CNBP Gene: CCHC-Type Zinc Finger Nucleic Acid Binding Protein
A key regulator of transcription and translation, implicated in myotonic dystrophy type 2 and other neuromuscular disorders.
Gene Information Card
| Symbol | CNBP |
|---|---|
| Full Name | CCHC-Type Zinc Finger Nucleic Acid Binding Protein |
| Gene Type | Protein coding |
| Chromosomal Location | 3q21.3 |
| NCBI Gene ID | 7555 ncbi.nlm.nih.gov/gene/7555 |
| Ensembl ID | ENSG00000169714 |
| UniProt ID | P62633 |
| OMIM ID | 116955 |
| HGNC ID | 13164 |
| Aliases | ZNF9, CNBP1, RNF163, PRO1995 |
Description
The CNBP gene encodes a highly conserved CCHC-type zinc finger protein that binds to single-stranded DNA and RNA. It functions as a transcriptional regulator and is involved in RNA processing, translation, and cell proliferation. Expansion of a CCTG repeat in intron 1 of CNBP causes myotonic dystrophy type 2 (DM2), a multisystemic disorder characterized by myotonia, muscle weakness, and cardiac abnormalities.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Myotonic Dystrophy Type 2 (DM2) | Expansion of a CCTG tetranucleotide repeat in intron 1 leads to RNA toxicity, sequestering splicing factors (e.g., MBNL1) and causing alternative splicing defects. | OMIM #602668; ClinVar pathogenic repeat expansions. |
| Hereditary Spastic Paraplegia (rare) | Missense mutations in CNBP have been reported in a small number of families with spastic paraplegia, though mechanism is unclear. | Case reports in literature; limited ClinVar entries. |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Brain | 12.5 | Medium |
| Heart | 9.8 | Medium |
| Skeletal Muscle | 15.2 | Medium |
| Liver | 7.1 | Low |
| Kidney | 8.3 | Low |
| Testis | 18.6 | High |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| HeLa | 14.2 | Medium |
| K562 | 11.5 | Medium |
| HEK293 | 13.0 | Medium |
| SH-SY5Y | 16.8 | High |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| CCTG repeat expansion (intron 1) | Repeat expansion (75-11,000 repeats) | Pathogenic in DM2 | RNA toxicity, splicing dysregulation |
| c.292C>T (p.Arg98Trp) | Missense | Rare | Unknown; possibly loss of function |
Mutation functional classification
Loss of Function (LOF)
Rare missense mutations (e.g., p.Arg98Trp) may reduce DNA/RNA binding affinity, but evidence is limited.
Gain of Function (GOF)
CCTG repeat expansions produce toxic RNA foci that sequester RNA-binding proteins, representing a gain-of-function mechanism.
Dominant Negative (DN)
Not established for CNBP.
View complete mutation data：
Gene Ontology (GO)
| • nucleic acid binding (GO:0003676) | • zinc ion binding (GO:0008270) |
| • nucleus (GO:0005634) | • cytoplasm (GO:0005737) |
| • negative regulation of mRNA splicing (GO:0048025) | • RNA binding (GO:0003723) |
Pathways
• Alternative splicing regulation (via MBNL1 sequestration in DM2)
• mRNA processing
Protein Summary
CNBP is a 177-amino acid protein containing seven CCHC-type zinc finger motifs. It binds single-stranded nucleic acids and is involved in transcriptional regulation, RNA metabolism, and cell cycle control. The protein is ubiquitously expressed, with highest levels in testis and skeletal muscle. Pathogenic CCTG repeat expansions in intron 1 cause myotonic dystrophy type 2 through a toxic RNA gain-of-function mechanism.
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