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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
CDK13
cyclin dependent kinase 13
Chromosome 7 Β· 7p14.1
NCBI Gene: 8621Ensembl: ENSG00000065883.19HGNC: HGNC:1733UniProt: Q14004
126PubMed Papers
21Diseases
4Drugs
88Pathogenic Variants
FUNCTIONAL ROLE
Kinase
RESEARCH IMPACT
Variant-Rich
CLINICAL
Clinical TrialsOMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
RNA bindingprotein bindingRNA polymerase II CTD heptapeptide repeat kinase activitycyclin bindingcongenital heart defects, dysmorphic facial features, and intellectual developmental disordergenetic disorderCardiac anomalies-developmental delay-facial dysmorphism syndromeneurodegenerative disease
✦AI Summary

CDK13 (cyclin dependent kinase 13) is a transcriptional regulatory kinase that phosphorylates the C-terminal domain (CTD) of RNA polymerase II, playing crucial roles in gene expression and RNA processing 1. As a CTD kinase functioning in complex with cyclin K, CDK13 regulates transcription elongation and RNA splicing, though it exhibits distinct functions from the related CDK12 1. CDK13 is essential for nuclear RNA surveillance pathways, where it phosphorylates ZC3H14 to promote degradation of defective transcripts, preventing accumulation of aberrant RNAs 2. The kinase also regulates lipid metabolism in prostate cancer by interacting with NSUN5 to enhance m5C modification of ACC1 mRNA, promoting fatty acid synthesis and lipid accumulation 3. Disease-wise, CDK13 mutations are associated with neurodevelopmental disorders, with the gene showing female-biased enrichment in de novo mutations 4. In cancer contexts, CDK13 mutations contribute to melanoma development through disrupted RNA surveillance 2, while therapeutic targeting of CDK13 (along with CDK12) shows promise in triple-negative breast cancer by inducing DNA damage response deficiencies 5. These findings establish CDK13 as a multifunctional kinase critical for proper gene expression, RNA quality control, and cellular metabolism.

Sources cited
1
CDK13 is a CTD kinase that functions with cyclin K and has distinct functions from CDK12
PMID: 30319007
2
CDK13 phosphorylates ZC3H14 for nuclear RNA surveillance and mutations cause aberrant RNA stabilization in melanoma
PMID: 37079685
3
CDK13 interacts with NSUN5 to regulate ACC1 mRNA modification and lipid metabolism in prostate cancer
PMID: 37845385
4
CDK13 shows female-biased de novo mutations in neurodevelopmental disorders
PMID: 31785789
5
CDK13 inhibition causes DNA damage response deficiencies in triple-negative breast cancer
PMID: 31668947
Disease Associationsβ“˜21
congenital heart defects, dysmorphic facial features, and intellectual developmental disorderOpen Targets
0.81Strong
genetic disorderOpen Targets
0.55Moderate
Cardiac anomalies-developmental delay-facial dysmorphism syndromeOpen Targets
0.53Moderate
neurodegenerative diseaseOpen Targets
0.53Moderate
Global developmental delayOpen Targets
0.46Moderate
syndromic intellectual disabilityOpen Targets
0.41Moderate
craniosynostosisOpen Targets
0.37Weak
autism spectrum disorderOpen Targets
0.34Weak
congenital heart diseaseOpen Targets
0.27Weak
Neurodevelopmental disorderOpen Targets
0.27Weak
Neurodevelopmental delayOpen Targets
0.27Weak
Abnormal heart morphologyOpen Targets
0.27Weak
marfanoid habitus and intellectual disabilityOpen Targets
0.27Weak
Neurodevelopmental abnormalityOpen Targets
0.27Weak
response to xenobiotic stimulusOpen Targets
0.26Weak
cervical carcinomaOpen Targets
0.23Weak
hypertrophic cardiomyopathyOpen Targets
0.18Weak
asthmaOpen Targets
0.17Weak
retinal degenerationOpen Targets
0.17Weak
neuroinflammatory disorderOpen Targets
0.15Weak
Congenital heart defects, dysmorphic facial features, and intellectual developmental disorderUniProt
Pathogenic Variants88
NM_003718.5(CDK13):c.2638C>T (p.Arg880Cys)Pathogenic
Congenital heart defects, dysmorphic facial features, and intellectual developmental disorder|not provided|Inborn genetic diseases
β˜…β˜…β˜†β˜†2026β†’ Residue 880
NM_003718.5(CDK13):c.3073C>T (p.Arg1025Ter)Pathogenic
not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 1025
NM_003718.5(CDK13):c.2563G>T (p.Asp855Tyr)Pathogenic
Congenital heart defects, dysmorphic facial features, and intellectual developmental disorder|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 855
NM_003718.5(CDK13):c.484dup (p.Ala162fs)Pathogenic
not provided|Congenital heart defects, dysmorphic facial features, and intellectual developmental disorder|CDK13-related disorder|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 162
NM_003718.5(CDK13):c.2525A>G (p.Asn842Ser)Pathogenic
not provided|Congenital heart defects, dysmorphic facial features, and intellectual developmental disorder|Inborn genetic diseases|Marfanoid habitus and intellectual disability|Global developmental delay
β˜…β˜…β˜†β˜†2025β†’ Residue 842
NM_003718.5(CDK13):c.2716G>A (p.Glu906Lys)Pathogenic
Inborn genetic diseases|not provided|Syndromic intellectual disability
β˜…β˜…β˜†β˜†2025β†’ Residue 906
NM_003718.5(CDK13):c.2579G>A (p.Arg860Gln)Pathogenic
not provided|Congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 860
NM_003718.5(CDK13):c.2141G>A (p.Gly714Asp)Pathogenic
not provided|Global developmental delay|Inborn genetic diseases|Congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 714
NM_003718.5(CDK13):c.2563G>A (p.Asp855Asn)Likely pathogenic
Congenital heart defects, dysmorphic facial features, and intellectual developmental disorder|Neurodevelopmental abnormality
β˜…β˜…β˜†β˜†2025β†’ Residue 855
NM_003718.5(CDK13):c.2201A>G (p.Lys734Arg)Pathogenic
Congenital heart defects, dysmorphic facial features, and intellectual developmental disorder|CDK13-related disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 734
NM_003718.5(CDK13):c.2570G>A (p.Gly857Glu)Pathogenic
Congenital heart defects, dysmorphic facial features, and intellectual developmental disorder|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 857
NM_003718.5(CDK13):c.2134G>A (p.Gly712Arg)Pathogenic
not provided|Heart, malformation of
β˜…β˜…β˜†β˜†2024β†’ Residue 712
NM_003718.5(CDK13):c.527dup (p.Ser177fs)Pathogenic
not provided|Inborn genetic diseases
β˜…β˜…β˜†β˜†2024β†’ Residue 177
NM_003718.5(CDK13):c.2524A>G (p.Asn842Asp)Pathogenic
Congenital heart defects, dysmorphic facial features, and intellectual developmental disorder|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 842
NM_003718.5(CDK13):c.2149G>A (p.Gly717Arg)Pathogenic
Congenital heart defects, dysmorphic facial features, and intellectual developmental disorder|not provided|Inborn genetic diseases|Autism spectrum disorder
β˜…β˜…β˜†β˜†2024β†’ Residue 717
NM_003718.5(CDK13):c.181del (p.Leu61fs)Pathogenic
Inborn genetic diseases|Congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
β˜…β˜…β˜†β˜†2023β†’ Residue 61
NM_003718.5(CDK13):c.2252G>A (p.Arg751Gln)Pathogenic
Congenital heart defects, dysmorphic facial features, and intellectual developmental disorder|not provided
β˜…β˜…β˜†β˜†2023β†’ Residue 751
NM_003718.5(CDK13):c.2209C>T (p.Arg737Cys)Pathogenic
not provided|Congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
β˜…β˜…β˜†β˜†2022β†’ Residue 737
NM_003718.5(CDK13):c.454C>T (p.Gln152Ter)Pathogenic
not provided|Congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
β˜…β˜…β˜†β˜†2021β†’ Residue 152
NM_003718.5(CDK13):c.2509G>A (p.Asp837Asn)Pathogenic
Congenital heart defects, dysmorphic facial features, and intellectual developmental disorder
β˜…β˜†β˜†β˜†2026β†’ Residue 837
View on ClinVar β†—
Drug Targets4
AT-7519Phase II
Cyclin-dependent kinase inhibitor
chronic lymphocytic leukemia
AZD-5438Phase I
Cyclin-dependent kinase inhibitor
PHA-793887Phase I
Cyclin-dependent kinase inhibitor
RONICICLIBPhase II
Cyclin-dependent kinase inhibitor
small cell lung carcinoma
Related Genes
CCNT1Protein interaction97%CCNT2Protein interaction96%MMP23BProtein interaction93%SUPT5HProtein interaction92%CCNHProtein interaction91%POLR2AProtein interaction90%
Tissue Expression6 tissues
Ovary
100%
Bone Marrow
83%
Liver
73%
Brain
67%
Heart
62%
Lung
62%
Gene Interaction Network
Click a node to explore
CDK13CCNT1CCNT2MMP23BSUPT5HCCNHPOLR2A
PROTEIN STRUCTURE
Preparing viewer…
PDB5EFQ Β· 2.00 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.43Moderately Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.31 [0.23–0.43]
RankingsWhere CDK13 stands among ~20K protein-coding genes
  • #3,712of 20,598
    Most Researched126 Β· top quartile
  • #857of 5,498
    Most Pathogenic Variants88 Β· top quartile
  • #2,344of 17,882
    Most Constrained (LOEUF)0.43 Β· top quartile
Genes detectedCDK13
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Sex-Based Analysis of De Novo Variants in Neurodevelopmental Disorders.
PMID: 31785789
Am J Hum Genet Β· 2019
1.00
2
Prevalence and architecture of de novo mutations in developmental disorders.
PMID: 28135719
Nature Β· 2017
0.90
3
Oncogenic
PMID: 37079685
Science Β· 2023
0.80
4
Therapeutic Targeting of CDK12/CDK13 in Triple-Negative Breast Cancer.
PMID: 31668947
Cancer Cell Β· 2019
0.70
5
Covalent targeting of remote cysteine residues to develop CDK12 and CDK13 inhibitors.
PMID: 27571479
Nat Chem Biol Β· 2016
0.60