CDK9
Chr 9cyclin dependent kinase 9
Also known as: C-2k, CDC2L4, CTK1, PITALRE, TAK
CDK9 encodes a cyclin-dependent kinase that phosphorylates RNA polymerase II and other proteins to regulate transcriptional elongation, forming the P-TEFb complex essential for productive gene transcription. Mutations cause autosomal dominant developmental delay, seizures, and dysmorphic features with onset in early childhood. The gene is not highly constrained against loss-of-function variants, suggesting the disorder may involve altered protein function rather than simple protein loss.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Typical tolerance to LoF variation
Moderately missense-constrained (top ~2.5%)
The highest-scoring mechanism for this gene is dominant-negative.
Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.
ClinVar Variant Classifications
96 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 0 | 0 | 38 | 0 | 38 |
Likely Pathogenic | 0 | 1 | 1 | 0 | 2 |
VUS | 0 | 33 | 2 | 0 | 35 |
Likely Benign | 1 | 0 | 2 | 5 | 8 |
Benign | 0 | 0 | 2 | 2 | 4 |
| Total | 1 | 34 | 45 | 7 | 87 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
CDK9 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
3D Protein StructureAlphaFold
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →External Resources
Links to major genomics databases and tools