CLEC3A

protein-coding

C-type lectin domain family 3 member A, the group of C-type lectin domain containing

Gene summary

Predicted to enable carbohydrate binding activity. Predicted to be involved in ossification. Predicted to be located in extracellular region. Predicted to be active in obsolete extracellular space. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

CLECSF1

MANE transcript

NM_005752.6

Inheritance

—

ClinVar variants

U:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.42

Max pathogenic AF

—

Genomic locus

chr16:78,022,515-78,066,761

External References & Databases

Ensembl (ENSG00000166509)

Transcript & Mutation Effects

hg38 • Region Span ~44.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CLEC3A variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 8

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005752.6. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			7 clinvar			7
nonsense						0
start loss			1 clinvar			1
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	8	0	0	8

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005752.6	RefSeq	NP_005743.5	3	MANE Select
ENST00000299642.10	Ensembl	ENSP00000299642.5	3	MANE Select
ENST00000567430.2	Ensembl	ENSP00000457211.2	2	Standard
ENST00000651443.1	Ensembl	ENSP00000499168.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

skeletal system development
ossification

Molecular Function

carbohydrate binding

Cellular Component

extracellular space

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000299642
Coding exons: 3
Length: 44247
Individuals with no LoFs: 125722
Homozygous LoFs: 0
Heterozygous LoFs: 24
Defined: 125746
p: 0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-2.65	198	117	1.69	0.00000632	1350
Missense (PolyPhen)		81	41.808	1.9374		516
Synonymous	-2.22	64	45.1	1.42	0.00000267	389
Loss of Function	-1.22	14	9.88	1.42	6.54e-7	96

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000092	0.000087	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00022	0.00022	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000071	0.000070	rare
South Asian	0.00020	0.00020	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Promotes cell adhesion to laminin-332 and fibronectin.;

Recessive Scores

pRec: 0.104

Intolerance Scores

RVIS EVS: 0.6
RVIS percentile EVS: 82.66

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.136

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium