CSNK1A1L

Chr 13

casein kinase 1 alpha 1 like

Also known as: CK1

NCBI Gene: 122011 ENSG00000180138 UniProt: Q8N752

Encodes a casein kinase that phosphorylates numerous protein substrates and participates in Wnt signaling pathways. Mutations cause amelogenesis imperfecta type IIIA, a disorder affecting tooth enamel formation, with autosomal dominant inheritance.

ResearchSummary from RefSeq, OMIM, UniProt

Predicted to enable protein serine/threonine kinase activity. Predicted to be involved in negative regulation of canonical Wnt signaling pathway and signal transduction. Predicted to be active in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Jul 2025]

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.15

LOEUF

Mechanism· predicted

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.15LOEUF

pLI 0.013

Z-score 1.31

OE 0.50 (0.25–1.15)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.17Z-score

OE missense 0.96 (0.85–1.09)

178 obs / 184.6 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.50 (0.25–1.15)

0≤0.351.4

Missense OE?0.96 (0.85–1.09)

0≤0.61.4

Synonymous OE?1.16

0≤1.21.6

LoF obs/exp: 4 / 8.0Missense obs/exp: 178 / 184.6Syn Z: -1.09

Background carrier burden — how many people carry a rare variant somewhere in CSNK1A1L?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 91

449 rare PASS variants

Rare truncating (LoF)

1 in 1,300

70 rare PASS variants

Rare synonymous (reference)

1 in 270

164 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for CSNK1A1L. 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 170	1 in 2,500
South Asian	~43k	1 in 160	1 in 570
Remaining (unassigned)	~30k	1 in 75	1 in 920
European (Finnish)	~27k	1 in 2,100	≈ 1 in 13,000
Admixed American	~22k	1 in 110	1 in 1,100
African / African American	~21k	1 in 100	1 in 1,200
East Asian	~20k	1 in 110	1 in 340
Ashkenazi Jewish	~13k	1 in 820	none seen
Middle Eastern	~2,884	1 in 110	1 in 410

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): All 1 coding exons well covered in gnomAD exomes and genomes.? see exons ↓