CHD7 Gene: Chromodomain Helicase DNA Binding Protein 7
Key regulator of chromatin remodeling and development; associated with CHARGE syndrome and multiple congenital anomalies.
Gene Information Card
| Symbol | CHD7 |
|---|---|
| Full Name | Chromodomain Helicase DNA Binding Protein 7 |
| Gene Type | Protein coding |
| Chromosomal Location | 8q12.2 |
| NCBI Gene ID | 55636 ncbi.nlm.nih.gov/gene/55636 |
| Ensembl ID | ENSG00000171316 |
| UniProt ID | Q9P2D1 |
| OMIM ID | 608892 |
| HGNC ID | 20626 |
| Aliases | KIAA1416, IS3, FLJ20357, CHD-7 |
Description
CHD7 encodes a member of the chromodomain helicase DNA-binding (CHD) protein family, which functions as an ATP-dependent chromatin remodeling factor. The protein contains two N-terminal chromodomains, a SNF2-like ATPase/helicase domain, and a DNA-binding domain. CHD7 is essential for normal development, particularly of the neural crest, and is a master regulator of gene expression through nucleosome remodeling. Heterozygous loss-of-function mutations in CHD7 are the primary cause of CHARGE syndrome, a complex multisystem disorder. CHD7 also plays roles in stem cell maintenance and is implicated in various cancers.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| CHARGE syndrome | Heterozygous loss-of-function mutations disrupt chromatin remodeling, leading to impaired neural crest cell migration and differentiation, causing coloboma, heart defects, choanal atresia, growth retardation, genital abnormalities, and ear anomalies. | ClinVar, OMIM #214800 |
| Hypogonadotropic hypogonadism | CHD7 mutations impair GnRH neuron development and migration, resulting in delayed or absent puberty and infertility. | ClinVar, OMIM #612370 |
| Isolated cleft palate | Rare CHD7 missense variants may disrupt craniofacial development pathways. | ClinVar |
| Autism spectrum disorder | De novo CHD7 variants have been identified in some ASD cohorts, suggesting a role in neurodevelopment. | ClinVar, NCBI |
| Colorectal cancer | Somatic CHD7 mutations (including frameshift and nonsense) are found in colorectal tumors, potentially affecting chromatin remodeling and gene expression. | COSMIC |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Brain | 12.5 | Medium |
| Heart | 8.2 | Low |
| Lung | 6.1 | Low |
| Liver | 4.3 | Low |
| Kidney | 7.8 | Low |
| Testis | 15.3 | Medium |
| Ovary | 9.0 | Low |
| Skeletal muscle | 3.5 | Not detected |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| HEK 293 | 10.2 | Embryonic kidney cells; moderate expression |
| HeLa | 8.5 | Cervical cancer cells; low expression |
| K562 | 6.0 | Leukemia cells; low expression |
| SH-SY5Y | 12.0 | Neuroblastoma cells; medium expression |
| HepG2 | 5.5 | Hepatocellular carcinoma cells; low expression |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| c.5404C>T (p.Arg1802*) | Nonsense | ~30% of CHARGE syndrome cases | Loss of function; premature termination |
| c.2929_2930del (p.Leu977Alafs*5) | Frameshift | ~5% of CHARGE syndrome cases | Loss of function; truncated protein |
| c.2011G>A (p.Gly671Arg) | Missense | ~2% of CHARGE syndrome cases | Loss of function; impaired ATPase activity |
| c.7888C>T (p.Arg2630*) | Nonsense | Somatic in colorectal cancer | Loss of function; tumor suppressor role |
| c.1234A>G (p.Lys412Glu) | Missense | Rare in hypogonadotropic hypogonadism | Likely loss of function; reduced chromatin binding |
Mutation functional classification
Loss of Function (LOF)
Most CHD7 mutations in CHARGE syndrome are heterozygous loss-of-function (nonsense, frameshift, splice-site, or missense that disrupt ATPase/helicase activity), leading to haploinsufficiency and impaired chromatin remodeling.
Gain of Function (GOF)
No well-established gain-of-function mutations reported for CHD7 in human disease.
Dominant Negative (DN)
Some missense mutations may exert dominant-negative effects by interfering with wild-type CHD7 function, though haploinsufficiency is the primary mechanism in CHARGE syndrome.
View complete mutation data：
Gene Ontology (GO)
Pathways
• Chromatin remodeling by ATP-dependent complexes (Reactome: R-HSA-5250913)
• Transcriptional regulation by CHD7 (Reactome: R-HSA-9018519)
• Neural crest differentiation (KEGG: hsa04350)
• Notch signaling pathway (KEGG: hsa04330)
Protein Summary
CHD7 is a 2997-amino acid ATP-dependent chromatin remodeling protein that belongs to the CHD family. It contains two chromodomains that recognize methylated histones, a SNF2-like ATPase domain that provides energy for nucleosome sliding, and a C-terminal DNA-binding domain. CHD7 regulates gene expression by altering chromatin accessibility, particularly at enhancer regions. It is essential for neural crest cell development, neurogenesis, and craniofacial morphogenesis. Mutations cause CHARGE syndrome, and somatic alterations are linked to cancer. The protein is widely expressed, with highest levels in brain and testis.
Related Services
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| CHD7 Knockout HEK293 Cell Line | EDJ-KQ12093 | Human | 55636 | Details Get a Quote |
| CHD7 Knockout HCT 116 Cell Line | EDJ-KQ39507 | Human | 55636 | Details Get a Quote |
| CHD7 Knockout A-549 Cell Line | EDJ-KQ40762 | Human | 55636 | Details Get a Quote |
| CHD7 Knockout HeLa Cell Line | EDJ-KQ40763 | Human | 55636 | Details Get a Quote |
