CDKL4
protein-codingcyclin dependent kinase like 4, the group of Cyclin dependent kinases
Gene summary
Predicted to enable protein serine/threonine kinase activity. Predicted to be involved in regulation of cell cycle. Predicted to be located in cytoplasm. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~75.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CDKL4 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001397900.1. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 38 | 38 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 38 | 0 | 0 | 38 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001384829.1 | 9 | MANE Select | |
| Ensembl | ENSP00000389833.2 | 9 | MANE Select | |
| RefSeq | NP_001009565.1 | 8 | Standard | |
| RefSeq | NP_001333840.1 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- protein phosphorylation
- regulation of cell cycle
Molecular Function
- cyclin-dependent protein serine/threonine kinase activity
- ATP binding
Cellular Component
- nucleus
- cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000378803
- Coding exons
- 8
- Length
- 53943
- Individuals with no LoFs
- 125383
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 362
- Defined
- 125747
- p
- 0.00145
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.0158 | 162 | 163 | 0.997 | 0.00000802 | 2073 |
| Missense (PolyPhen) | 63 | 60.978 | 1.0332 | 802 | ||
| Synonymous | 0.251 | 54 | 56.4 | 0.957 | 0.00000297 | 574 |
| Loss of Function | -0.551 | 19 | 16.6 | 1.15 | 8.83e-7 | 209 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00018 | rare |
| Latino/Admixed American | 0.0037 | 0.0036 | notable |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.010 | 0.010 | notable |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00021 | 0.00018 | rare |
| South Asian | 0.00091 | 0.00085 | rare |
| Other | 0.00066 | 0.00065 | rare |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.0869
Intolerance Scores
- LoFtool
- 0.711
- RVIS EVS
- 0.04
- RVIS percentile EVS
- 57.15
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0449
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |