CLEC7A

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

Basic information

Region (hg38): 12:10116776-10130258

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

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Candidiasis, familial, 4	AR	Allergy/Immunology/Infectious	Individuals are highly susceptible to recurrent fungal infections, and recognition may allow prompt treatment, which may be beneficial	Allergy/Immunology/Infectious	18946062; 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.

• Inborn genetic diseases (11 variants)
• not provided (6 variants)
• Familial chronic mucocutaneous candidiasis;Aspergillosis, susceptibility to (3 variants)
• Familial chronic mucocutaneous candidiasis (3 variants)
• not specified (2 variants)
• Aspergillosis, susceptibility to (1 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.

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			1	2		3
missense			12	1	3	16
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	13	4	4

Variants in CLEC7A

This is a list of pathogenic ClinVar variants found in the CLEC7A region.

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

Position	Type	Phenotype	Significance	ClinVar
12-10118456-T-C		not specified	Benign (Mar 29, 2016)
12-10118463-T-A		CLEC7A-related disorder	Likely benign (May 22, 2023)
12-10118488-A-C		Familial chronic mucocutaneous candidiasis • Aspergillosis, susceptibility to • not specified • Aspergillosis, susceptibility to;Familial chronic mucocutaneous candidiasis • CLEC7A-related disorder	Benign/Likely benign (May 10, 2022)
12-10118498-A-G		not specified	Uncertain significance (Sep 27, 2021)
12-10118529-C-T		not specified	Uncertain significance (Oct 26, 2022)
12-10118534-A-C			Benign (Mar 28, 2018)
12-10123309-G-A			Benign/Likely benign (Dec 01, 2023)
12-10123320-A-G		Familial chronic mucocutaneous candidiasis	Uncertain significance (Jul 23, 2019)
12-10123326-T-G		not specified	Uncertain significance (Nov 22, 2022)
12-10123373-A-G		CLEC7A-related disorder	Likely benign (Aug 09, 2019)
12-10125307-G-A			Benign (Aug 21, 2018)
12-10125375-T-C		Familial chronic mucocutaneous candidiasis • Familial chronic mucocutaneous candidiasis;Aspergillosis, susceptibility to	Uncertain significance (Mar 30, 2021)
12-10125382-A-C		not specified	Uncertain significance (Jul 06, 2021)
12-10125392-G-A		Familial chronic mucocutaneous candidiasis;Aspergillosis, susceptibility to	Benign/Likely benign (Mar 01, 2024)
12-10125404-T-C		not specified	Uncertain significance (Mar 16, 2022)
12-10126562-T-C		CLEC7A-related disorder	Likely benign (Jun 25, 2019)
12-10126607-C-G		not specified	Uncertain significance (Apr 12, 2022)
12-10126643-C-T		not specified	Uncertain significance (Jan 06, 2023)
12-10126667-C-T		not specified	Uncertain significance (Nov 12, 2021)
12-10127760-G-A			Likely benign (Jun 08, 2018)
12-10127818-C-T		not specified	Uncertain significance (Apr 08, 2022)
12-10127819-G-A		not specified	Uncertain significance (May 23, 2023)
12-10127827-G-A		not specified	Uncertain significance (Jun 27, 2023)
12-10127828-G-C		not specified	Uncertain significance (Dec 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLEC7A	protein_coding	protein_coding	ENST00000304084	6	13482

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.51e-12	0.00851	125727	0	19	125746	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.119	120	124	0.970	0.00000575	1589
Missense in Polyphen		30	35.771	0.83866		482
Synonymous	0.0564	43	43.5	0.989	0.00000203	457
Loss of Function	-1.08	15	11.1	1.35	4.70e-7	142

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000472	0.000460
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000357	0.0000352
Middle Eastern	0.000109	0.000109
South Asian	0.000131	0.000131
Other	0.000163	0.000163

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

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

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