CLEC4A
C-type lectin domain family 4 member A, the group of C-type lectin domain containing|CD molecules
Basic information
Region (hg38): 12:8123616-8138607
Previous symbols: [ "CLECSF6" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLEC4A 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 | 13 | 15 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 13 | 2 | 0 |
Variants in CLEC4A
This is a list of pathogenic ClinVar variants found in the CLEC4A region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-8123886-C-T | not specified | Uncertain significance (Dec 02, 2022) | ||
| 12-8123939-A-T | not specified | Uncertain significance (May 28, 2024) | ||
| 12-8123940-T-C | not specified | Likely benign (Jun 10, 2024) | ||
| 12-8129314-C-A | not specified | Uncertain significance (Mar 31, 2024) | ||
| 12-8129339-T-C | not specified | Uncertain significance (May 01, 2022) | ||
| 12-8129356-G-A | not specified | Likely benign (Oct 05, 2023) | ||
| 12-8135588-C-T | not specified | Uncertain significance (Oct 05, 2022) | ||
| 12-8135596-A-T | not specified | Uncertain significance (Dec 09, 2023) | ||
| 12-8136830-G-A | not specified | Uncertain significance (Apr 05, 2023) | ||
| 12-8136858-G-A | not specified | Uncertain significance (Sep 25, 2023) | ||
| 12-8138153-C-T | not specified | Uncertain significance (May 26, 2024) | ||
| 12-8138154-G-A | not specified | Likely benign (Mar 28, 2024) | ||
| 12-8138162-A-T | not specified | Uncertain significance (May 15, 2023) | ||
| 12-8138163-G-A | not specified | Likely benign (May 15, 2023) | ||
| 12-8138177-C-T | not specified | Uncertain significance (Nov 18, 2022) | ||
| 12-8138198-C-T | not specified | Uncertain significance (Aug 26, 2022) | ||
| 12-8138220-G-A | not specified | Uncertain significance (Nov 10, 2022) | ||
| 12-8138246-C-T | not specified | Uncertain significance (Oct 29, 2021) | ||
| 12-8138250-A-C | not specified | Uncertain significance (Feb 23, 2023) | ||
| 12-8138264-G-A | not specified | Likely benign (Mar 28, 2024) | ||
| 12-8138285-T-C | Benign (Dec 31, 2019) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CLEC4A | protein_coding | protein_coding | ENST00000229332 | 6 | 14976 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000419 | 0.644 | 125714 | 0 | 33 | 125747 | 0.000131 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.545 | 107 | 124 | 0.862 | 0.00000620 | 1571 |
| Missense in Polyphen | 25 | 28.052 | 0.89121 | 396 | ||
| Synonymous | -0.484 | 48 | 43.9 | 1.09 | 0.00000223 | 418 |
| Loss of Function | 0.849 | 8 | 11.0 | 0.724 | 5.65e-7 | 135 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000607 | 0.000607 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000123 | 0.000123 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000131 | 0.000131 |
| Other | 0.000326 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: C-type lectin receptor that binds carbohydrates mannose and fucose but also weakly interacts with N-acetylglucosamine (GlcNAc) in a Ca(2+)-dependent manner (PubMed:27015765). Involved in regulating immune reactivity (PubMed:18258799, PubMed:10438934). Once triggered by antigen, it is internalized by clathrin-dependent endocytosis and delivers its antigenic cargo into the antigen presentation pathway resulting in cross-priming of CD8(+) T cells. This cross-presentation and cross-priming are enhanced by TLR7 and TLR8 agonists with increased expansion of the CD8(+) T cells, high production of IFNG and TNF with reduced levels of IL4, IL5 and IL13 (PubMed:18258799, PubMed:20530286). In plasmacytoid dendritic cells, inhibits TLR9-mediated IFNA and TNF production (PubMed:18258799). May be involved via its ITIM motif (immunoreceptor tyrosine-based inhibitory motifs) in the inhibition of B-cell-receptor-mediated calcium mobilization and protein tyrosine phosphorylation (PubMed:10438934). {ECO:0000269|PubMed:10438934, ECO:0000269|PubMed:18258799, ECO:0000269|PubMed:20530286, ECO:0000269|PubMed:27015765}.;
- Pathway
- Dectin-2 family;C-type lectin receptors (CLRs);Innate Immune System;Immune System
(Consensus)
Recessive Scores
- pRec
- 0.0810
Intolerance Scores
- loftool
- 0.991
- rvis_EVS
- 0.71
- rvis_percentile_EVS
- 85.53
Haploinsufficiency Scores
- pHI
- 0.0237
- hipred
- N
- hipred_score
- 0.112
- ghis
- 0.396
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.144
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Clec4a2
- Phenotype
- homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; reproductive system phenotype; hematopoietic system phenotype; digestive/alimentary phenotype; skeleton phenotype; immune system phenotype;
Gene ontology
- Biological process
- negative regulation of cytokine production;stimulatory C-type lectin receptor signaling pathway;adaptive immune response;plasmacytoid dendritic cell antigen processing and presentation;cell adhesion;cell surface receptor signaling pathway;negative regulation of tumor necrosis factor production;CD8-positive, alpha-beta T cell activation;antigen processing and presentation of exogenous peptide antigen via MHC class I;innate immune response
- Cellular component
- plasma membrane;integral component of plasma membrane
- Molecular function
- transmembrane signaling receptor activity;calcium ion binding;mannose binding;carbohydrate binding