COLEC10

Chr 8AR

collectin subfamily member 10

Also known as: 3MC3, CL-10, CL-34, CLL1

NCBI Gene: 10584 ENSG00000184374 UniProt: Q9Y6Z7 OMIM: 607620

This gene encodes a cytosolic lectin that binds to various sugars and acts as a chemoattractant involved in regulating cell migration. Mutations cause 3MC syndrome 3, a developmental disorder with craniofacial, skeletal, and other congenital anomalies. The condition follows autosomal recessive inheritance.

OMIM ResearchSummary from RefSeq, OMIM, UniProt

This gene encodes a member of the C-lectin family, proteins that possess collagen-like sequences and carbohydrate recognition domains. The other members of this family are secreted proteins and bind to carbohydrate antigens on microorganisms facilitating their recognition and removal. This gene product is a cytosolic protein, a characteristic that suggests that it may have different biological functions than other C-lectins. [provided by RefSeq, Jul 2008]

OMIM ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

3MC syndrome 3MIM #248340

Clinical highlights

Gene–disease validity

Not independently assessedOMIM lists 3MC syndrome 3; no ClinGen or GenCC tier

Interpreting a novel variant

Loss of function is the curated mechanism (Gene2Phenotype), though the gene is not strongly LoF-constrained in the population — weigh truncating variants against that tolerance.Curated gene-level mechanism — a prior for triage, not a per-variant call.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.96

LOEUF

LOF

Mechanism· G2P

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.96LOEUF

pLI 0.003

Z-score 1.66

OE 0.49 (0.27–0.96)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.03Z-score

OE missense 0.99 (0.87–1.13)

158 obs / 159.0 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.49 (0.27–0.96)

0≤0.351.4

Missense OE?0.99 (0.87–1.13)

0≤0.61.4

Synonymous OE?0.88

0≤1.21.6

LoF obs/exp: 6 / 12.3Missense obs/exp: 158 / 159.0Syn Z: 0.71

Background carrier burden — how many people carry a rare variant somewhere in COLEC10?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 150

384 rare PASS variants

Rare truncating (LoF)

1 in 2,800

50 rare PASS variants

Rare synonymous (reference)

1 in 330

138 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for COLEC10. 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 280	1 in 3,500
South Asian	~43k	1 in 250	1 in 1,300
Remaining (unassigned)	~30k	1 in 130	1 in 3,800
European (Finnish)	~27k	1 in 570	≈ 1 in 13,000
Admixed American	~22k	1 in 140	1 in 3,800
African / African American	~21k	1 in 97	1 in 4,000
East Asian	~20k	1 in 110	≈ 1 in 5,000
Ashkenazi Jewish	~13k	1 in 450	≈ 1 in 6,500
Middle Eastern	~2,884	1 in 180	≈ 1 in 2,900

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 ↓