CDKL1
protein-codingcyclin dependent kinase like 1, the group of Cyclin dependent kinases
Gene summary
This gene product is a member of a large family of CDC2-related serine/threonine protein kinases that accumulates primarily in the nucleus. [provided by RefSeq, Nov 2018]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~90.2 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 CDKL1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_004196.7. 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 | 2 | 2 | ||||
| missense | 41 | 1 | 42 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 45 | 1 | 0 | 46 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_004187.3 | 9 | MANE Select | |
| Ensembl | ENSP00000379176.2 | 9 | MANE Select | |
| RefSeq | NP_001269165.2 | 8 | Standard | |
| RefSeq | NP_001353993.2 | 8 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| cdkl1 | Danio rerio | Structure: post-vent region Quality: kinked abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- protein phosphorylation
- heart development
- regulation of cell cycle
- regulation of cilium assembly
Molecular Function
- cyclin-dependent protein serine/threonine kinase activity
- ATP binding
Cellular Component
- nucleus
- nucleoplasm
- cytoplasm
- ciliary transition zone
- intracellular membrane-bounded organelle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000395834
- Coding exons
- 9
- Length
- 86870
- Individuals with no LoFs
- 125502
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 246
- Defined
- 125748
- p
- 0.000979
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.818 | 165 | 197 | 0.836 | 0.0000105 | 2354 |
| Missense (PolyPhen) | 47 | 62.209 | 0.75552 | 701 | ||
| Synonymous | 0.383 | 72 | 76.3 | 0.944 | 0.00000428 | 672 |
| Loss of Function | 1.28 | 13 | 19.0 | 0.683 | 9.74e-7 | 224 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00018 | 0.00018 | rare |
| Latino/Admixed American | 0.000087 | 0.000087 | rare |
| Ashkenazi Jewish | 0.00040 | 0.00040 | rare |
| East Asian | 0.00033 | 0.00033 | rare |
| Finnish | 0.0040 | 0.0040 | notable |
| European (Non-Finnish) | 0.00067 | 0.00067 | rare |
| South Asian | 0.0018 | 0.0018 | notable |
| Other | 0.0018 | 0.0018 | notable |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- LoFtool
- 0.791
- RVIS EVS
- 0.6
- RVIS percentile EVS
- 82.66
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0167
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |