CSNK1E

Chr 22

casein kinase 1 epsilon

Also known as: CKIe, CKIepsilon, HCKIE

NCBI Gene: 1454ENSG00000213923UniProt: P49674

The protein encoded by this gene is a serine/threonine protein kinase and a member of the casein kinase I protein family, whose members have been implicated in the control of cytoplasmic and nuclear processes, including DNA replication and repair. The encoded protein is found in the cytoplasm as a monomer and can phosphorylate a variety of proteins, including itself. This protein has been shown to phosphorylate period, a circadian rhythm protein. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Feb 2014]

0
ClinVar variants
0
Pathogenic / LP
1.00
pLI score· haploinsufficient
0
Active trials
Clinical Summary— CSNK1E
⚡
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.

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Dual constrained — LoF & missense intolerant
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.14LOEUF
pLI 0.999
Z-score 4.23
OE 0.00 (0.00–0.14)
Highly constrained

Among the most LoF-intolerant genes (~top 3%)

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
3.18Z-score
OE missense 0.47 (0.41–0.55)
136 obs / 287.8 exp
Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.00 (0.00–0.14)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.47 (0.41–0.55)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.97
0≤1.21.6
LoF obs/exp: 0 / 20.8Missense obs/exp: 136 / 287.8Syn Z: 0.24

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

CSNK1E · protein map & ClinVar variants

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

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Casein kinase 1 family member CSNK1E can regulate proliferation and migration in hepatocellular carcinoma.
Zhou J et al.·J Cancer Res Clin Oncol
2025
Exome sequencing identifies genes for socioeconomic status in 350,770 individuals.
Wu XR et al.·Proc Natl Acad Sci U S A
2025
A de novo pathogenic CSNK1E mutation identified by exome sequencing in family trios with epileptic encephalopathy.
Chen X et al.·Hum Mutat
2019
A CGG Repeat Expansion in CSNK1E Associated with Progressive Myoclonic Epilepsy with Incomplete Penetrance.
Akçimen F et al.·Mov Disord
2025Case report
Genetic association study of CSNK1E gene in bipolar disorder and circadian characteristics.
Lee KY et al.·Nord J Psychiatry
2018
A signature of circadian rhythm genes in driving anaplastic thyroid carcinoma malignant progression.
Xu T et al.·Cell Signal
2022
Circadian pathway genes in relation to glioma risk and outcome.
Madden MH et al.·Cancer Causes Control
2014
Epigenome-wide DNA methylation study of whole blood in patients with sporadic amyotrophic lateral sclerosis.
Cai Z et al.·Chin Med J (Engl)
2022Cohort
Genetic variation in the NOC gene is associated with body mass index in Chinese subjects.
Chang YC et al.·PLoS One
2013
Concurrent gene signatures for han chinese breast cancers.
Huang CC et al.·PLoS One
2013
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools