CLEC6A

Chr 12

C-type lectin domain containing 6A

Also known as: CLEC4N, CLECSF10, dectin-2, hDECTIN-2

NCBI Gene: 93978ENSG00000205846UniProt: Q6EIG7

CLEC6A encodes a calcium-dependent lectin that functions as a pattern recognition receptor in the innate immune system, specifically recognizing alpha-mannans on fungal pathogens and allergens to trigger immune responses through the CARD9-NF-kappa-B pathway. The gene shows very low constraint against loss-of-function variants (pLI near 0, LOEUF 1.44), and no definitive disease associations have been established in the provided data. This receptor plays a role in antigen presentation and T-helper cell differentiation but lacks clear Mendelian disease phenotypes.

Summary from RefSeq, UniProt
Research Assistant →
0
Active trials
2
Pubs (1 yr)
39
P/LP submissions
0%
P/LP missense
1.44
LOEUF
Multiple*
Mechanism· predicted
Clinical Summary— CLEC6A
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
38 unique Pathogenic / Likely Pathogenic· 27 VUS of 74 total submissions
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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.44LOEUF
pLI 0.000
Z-score 0.47
OE 0.85 (0.52–1.44)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
-0.03Z-score
OE missense 1.01 (0.86–1.19)
104 obs / 103.2 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE0.85 (0.52–1.44)
0≤0.351.4
Missense OE1.01 (0.86–1.19)
0≤0.61.4
Synonymous OE0.97
0≤1.21.6
LoF obs/exp: 10 / 11.7Missense obs/exp: 104 / 103.2Syn Z: 0.13
DN
0.7228th %ile
GOF
0.7028th %ile
LOF
0.2289th %ile

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.

DNprediction above median
GOFprediction above median

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

74 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic36
Likely Pathogenic2
VUS27
Likely Benign5
36
Pathogenic
2
Likely Pathogenic
27
VUS
5
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
36
0
36
Likely Pathogenic
0
0
2
0
2
VUS
0
22
5
0
27
Likely Benign
0
4
1
0
5
Benign
0
0
0
0
0
Total02644070

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

CLEC6A · protein map & ClinVar variants

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

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 4 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC

No open access results found

Top 5 resultsSearch Europe PMC ↗

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