CDK11A
protein-codingcyclin dependent kinase 11A, the group of Cyclin dependent kinases
Gene summary
This gene encodes a member of the serine/threonine protein kinase family. Members of this kinase family are known to be essential for eukaryotic cell cycle control. Due to a segmental duplication, this gene shares very high sequence identity with a neighboring gene. These two genes are frequently deleted or altered in neuroblastoma. The protein kinase encoded by this gene can be cleaved by caspases and may play a role in cell apoptosis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2015]
- CDC2L3
- CDC2L2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~22.0 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 CDK11A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_024011.4. 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 | 6 | 6 | ||||
| missense | 121 | 3 | 124 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 4 | 4 | ||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 126 | 9 | 0 | 135 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_076916.2 | 19 | MANE Select | |
| Ensembl | ENSP00000384442.3 | 19 | MANE Select | |
| RefSeq | NP_001300825.1 | 19 | Standard | |
| RefSeq | NP_001300911.1 | 19 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- terminal <i>O</i>-glycans residues modification
- Recruitment of mitotic centrosome proteins and complexes
- Centrosome maturation
- G2/M Transition
- Mitotic G2-G2/M phases
Biological Process
- mitotic cell cycle
- regulation of cell growth
- regulation of transcription, DNA-templated
- protein phosphorylation
- apoptotic process
Molecular Function
- protein kinase activity
- protein serine/threonine kinase activity
- 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
- ENST00000404249
- Coding exons
- 19
- Length
- 21598
- Individuals with no LoFs
- 124054
- Homozygous LoFs
- 4
- Heterozygous LoFs
- 583
- Defined
- 124641
- p
- 0.00236
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.828 | 339 | 299 | 1.13 | 0.0000188 | 5028 |
| Missense (PolyPhen) | 54 | 63.928 | 0.8447 | 1211 | ||
| Synonymous | -3.12 | 163 | 120 | 1.36 | 0.00000791 | 1336 |
| Loss of Function | 0.316 | 27 | 28.8 | 0.936 | 0.00000155 | 525 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00052 | 0.00052 | rare |
| Latino/Admixed American | 0.00073 | 0.00072 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0.012 | 0.012 | notable |
| European (Non-Finnish) | 0.0020 | 0.0019 | notable |
| South Asian | 0.0021 | 0.0020 | notable |
| Other | 0.0029 | 0.0028 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Appears to play multiple roles in cell cycle progression, cytokinesis and apoptosis. The p110 isoforms have been suggested to be involved in pre-mRNA splicing, potentially by phosphorylating the splicing protein SFRS7. The p58 isoform may act as a negative regulator of normal cell cycle progression. {ECO:0000269|PubMed:12501247, ECO:0000269|PubMed:12624090}.;
Recessive Scores
- pRec
- 0.141
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.781
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | High | High | High |
| Primary Immunodeficiency | High | High | High |
| Cancer | High | High | High |