CSNK1G1

Chr 15

casein kinase 1 gamma 1

Also known as: CK1gamma1

NCBI Gene: 53944 ENSG00000169118 UniProt: Q9HCP0 OMIM: 606274

This gene encodes a member of the casein kinase I gene family. This family is comprised of serine/threonine kinases that phosphorylate acidic proteins such as caseins. The encoded kinase plays a role in cell cycle checkpoint arrest in response to stalled replication forks by phosphorylating Claspin. A mutation in this gene may be associated with non-syndromic early-onset epilepsy (NSEOE). [provided by RefSeq, Jul 2016]

OMIM Research

OMIM ResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant

This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Curated gene-level mechanism — a prior for triage, not a per-variant call.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.22

LOEUF· LoF intol.

LOF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

LoF intolerant — likely haploinsufficient

LoF Constraint?

0.22LOEUF

pLI 0.999

Z-score 4.66

OE 0.07 (0.03–0.22)

Highly constrained

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

Missense Constraint?

1.99Z-score

OE missense 0.64 (0.56–0.73)

151 obs / 237.3 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.07 (0.03–0.22)

0≤0.351.4

Missense OE?0.64 (0.56–0.73)

0≤0.61.4

Synonymous OE?0.97

0≤1.21.6

LoF obs/exp: 2 / 29.1Missense obs/exp: 151 / 237.3Syn Z: 0.22

Background carrier burden — how many people carry a rare variant somewhere in CSNK1G1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 90

608 rare PASS variants

Rare truncating (LoF)

1 in 620

80 rare PASS variants

Rare synonymous (reference)

1 in 250

277 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for CSNK1G1. 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 96	1 in 2,500
South Asian	~43k	1 in 120	1 in 700
Remaining (unassigned)	~30k	1 in 83	1 in 750
European (Finnish)	~27k	1 in 350	≈ 1 in 13,000
Admixed American	~22k	1 in 170	1 in 390
African / African American	~21k	1 in 100	1 in 1,600
East Asian	~20k	1 in 160	1 in 2,300
Ashkenazi Jewish	~13k	1 in 420	≈ 1 in 9,700
Middle Eastern	~2,884	1 in 120	≈ 1 in 720

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.

Exome coverage (gnomAD): 9 of 11 coding exons well covered in gnomAD exomes; exons 3, 8 marginal. Genomes: all 11.? see exons ↓