CLEC3B

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

Basic information

Region (hg38): 3:45001548-45036071

Previous symbols: [ "TNA" ]

Links

ENSG00000163815 ∙ NCBI:7123 ∙ OMIM:187520 ∙ HGNC:11891 ∙ Uniprot:P05452 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• macular dystrophy, retinal, 4 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Macular dystrophy, retinal, 4	AD	General	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	Ophthalmologic	35331648

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CLEC3B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLEC3B gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in CLEC3B

This is a list of pathogenic ClinVar variants found in the CLEC3B region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-45001562-T-G		not specified	Uncertain significance (Dec 02, 2024)
3-45005316-G-C		not specified	Uncertain significance (Aug 28, 2024)
3-45005319-G-A		not specified	Uncertain significance (Dec 15, 2024)
3-45005354-C-G		not specified	Uncertain significance (Feb 16, 2023)
3-45005371-G-A		not specified	Uncertain significance (Dec 13, 2022)
3-45007433-A-G		not specified	Uncertain significance (Aug 26, 2022)
3-45007541-G-C		not specified	Uncertain significance (Mar 12, 2024)
3-45007567-A-G		not specified	Uncertain significance (Aug 13, 2021)
3-45007567-A-T		not specified	Uncertain significance (Dec 18, 2023)
3-45011299-G-A		not specified	Uncertain significance (Aug 04, 2023)
3-45011301-C-G		not specified	Uncertain significance (Aug 27, 2024)
3-45026394-G-A		not specified	Uncertain significance (Jun 22, 2021)
3-45026426-G-A		not specified	Uncertain significance (Sep 29, 2022)
3-45035536-G-A		not specified	Uncertain significance (Jun 24, 2022)
3-45035684-G-C		not specified	Uncertain significance (Sep 27, 2021)
3-45035688-G-T		not specified	Uncertain significance (Jan 04, 2024)
3-45035703-G-A		not specified	Uncertain significance (Jan 17, 2024)
3-45035736-G-A		not specified	Uncertain significance (Feb 07, 2023)
3-45035772-G-T		not specified	Uncertain significance (Aug 17, 2022)
3-45035800-C-T		not specified	Uncertain significance (May 30, 2023)
3-45035854-C-A		Macular dystrophy, retinal, 4	Pathogenic (Jul 26, 2022)
3-45035876-G-C		not specified	Uncertain significance (May 23, 2024)
3-45035902-T-C		not specified	Uncertain significance (Nov 13, 2024)
3-45035919-G-A		not specified	Uncertain significance (May 10, 2023)
3-45035919-G-C		not specified	Uncertain significance (Feb 18, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLEC3B	protein_coding	protein_coding	ENST00000296130	3	34524

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00210	0.763	125703	0	11	125714	0.0000438

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.33	87	130	0.670	0.00000757	1306
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000196	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000534	0.0000528
Middle Eastern	0.000196	0.000163
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Tetranectin binds to plasminogen and to isolated kringle 4. May be involved in the packaging of molecules destined for exocytosis.
• Pathway: Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.232

Intolerance Scores

• loftool: 0.533
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.26

Haploinsufficiency Scores

• pHI: 0.322
• hipred: N
• hipred_score: 0.332
• ghis: 0.532

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.860

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clec3b
• Phenotype: skeleton phenotype

Gene ontology

• Biological process: ossification;platelet degranulation;positive regulation of plasminogen activation;bone mineralization;cellular response to organic substance;cellular response to transforming growth factor beta stimulus
• Cellular component: granular component;extracellular region;extracellular space;cytoplasm;platelet dense granule lumen;collagen-containing extracellular matrix;extracellular exosome
• Molecular function: calcium ion binding;heparin binding;carbohydrate binding;kringle domain binding