CLEC3B

protein-coding

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

Gene summary

Enables calcium ion binding activity; heparin binding activity; and kringle domain binding activity. Involved in bone mineralization. Located in cytoplasm; granular component; and obsolete extracellular space. Implicated in osteoarthritis and retinal macular dystrophy 4. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

MANE transcript

NM_003278.3

Inheritance

ClinVar variants

P:1U:27

Top phenotype

Macular dystrophy, retinal, 4

gnomAD constraint

pLI —, LoF o/e 0.64

Max pathogenic AF

—

Genomic locus

chr3:45,001,548-45,036,071

External References & Databases

Ensembl (ENSG00000163815)

Transcript & Mutation Effects

hg38 • Region Span ~34.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

macular dystrophy, retinal, 4STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0859568

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Macular dystrophy, retinal, 4AD

Manifestation: Ophthalmologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 35331648

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CLEC3B variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 25

not providedTotal: 1

Macular dystrophy, retinal, 4Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003278.3. 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	1 clinvar		27 clinvar			28
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	1	0	27	0	0	28

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003278.3	RefSeq	NP_003269.2	3	MANE Select
ENST00000296130.5	Ensembl	ENSP00000296130.4	3	MANE Select
NM_001308394.2	RefSeq	NP_001295323.1	2	Standard
ENST00000428034.1	Ensembl	ENSP00000396013.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Platelet degranulation
Response to elevated platelet cytosolic Ca2+
Platelet activation, signaling and aggregation
Hemostasis

Biological Process

ossification
platelet degranulation
positive regulation of plasminogen activation
bone mineralization
cellular response to organic substance

Molecular Function

calcium ion binding
heparin binding
carbohydrate binding
kringle domain binding

Cellular Component

granular component
extracellular region
extracellular space
cytoplasm
platelet dense granule lumen

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000296130
Coding exons: 3
Length: 34524
Individuals with no LoFs: 125703
Homozygous LoFs: 0
Heterozygous LoFs: 11
Defined: 125714
p: 0.0000438

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.33	87	130	0.670	0.00000757	1306
Missense (PolyPhen)		34	49.256	0.69027		542
Synonymous	1.05	49	59.3	0.826	0.00000409	393
Loss of Function	0.937	5	7.83	0.639	3.34e-7	87

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00020	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000053	0.000053	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Tetranectin binds to plasminogen and to isolated kringle 4. May be involved in the packaging of molecules destined for exocytosis.;

Recessive Scores

pRec: 0.232

Intolerance Scores

LoFtool: 0.533
RVIS EVS: 0.06
RVIS percentile EVS: 58.26

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.860

Gene Damage Prediction

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