CSNK2A2

Chr 16

casein kinase 2 alpha 2

Also known as: CK2A2, CK2alpha', CSNK2A1

The protein functions as a catalytic subunit of casein kinase 2, a constitutively active serine/threonine kinase that phosphorylates numerous substrates and regulates critical cellular processes including cell cycle progression, apoptosis, transcription, and DNA repair. Loss-of-function mutations in this gene cause autosomal dominant neurodevelopmental disorders, with the gene showing extreme intolerance to loss-of-function variants (pLI = 0.999, LOEUF = 0.184). The pathogenic mechanism involves haploinsufficiency, where reduced kinase activity disrupts the coordinated cellular signaling networks essential for normal neurological development.

Summary from RefSeq, UniProt, Mechanism
1
Active trials
7
Pubs (1 yr)
0
P/LP submissions
P/LP missense
0.18
LOEUF· LoF intol.
LOF
Mechanism· predicted
Clinical SummaryCSNK2A2
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.
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Clinical Trials
1 active or recruiting trial — potential therapeutic options may be available

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Dual constrained — LoF & missense intolerant
LoF Constraint
0.18LOEUF
pLI 0.999
Z-score 4.53
OE 0.04 (0.010.18)
Highly constrained

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

Missense Constraint
3.15Z-score
OE missense 0.36 (0.300.44)
70 obs / 193.5 exp
Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios
LoF OE0.04 (0.010.18)
00.351.4
Missense OE0.36 (0.300.44)
00.61.4
Synonymous OE0.63
01.21.6
LoF obs/exp: 1 / 25.8Missense obs/exp: 70 / 193.5Syn Z: 2.37
DN
0.3296th %ile
GOF
0.3986th %ile
LOF
0.75top 10%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · LOEUF 0.18

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

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

CSNK2A2 · protein map & ClinVar variants

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

Clinical Literature
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