CLEC4D
protein-codingC-type lectin domain family 4 member D, the group of CD molecules|C-type lectin domain containing
Gene summary
This gene encodes a member of the C-type lectin/C-type lectin-like domain (CTL/CTLD) superfamily. Members of this family share a common protein fold and have diverse functions, such as cell adhesion, cell-cell signalling, glycoprotein turnover, and roles in inflammation and immune response. This gene is closely linked to other CTL/CTLD superfamily members on chromosome 12p13 in the natural killer gene complex region. [provided by RefSeq, Jul 2008]
- CLECSF8
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~12.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CLEC4D variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_080387.5. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 35 | 3 | 38 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 36 | 4 | 0 | 40 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_525126.2 | 6 | MANE Select | |
| Ensembl | ENSP00000299665.2 | 6 | MANE Select | |
| Ensembl | ENSP00000371496.2 | 5 | Standard | |
| Ensembl | ENSP00000629706.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- C-type lectin receptor signaling pathway - Homo sapiens (human)
- Neutrophil degranulation
- Dectin-2 family
- C-type lectin receptors (CLRs)
- Innate Immune System
Biological Process
- stimulatory C-type lectin receptor signaling pathway
- adaptive immune response
- T cell differentiation involved in immune response
- positive regulation of myeloid dendritic cell activation
- Fc-gamma receptor signaling pathway
Molecular Function
- protein binding
- carbohydrate binding
- immunoglobulin receptor binding
- metal ion binding
Cellular Component
- plasma membrane
- integral component of membrane
- specific granule membrane
- tertiary granule membrane
- ficolin-1-rich granule membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000299665
- Coding exons
- 6
- Length
- 12892
- Individuals with no LoFs
- 125719
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 24
- Defined
- 125744
- p
- 0.0000994
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.116 | 120 | 116 | 1.03 | 0.00000594 | 1432 |
| Missense (PolyPhen) | 32 | 27.127 | 1.1796 | 385 | ||
| Synonymous | 0.0934 | 38 | 38.7 | 0.981 | 0.00000208 | 368 |
| Loss of Function | 0.252 | 9 | 9.85 | 0.913 | 4.86e-7 | 124 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00025 | 0.00025 | rare |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000053 | 0.000053 | rare |
| South Asian | 0.00039 | 0.00036 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: A calcium-dependent lectin involved in innate recognition of pathogen-associated molecular patterns (PAMPs). Interacts with signaling adapter Fc receptor gamma chain/FCER1G, likely via CLEC4E, to form a functional complex in myeloid cells (By similarity). 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 (PubMed:23602766). Functions as an endocytic receptor. May be involved in antigen uptake at the site of infection, either for clearance of the antigen, or for processing and further presentation to T cells (PubMed:14971047). {ECO:0000250|UniProtKB:Q69FH1, ECO:0000269|PubMed:14971047, ECO:0000269|PubMed:23602766}.;
Recessive Scores
- pRec
- 0.0707
Intolerance Scores
- LoFtool
- 0.858
- RVIS EVS
- 0.35
- RVIS percentile EVS
- 74.37
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.192
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |