CLEC6A

C-type lectin domain containing 6A, the group of C-type lectin domain containing

Basic information

Region (hg38): 12:8455962-8478330

Previous symbols: [ "CLECSF10" ]

Links

ENSG00000205846 ∙ NCBI:93978 ∙ OMIM:613579 ∙ HGNC:14556 ∙ Uniprot:Q6EIG7 ∙ 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 CLEC6A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLEC6A 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			6	1		7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	1	0

Variants in CLEC6A

This is a list of pathogenic ClinVar variants found in the CLEC6A region.

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

Position	Type	Phenotype	Significance	ClinVar
12-8465555-G-T		not specified	Likely benign (Sep 13, 2023)
12-8465590-G-A		not specified	Uncertain significance (Jul 19, 2022)
12-8476149-G-A		not specified	Uncertain significance (Sep 20, 2023)
12-8476182-C-A		not specified	Uncertain significance (Feb 23, 2023)
12-8476191-A-G		not specified	Uncertain significance (Jul 13, 2021)
12-8476222-C-T		not specified	Uncertain significance (Jan 10, 2023)
12-8477343-A-G		not specified	Uncertain significance (Sep 16, 2021)
12-8477408-G-T		not specified	Uncertain significance (Mar 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLEC6A	protein_coding	protein_coding	ENST00000382073	6	22405

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000113	0.361	125727	0	19	125746	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0265	104	103	1.01	0.00000434	1377
Missense in Polyphen		25	27.38	0.91306		377
Synonymous	0.131	33	34.0	0.971	0.00000146	354
Loss of Function	0.472	10	11.7	0.851	5.01e-7	133

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000661	0.0000462
European (Non-Finnish)	0.0000898	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.000186	0.000163
Other	0.000173	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds high-mannose carbohydrates in a Ca(2+)-dependent manner (PubMed:28652405). Functional receptor for alpha-mannans on C.albicans hypheas. Plays an important role in the host defense against C.albicans infection by inducing TH17 cell differentiation. Recognizes also, in a mannose-dependent manner, allergens from house dust mite and fungi, by promoting cysteinyl leukotriene production. Recognizes soluble elements from the eggs of Shistosoma mansoni altering adaptive immune responses. Transduces signals through an Fc receptor gamma chain /FCER1G and Syk-CARD9-NF-kappa-B-dependent pathway (By similarity). {ECO:0000250|UniProtKB:Q9JKF4, ECO:0000269|PubMed:28652405}.
• Pathway: C-type lectin receptor signaling pathway - Homo sapiens (human);Ebola Virus Pathway on Host;Ebola Virus Pathway on Host;Dectin-2 family;C-type lectin receptors (CLRs);Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.0596

Intolerance Scores

• rvis_EVS: 0.95
• rvis_percentile_EVS: 89.96

Haploinsufficiency Scores

• pHI: 0.0282
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0696

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clec4n
• Phenotype: immune system phenotype; renal/urinary system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype

Gene ontology

• Biological process: stimulatory C-type lectin receptor signaling pathway;adaptive immune response;positive regulation of I-kappaB kinase/NF-kappaB signaling;innate immune response;positive regulation of cytokine secretion;defense response to fungus
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: calcium ion binding;mannose binding;carbohydrate binding