CLEC4E
C-type lectin domain family 4 member E, the group of C-type lectin domain containing
Basic information
Region (hg38): 12:8533305-8540905
Previous symbols: [ "CLECSF9" ]
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 CLEC4E 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 | 14 | ||||
| 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 | 1 | 0 |
Variants in CLEC4E
This is a list of pathogenic ClinVar variants found in the CLEC4E region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-8534656-G-T | not specified | Uncertain significance (Oct 06, 2023) | ||
| 12-8534699-T-C | not specified | Likely benign (May 24, 2024) | ||
| 12-8534732-C-T | not specified | Uncertain significance (Mar 01, 2024) | ||
| 12-8534799-C-T | not specified | Uncertain significance (Sep 16, 2021) | ||
| 12-8536115-C-T | not specified | Uncertain significance (Dec 27, 2023) | ||
| 12-8536135-C-A | not specified | Uncertain significance (Sep 25, 2023) | ||
| 12-8536162-A-G | not specified | Uncertain significance (Dec 04, 2023) | ||
| 12-8537182-G-A | not specified | Uncertain significance (Feb 28, 2023) | ||
| 12-8537182-G-T | not specified | Uncertain significance (Dec 16, 2023) | ||
| 12-8537201-T-C | not specified | Uncertain significance (Jan 23, 2024) | ||
| 12-8537242-A-G | not specified | Likely benign (Mar 07, 2024) | ||
| 12-8539264-T-C | not specified | Uncertain significance (Aug 21, 2023) | ||
| 12-8539282-C-T | not specified | Uncertain significance (Jan 09, 2024) | ||
| 12-8539295-T-C | not specified | Uncertain significance (Jan 03, 2024) | ||
| 12-8540794-T-G | not specified | Uncertain significance (Jan 05, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CLEC4E | protein_coding | protein_coding | ENST00000299663 | 6 | 7659 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000114 | 0.603 | 125689 | 0 | 57 | 125746 | 0.000227 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.117 | 110 | 114 | 0.969 | 0.00000533 | 1446 |
| Missense in Polyphen | 30 | 37.738 | 0.79495 | 490 | ||
| Synonymous | -0.868 | 47 | 40.0 | 1.17 | 0.00000199 | 381 |
| Loss of Function | 0.837 | 9 | 12.2 | 0.741 | 5.13e-7 | 149 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00107 | 0.00107 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000163 | 0.000163 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000256 | 0.000255 |
| Middle Eastern | 0.000163 | 0.000163 |
| South Asian | 0.000133 | 0.000131 |
| Other | 0.000330 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: A calcium-dependent lectin that acts as a pattern recognition receptor of the innate immune system. Recognizes damage-associated molecular patterns (DAMPs) of abnormal self and pathogen-associated molecular patterns (PAMPs) of bacteria and fungi (PubMed:18509109, PubMed:23602766). The PAMPs notably include mycobacterial trehalose 6,6'-dimycolate (TDM), a cell wall glycolipid with potent adjuvant immunomodulatory functions (PubMed:23602766, PubMed:24101491). Interacts with signaling adapter Fc receptor gamma chain/FCER1G to form a functional complex in myeloid cells. Binding of mycobacterial trehalose 6,6'- dimycolate (TDM) to this receptor complex leads to phosphorylation of the immunoreceptor tyrosine-based activation motif (ITAM) of FCER1G, triggering activation of SYK, CARD9 and NF-kappa-B, consequently driving maturation of antigen-presenting cells and shaping antigen-specific priming of T-cells toward effector T- helper 1 and T-helper 17 cell subtypes. Specifically recognizes alpha-mannose residues on pathogenic fungi of the genus Malassezia and mediates macrophage activation. Through recognition of DAMPs released upon nonhomeostatic cell death, enables immune sensing of damaged self and promotes inflammatory cell infiltration into the damaged tissue (By similarity). {ECO:0000250|UniProtKB:Q9R0Q8, ECO:0000269|PubMed:18509109, ECO:0000269|PubMed:23602766, ECO:0000269|PubMed:24101491}.;
- Pathway
- C-type lectin receptor signaling pathway - Homo sapiens (human);Tuberculosis - Homo sapiens (human);Dectin-2 family;C-type lectin receptors (CLRs);Innate Immune System;Immune System
(Consensus)
Intolerance Scores
- loftool
- 0.674
- rvis_EVS
- 0.08
- rvis_percentile_EVS
- 60.09
Haploinsufficiency Scores
- pHI
- 0.388
- hipred
- N
- hipred_score
- 0.112
- ghis
- 0.492
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Clec4e
- Phenotype
- immune system phenotype; homeostasis/metabolism phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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);
Gene ontology
- Biological process
- stimulatory C-type lectin receptor signaling pathway;T cell differentiation involved in immune response;Fc-gamma receptor signaling pathway;defense response to bacterium;innate immune response;positive regulation of cytokine secretion
- Cellular component
- plasma membrane;integral component of membrane
- Molecular function
- carbohydrate binding;signaling receptor activity;metal ion binding