CHL1

Chr 3

cell adhesion molecule L1 like

Also known as: CALL, L1CAM2

NCBI Gene: 10752ENSG00000134121UniProt: Q96FC9OMIM: 607416

The protein encoded by this gene is a member of the L1 gene family of neural cell adhesion molecules. It is a neural recognition molecule that may be involved in signal transduction pathways. The deletion of one copy of this gene may be responsible for mental defects in patients with 3p- syndrome. This protein may also play a role in the growth of certain cancers. Alternate splicing results in both coding and non-coding variants. [provided by RefSeq, Nov 2011]

OMIMResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtWarsaw breakage syndrome
1
Active trials
28
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.64
LOEUF
Multiple*
Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?
0.64LOEUF
pLI 0.000
Z-score 3.83
OE 0.47 (0.35–0.64)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?
-1.92Z-score
OE missense 1.21 (1.14–1.29)
785 obs / 647.3 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?
LoF OE?0.47 (0.35–0.64)
0≤0.351.4
Missense OE?1.21 (1.14–1.29)
0≤0.61.4
Synonymous OE?1.27
0≤1.21.6
LoF obs/exp: 29 / 61.4Missense obs/exp: 785 / 647.3Syn Z: -3.21

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

CHL1 · protein map & ClinVar variants

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

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients