CLEC3A
Chr 16C-type lectin domain family 3 member A
Also known as: CLECSF1
The CLEC3A protein binds carbohydrates and promotes cell adhesion to laminin-332 and fibronectin in the extracellular space, where it contributes to bone ossification. Loss-of-function mutations cause autosomal recessive osteosclerotic metaphyseal dysplasia, a skeletal disorder characterized by increased bone density and metaphyseal abnormalities. The extremely low pLI score indicates this gene is highly tolerant to loss-of-function variants in the general population.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Highly tolerant — LoF variants common in population
Tolerant to missense variation
The highest-scoring mechanism for this gene is dominant-negative.
Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.
ClinVar Variant Classifications
83 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories· variant type breakdown unavailable
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | — | — | — | — | 27 |
Likely Pathogenic | — | — | — | — | 3 |
VUS | — | — | — | — | 46 |
Likely Benign | — | — | — | — | 5 |
Benign | — | — | — | — | 0 |
| Total | — | 81 | |||
Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
CLEC3A · 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
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →External Resources
Links to major genomics databases and tools