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.

not_specified (22 variants)
not_provided (1 variants)
Macular_dystrophy,_retinal,_4 (1 variants)

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. These statistics are base on transcript: NM_000003278.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense	1 clinvar		23 clinvar			24
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	1	0	23	0	0

Loading clinvar variants...

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