CSNK1G2

Chr 19

casein kinase 1 gamma 2

Also known as: CK1g2

NCBI Gene: 1455 ENSG00000133275 UniProt: P78368 OMIM: 602214

Enables protein serine/threonine kinase activity. Predicted to be involved in endocytosis; positive regulation of canonical Wnt signaling pathway; and signal transduction. Located in membrane. [provided by Alliance of Genome Resources, Jul 2025]

OMIM Research

OMIM ResearchGenerating clinical summary…

LOFmechanismLOEUF 0.25

Clinical Summary— CSNK1G2

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Population Constraint (gnomAD)

Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.99). One damaged copy is likely sufficient to cause disease.

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ClinVar Variants

37 VUS of 60 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

LoF intolerant — likely haploinsufficient

LoF Constraint?

0.25LOEUF

pLI 0.991

Z-score 3.79

OE 0.05 (0.02–0.25)

Highly constrained

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

Missense Constraint?

2.80Z-score

OE missense 0.51 (0.45–0.59)

134 obs / 261.2 exp

Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?

LoF OE?0.05 (0.02–0.25)

0≤0.351.4

Missense OE?0.51 (0.45–0.59)

0≤0.61.4

Synonymous OE?1.23

0≤1.21.6

LoF obs/exp: 1 / 18.6Missense obs/exp: 134 / 261.2Syn Z: -1.93

This gene — mechanism propensity

0.4983th %ile

GOF

0.4184th %ile

LOF

0.69top 10%

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

LOFprediction above median · LOEUF 0.25

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

60 submitted variants in ClinVar

ClinVar

Classification Summary

VUS37

Likely Benign4

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Synonymous	Total
Pathogenic	0	0	0
Likely Pathogenic	0	0	0
VUS	37	0	37
Likely Benign	2	2	4
Benign	0	0	0
Total	39	2	41

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

View in ClinVar →

24 pathogenic / likely-pathogenic (of 40) ClinVar copy-number / structural variants overlap CSNK1G2 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →