CLEC3A

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

Basic information

Region (hg38): 16:78022514-78066761

Previous symbols: [ "CLECSF1" ]

Links

ENSG00000166509 ∙ NCBI:10143 ∙ OMIM:613588 ∙ HGNC:2052 ∙ Uniprot:O75596 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CLEC3A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLEC3A 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			3			3
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	0

Variants in CLEC3A

This is a list of pathogenic ClinVar variants found in the CLEC3A region.

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

Position	Type	Phenotype	Significance	ClinVar
16-78022627-A-G		not specified	Uncertain significance (Aug 09, 2021)
16-78028131-A-G		not specified	Uncertain significance (Dec 27, 2022)
16-78030593-G-A		not specified	Uncertain significance (Sep 30, 2021)
16-78030803-A-G		not specified	Uncertain significance (Feb 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLEC3A	protein_coding	protein_coding	ENST00000299642	3	44247

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.00e-11	0.00944	125722	0	24	125746	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.65	198	117	1.69	0.00000632	1350
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000155	0.000154
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000219	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.0000708	0.0000703
Middle Eastern	0.000219	0.000217
South Asian	0.000200	0.000196
Other	0.000169	0.000163

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.215
• hipred: N
• hipred_score: 0.254

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.136

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clec3a

Gene ontology

• Biological process: skeletal system development;ossification
• Cellular component: extracellular space
• Molecular function: carbohydrate binding