GeneBe

CLEC7A

C-type lectin domain containing 7A, the group of C-type lectin domain containing|CD molecules|Scavenger receptors

Basic information

Region (hg38): 12:10116777-10130258

Previous symbols: [ "CLECSF12" ]

Links

ENSG00000172243 ∙ NCBI:64581 ∙ OMIM:606264 ∙ HGNC:14558 ∙ Uniprot:Q9BXN2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • chronic mucocutaneous candidiasis (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Candidiasis, familial, 4ARAllergy/Immunology/InfectiousIndividuals are highly susceptible to recurrent fungal infections, and recognition may allow prompt treatment, which may be beneficialAllergy/Immunology/Infectious18946062; 19864674; 20807886; 20107226; 22674328; 23374272
Heterozygous variants may result in milder manifestations

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CLEC7A gene.

  • not_specified (27 variants)
  • not_provided (6 variants)
  • Familial_chronic_mucocutaneous_candidiasis (4 variants)
  • Aspergillosis,_susceptibility_to (3 variants)
  • CLEC7A-related_disorder (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLEC7A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000197947.3. 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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
3
clinvar
 4
missense
27
clinvar
2
clinvar
2
clinvar
 31
nonsense
1
clinvar
 1
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 29 5 2
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CLEC7Aprotein_codingprotein_codingENST00000304084 613482
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
5.51e-120.008511257270191257460.0000756
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.1191201240.9700.000005751589
Missense in Polyphen3035.7710.83866482
Synonymous0.05644343.50.9890.00000203457
Loss of Function-1.081511.11.354.70e-7142

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004720.000460
Ashkenazi Jewish0.000.00
East Asian0.0001090.000109
Finnish0.000.00
European (Non-Finnish)0.00003570.0000352
Middle Eastern0.0001090.000109
South Asian0.0001310.000131
Other0.0001630.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: Lectin that functions as pattern receptor specific for beta-1,3-linked and beta-1,6-linked glucans, such as cell wall constituents from pathogenic bacteria and fungi. Necessary for the TLR2-mediated inflammatory response and for TLR2-mediated activation of NF-kappa-B. Enhances cytokine production in macrophages and dendritic cells. Mediates production of reactive oxygen species in the cell. Mediates phagocytosis of C.albicans conidia. Binds T-cells in a way that does not involve their surface glycans and plays a role in T-cell activation. Stimulates T-cell proliferation (By similarity). {ECO:0000250, ECO:0000269|PubMed:11567029, ECO:0000269|PubMed:12423684, ECO:0000269|PubMed:17230442}.;
Disease
DISEASE: Candidiasis, familial, 4 (CANDF4) [MIM:613108]: A primary immunodeficiency disorder with altered immune responses and impaired clearance of fungal infections, selective against Candida. It is characterized by persistent and/or recurrent infections of the skin, nails and mucous membranes caused by organisms of the genus Candida, mainly Candida albicans. {ECO:0000269|PubMed:19864674}. Note=The disease may be caused by mutations affecting the gene represented in this entry.;
Pathway
Phagosome - Homo sapiens (human);C-type lectin receptor signaling pathway - Homo sapiens (human);Tuberculosis - Homo sapiens (human);CLEC7A (Dectin-1) signaling;C-type lectin receptors (CLRs);Innate Immune System;Immune System (Consensus)

Recessive Scores

pRec
0.148

Intolerance Scores

loftool
0.770
rvis_EVS
0.35
rvis_percentile_EVS
74.37

Haploinsufficiency Scores

pHI
0.0805
hipred
N
hipred_score
0.112
ghis
0.425

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.00481

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Clec7a
Phenotype
homeostasis/metabolism phenotype; immune system phenotype; digestive/alimentary 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; respiratory system phenotype;

Gene ontology

Biological process
pattern recognition receptor signaling pathway;phagocytosis, recognition;inflammatory response;cell recognition;carbohydrate mediated signaling;T cell activation;defense response to protozoan;innate immune response
Cellular component
nucleoplasm;cytoplasm;plasma membrane;integral component of membrane;intracellular membrane-bounded organelle
Molecular function
protein binding;signaling pattern recognition receptor activity;carbohydrate binding;MHC protein binding;metal ion binding