CLEC2A
Chr 12C-type lectin domain family 2 member A
Also known as: INPE5792, KACL, PILAR, UNQ5792
CLEC2A encodes a membrane-bound protein expressed on keratinocytes that serves as a ligand for the NKp65 receptor on natural killer cells, facilitating immune recognition and NK cell-mediated cytotoxicity while also modulating T-cell expansion. The gene shows extremely high constraint against loss-of-function variants (pLI = 1.0, LOEUF = 1.841), suggesting that haploinsufficiency would likely be pathogenic, but no specific Mendelian diseases have been definitively associated with CLEC2A mutations to date.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Highly tolerant — LoF variants common in population
Mild missense constraint
This gene has evidence for multiple mechanisms of pathogenicity (dominant-negative and gain-of-function). Both the Badonyi & Marsh prediction and the broader genomic evidence point to dominant-negative as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.
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
107 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 0 | 0 | 34 | 0 | 34 |
Likely Pathogenic | 0 | 0 | 2 | 0 | 2 |
VUS | 0 | 59 | 5 | 0 | 64 |
Likely Benign | 0 | 3 | 1 | 0 | 4 |
Benign | 0 | 0 | 0 | 0 | 0 |
| Total | 0 | 62 | 42 | 0 | 104 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
CLEC2A · 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