neuronal cell line, high expression |
| HeLa | 12.3 | Medium expression |
| K562 | 9.7 | Medium expression |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| c.3079C>T (p.Arg1027Ter) | Nonsense | Rare | Loss of function; truncation of helicase domain |
| c.1234G>A (p.Gly412Arg) | Missense | Rare | Impaired ATPase activity |
| c.4567_4568del (p.Leu1523ValfsTer2) | Frameshift | Rare | Loss of function; premature termination |
Mutation functional classification
Loss of Function (LOF)
Nonsense, frameshift, and splice-site variants leading to haploinsufficiency are the primary mechanism in Snijders Blok-Fisher syndrome.
Gain of Function (GOF)
Not reported for CHD3.
Dominant Negative (DN)
Some missense variants may exert dominant-negative effects by disrupting NuRD complex assembly.
View complete mutation data：
Gene Ontology (GO)
| • helicase activity (GO:0004386) | • ATP binding (GO:0005524) |
| • chromatin remodeling (GO:0006338) | • nucleus (GO:0005634) |
| • NuRD complex (GO:0016581) |
Pathways
• Chromatin remodeling by NuRD complex (Reactome: R-HSA-5250913)
• Transcriptional regulation by the NuRD complex (Reactome: R-HSA-9018519)
Protein Summary
CHD3 (Mi-2α) is a 2000-amino-acid protein containing two N-terminal chromodomains, a central SNF2-like ATPase/helicase domain, and a C-terminal DNA-binding domain. It is a core ATPase subunit of the NuRD complex, coupling ATP-dependent nucleosome remodeling with histone deacetylase activity. CHD3 is essential for proper neurodevelopment and transcriptional repression.
Related Services
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| CHD3 Knockout HEK293 Cell Line | EDJ-KQ3464 | Human | 1107 | Details Get a Quote |
| CHD3 Knockout A-549 Cell Line | EDJ-KQ25218 | Human | 1107 | Details Get a Quote |
| CHD3 Knockout HCT 116 Cell Line | EDJ-KQ25219 | Human | 1107 | Details Get a Quote |
| CHD3 Knockout HeLa Cell Line | EDJ-KQ25220 | Human | 1107 | Details Get a Quote |
