CDK13

Chr 7AD

cyclin dependent kinase 13

Also known as: CDC2L, CDC2L5, CHDFIDD, CHED, hCDK13

NCBI Gene: 8621ENSG00000065883UniProt: Q14004OMIM: 603309

The protein is a cyclin-dependent serine/threonine kinase that localizes to nuclear speckles and likely functions in mRNA processing. Loss-of-function mutations cause an autosomal dominant syndrome characterized by congenital heart defects, dysmorphic facial features, and intellectual developmental disorder. The gene is highly intolerant to loss-of-function variants, supporting haploinsufficiency as the disease mechanism.

GeneReviewsOMIMResearchSummary from RefSeq, OMIM, UniProt, Mechanism
MultiplemechanismADLOEUF 0.321 OMIM phenotype
Clinical Summary— CDK13
🧬
Gene-Disease Validity (ClinGen)
syndromic intellectual disability · ADDefinitive

Definitive — sufficient evidence for diagnostic panels

⚡
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.91). One damaged copy is likely sufficient to cause disease.
📋
ClinVar Variants
27 unique Pathogenic / Likely Pathogenic· 241 VUS of 400 total submissions
Explore recent and relevant literature in Research Assistant →
📖
GeneReview available — CDK13
Authoritative clinical overview · Recommended first read
Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint
0.32LOEUF
pLI 0.908
Z-score 5.58
OE 0.20 (0.12–0.32)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint
2.35Z-score
OE missense 0.75 (0.69–0.80)
510 obs / 682.6 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios
LoF OE0.20 (0.12–0.32)
0≤0.351.4
Missense OE0.75 (0.69–0.80)
0≤0.61.4
Synonymous OE1.12
0≤1.21.6
LoF obs/exp: 11 / 56.2Missense obs/exp: 510 / 682.6Syn Z: -1.51
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
definitiveCDK13-related syndromic intellectual disability with or without congenital heart diseaseOTHERAD
DN
0.3196th %ile
GOF
0.3094th %ile
LOF
0.82top 5%

This gene has evidence for multiple mechanisms of pathogenicity (loss-of-function and dominant-negative). Both the Badonyi & Marsh prediction and the broader genomic evidence point to loss-of-function as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

LOFprediction above median · 44% of P/LP variants are LoF · LOEUF 0.32
DN1 literature citation

Literature Evidence

DNThese patients demonstrate that heterozygous, likely dominant negative mutations affecting the protein kinase domain of the CDK13 gene result in a recognisable, syndromic form of intellectual disability, with or without congenital heart disease.PMID:29021403

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

400 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic14
Likely Pathogenic13
VUS241
Likely Benign98
Benign10
Conflicting9
14
Pathogenic
13
Likely Pathogenic
241
VUS
98
Likely Benign
10
Benign
9
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
10
3
1
0
14
Likely Pathogenic
2
9
2
0
13
VUS
22
205
13
1
241
Likely Benign
0
9
15
74
98
Benign
0
10
0
0
10
Conflicting
—9
Total342363175385

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

CDK13 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients