CDK13 Gene: Cyclin-Dependent Kinase 13 – Function, Disease Associations, and Research Insights
Explore the CDK13 gene, its role in transcription regulation, associated genetic disorders, expression patterns, and mutation landscape.
Gene Information Card
| Symbol | CDK13 |
|---|---|
| Full Name | Cyclin Dependent Kinase 13 |
| Gene Type | Protein coding |
| Chromosomal Location | 7p14.1 |
| NCBI Gene ID | 8621 ncbi.nlm.nih.gov/gene/8621 |
| Ensembl ID | ENSG00000187486 |
| UniProt ID | Q14004 |
| OMIM ID | 603309 |
| HGNC ID | 1733 |
| Aliases | CDC2L5, CHED, DKFZp686K1770, FLJ12056, hCDK13 |
Description
The CDK13 gene encodes cyclin-dependent kinase 13, a serine/threonine protein kinase that plays a critical role in regulating transcription, RNA processing, and cell cycle progression. It is part of the cyclin-dependent kinase family and functions as a transcriptional regulator, particularly in the phosphorylation of RNA Polymerase II. Mutations in CDK13 are associated with a rare neurodevelopmental disorder characterized by congenital heart defects, facial dysmorphism, and intellectual developmental disorder (CHDFIDD).
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Disease | Mechanism | Evidence |
| Congenital heart defects, dysmorphic facial features, and intellectual developmental disorder (CHDFIDD) | Heterozygous loss-of-function mutations (including missense, frameshift, and nonsense variants) in CDK13 are thought to cause haploinsufficiency or dominant-negative effects, disrupting normal transcriptional regulation during development. | ClinVar, OMIM (OMIM: 603309), multiple case reports and cohort studies. |
| Intellectual Disability | Pathogenic variants in CDK13 lead to impaired kinase activity or reduced protein levels, affecting neuronal gene expression and synaptic function. | ClinVar, published clinical case series. |
| Congenital Heart Defects | Disruption of CDK13 function alters the expression of genes critical for cardiac morphogenesis, likely through dysregulation of RNA Polymerase II phosphorylation and transcription. | ClinVar, OMIM, clinical literature. |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Tissue | nTPM | Level |
| Testis | 25.4 | Medium |
| Brain (Cerebellum) | 18.7 | Medium |
| Thyroid | 17.9 | Medium |
| Adrenal Gland | 16.8 | Medium |
| Lymph Node | 15.2 | Low |
| Liver | 8.5 | Low |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| Cell Line | nTPM | Notes |
| K-562 (Leukemia) | 22.1 | High expression in this myeloid leukemia cell line. |
| MCF-7 (Breast Cancer) | 18.5 | Moderate expression in breast adenocarcinoma cells. |
| HeLa (Cervical Cancer) | 16.3 | Moderate expression in cervical cancer cells. |
| A549 (Lung Cancer) | 14.8 | Moderate expression in lung carcinoma cells. |
| HepG2 (Liver Cancer) | 10.2 | Lower expression in hepatocellular carcinoma cells. |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| Variant | Type | Frequency | Effect |
| c.1048C>T (p.Arg350Trp) | Missense | Recurrent in CHDFIDD cases | Likely affects kinase activity or protein stability, leading to loss-of-function. |
| c.2440G>A (p.Glu814Lys) | Missense | Rare | Predicted to be damaging; disrupts ATP binding or substrate recognition. |
| c.2785C>T (p.Arg929*) | Nonsense | Rare | Introduces a premature stop codon, leading to nonsense-mediated decay and haploinsufficiency. |
| c.1234_1235del (p.Lys412ValfsTer3) | Frameshift | Rare | Causes a frameshift and premature termination, resulting in a truncated non-functional protein. |
Mutation functional classification
Loss of Function (LOF)
The majority of pathogenic CDK13 variants are predicted to result in loss-of-function, either through nonsense-mediated decay of the mRNA or by producing a truncated or misfolded protein that lacks kinase activity. This leads to haploinsufficiency, where the single functional copy of the gene is insufficient for normal development.
Gain of Function (GOF)
There is currently no strong evidence for gain-of-function mutations in CDK13. The predominant disease mechanism is loss-of-function.
Dominant Negative (DN)
Some missense mutations, particularly those in the kinase domain, may exert a dominant-negative effect. The mutant protein could compete with the wild-type protein for binding to cyclin partners or substrates, thereby inhibiting the function of the normal allele.
View complete mutation data：
Gene Ontology (GO)
| • protein serine/threonine kinase activity | • ATP binding |
| • RNA polymerase II C-terminal domain binding | • regulation of transcription by RNA polymerase II |
| • cell cycle | • mRNA processing |
| • phosphorylation | • nucleus |
| • nucleoplasm | • cytoplasm |
Pathways
• RNA Polymerase II Transcription
• Cell Cycle
• Gene Expression
Protein Summary
The CDK13 protein is a large serine/threonine kinase (approximately 164 kDa) that contains a cyclin-binding domain and a protein kinase domain. It associates with cyclin K to form an active complex. This complex phosphorylates the C-terminal domain (CTD) of RNA Polymerase II, particularly at serine 2 and serine 5 residues, which is a key step in the transition from transcription initiation to elongation. CDK13 is also involved in pre-mRNA splicing and other RNA processing events. It is ubiquitously expressed but shows higher levels in certain tissues, suggesting a role in tissue-specific gene regulation.
Related Services
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| CDK13 Knockout HEK293 Cell Line | EDJ-KQ1111 | Human | 8621 | Details Get a Quote |
| CDK13 Knockout A-549 Cell Line | EDJ-KQ20296 | Human | 8621 | Details Get a Quote |
| CDK13 Knockout HCT 116 Cell Line | EDJ-KQ20297 | Human | 8621 | Details Get a Quote |
| CDK13 Knockout HeLa Cell Line | EDJ-KQ20298 | Human | 8621 | Details Get a Quote |
