CLEC1A

Chr 12

C-type lectin domain family 1 member A

Also known as: CLEC-1, CLEC1

NCBI Gene: 51267 ENSG00000150048 UniProt: Q8NC01 OMIM: 606782

This gene encodes a C-type lectin that functions in cell adhesion, cell-cell signaling, and immune response regulation, particularly in dendritic cell function. Mutations cause increased susceptibility to aspergillosis, a fungal infection that can affect multiple organ systems including the lungs and central nervous system. The gene shows autosomal inheritance and is not highly constrained against loss-of-function variants.

OMIM ResearchSummary from RefSeq, OMIM

This gene encodes a member of the C-type lectin/C-type lectin-like domain (CTL/CTLD) superfamily. Members of this family share a common protein fold and have diverse functions, such as cell adhesion, cell-cell signaling, glycoprotein turnover, and roles in inflammation and immune response. The encoded protein may play a role in regulating dendritic cell function. This gene is closely linked to other CTL/CTLD superfamily members on chromosome 12p13 in the natural killer gene complex region. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

OMIM ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

{Aspergillosis, susceptibility to}MIM #614079

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.93

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.93LOEUF

pLI 0.000

Z-score -1.86

OE 1.55 (1.08–1.93)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.15Z-score

OE missense 1.03 (0.91–1.18)

155 obs / 149.8 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?1.55 (1.08–1.93)

0≤0.351.4

Missense OE?1.03 (0.91–1.18)

0≤0.61.4

Synonymous OE?0.90

0≤1.21.6

LoF obs/exp: 21 / 13.6Missense obs/exp: 155 / 149.8Syn Z: 0.59

Background carrier burden — how many people carry a rare variant somewhere in CLEC1A?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 160

405 rare PASS variants

Rare truncating (LoF)

1 in 830

89 rare PASS variants

Rare synonymous (reference)

1 in 400

125 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for CLEC1A. 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 210	1 in 1,100
South Asian	~43k	1 in 140	1 in 1,400
Remaining (unassigned)	~30k	1 in 100	1 in 740
European (Finnish)	~27k	1 in 440	≈ 1 in 6,600
Admixed American	~22k	1 in 160	1 in 780
African / African American	~21k	1 in 220	1 in 1,200
East Asian	~20k	1 in 130	1 in 460
Ashkenazi Jewish	~13k	1 in 2,600	≈ 1 in 4,300
Middle Eastern	~2,884	1 in 120	≈ 1 in 1,400

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 6 coding exons well covered in gnomAD exomes and genomes.? see exons ↓