CLEC2A

C-type lectin domain family 2 member A, the group of C-type lectin domain containing

Basic information

Region (hg38): 12:9898673-9932370

Links

ENSG00000188393 ∙ NCBI:387836 ∙ OMIM:612087 ∙ HGNC:24191 ∙ Uniprot:Q6UVW9 ∙ 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 CLEC2A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLEC2A 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			8			8
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	1	0

Variants in CLEC2A

This is a list of pathogenic ClinVar variants found in the CLEC2A region.

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

Position	Type	Phenotype	Significance	ClinVar
12-9913625-T-G		not specified	Uncertain significance (Nov 09, 2021)
12-9913680-C-T			Likely benign (Mar 01, 2023)
12-9916718-C-T		not specified	Uncertain significance (Jan 09, 2024)
12-9916785-C-T		not specified	Uncertain significance (Aug 23, 2021)
12-9922069-G-T		not specified	Uncertain significance (Jan 10, 2023)
12-9922123-T-G		not specified	Uncertain significance (Jun 29, 2023)
12-9922130-G-C		not specified	Uncertain significance (Nov 18, 2022)
12-9922199-C-T		not specified	Uncertain significance (Jul 08, 2022)
12-9926268-A-G		not specified	Uncertain significance (Oct 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLEC2A	protein_coding	protein_coding	ENST00000455827	5	33709

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000219	0.161	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.658	65	81.7	0.795	0.00000394	1163
Missense in Polyphen		11	16.486	0.66725		257
Synonymous	0.740	21	25.8	0.815	0.00000128	289
Loss of Function	-0.401	8	6.87	1.17	2.91e-7	92

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in modulating the extent of T-cell expansion. Enhances the expansion of TCR-stimulated T-cells by increasing their survival through enhanced expression of anti- apoptotic proteins. May modulate the capacity of T-cells to home to lymph nodes through SELL. Facilitates dedicated immune recognition of keratinocytes via interaction with its receptor KLRF2 by stimulating natural killer cell mediated cytotoxicity. {ECO:0000269|PubMed:18550855, ECO:0000269|PubMed:20194751}.

Recessive Scores

• pRec: 0.0464

Intolerance Scores

• rvis_EVS: 1.75
• rvis_percentile_EVS: 96.64

Haploinsufficiency Scores

• pHI: 0.0705

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0658

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clec2f

Gene ontology

• Biological process: natural killer cell mediated cytotoxicity
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: protein binding;carbohydrate binding;protein homodimerization activity