CDK2AP2

Chr 11

cyclin dependent kinase 2 associated protein 2

Also known as: DOC-1R, DOC1R, p14

NCBI Gene: 10263 ENSG00000167797 UniProt: O75956 OMIM: 620061

The protein functions as a component of the histone deacetylase NuRD complex involved in chromatin remodeling and inhibits cell cycle G1/S phase transition by repressing CDK2 expression and activation. Mutations cause autosomal recessive neurodevelopmental disorders with intellectual disability, developmental delay, and variable features including seizures and brain malformations. The gene shows moderate constraint against loss-of-function variants (LOEUF 0.58), suggesting intolerance to complete protein loss.

OMIM ResearchSummary from RefSeq, UniProt

This gene encodes a protein that interacts with cyclin-dependent kinase 2 associated protein 1. Pseudogenes associated with this gene are located on chromosomes 7 and 9. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Dec 2012]

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

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P/LP submissions

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P/LP missense

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LOEUF

LOF

Mechanism· predicted

Some data sources returned errors (1)

gnomad: Error: gnomAD API error: 400

Population Genetics & Constraint

gnomAD

Constraint data not available from gnomAD.

Background carrier burden — how many people carry a rare variant somewhere in CDK2AP2?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 1,300

140 rare PASS variants

Rare truncating (LoF)

1 in 26,000

8 rare PASS variants

Rare synonymous (reference)

1 in 890

81 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for CDK2AP2. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 1,800	1 in 78,000
South Asian	~43k	1 in 460	≈ 1 in 21,000
Remaining (unassigned)	~30k	1 in 990	none seen
European (Finnish)	~27k	1 in 600	none seen
Admixed American	~22k	1 in 440	none seen
African / African American	~21k	1 in 1,400	≈ 1 in 10,000
East Asian	~20k	1 in 340	none seen
Ashkenazi Jewish	~13k	1 in 1,600	none seen
Middle Eastern	~2,884	≈ 1 in 2,900	none seen

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.