CLEC1B
protein-codingC-type lectin domain family 1 member B, the group of C-type lectin domain containing
Gene summary
Natural killer (NK) cells express multiple calcium-dependent (C-type) lectin-like receptors, such as CD94 (KLRD1; MIM 602894) and NKG2D (KLRC4; MIM 602893), that interact with major histocompatibility complex class I molecules and either inhibit or activate cytotoxicity and cytokine secretion. CLEC2 is a C-type lectin-like receptor expressed in myeloid cells and NK cells (Colonna et al., 2000 [PubMed 10671229]).[supplied by OMIM, Jan 2011]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~27.8 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 CLEC1B variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_016509.4. 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 | 0 | |||||
| missense | 48 | 5 | 53 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 49 | 5 | 0 | 54 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_057593.3 | 6 | MANE Select | |
| Ensembl | ENSP00000298527.6 | 6 | MANE Select | |
| RefSeq | NP_001092901.1 | 5 | Standard | |
| RefSeq | NP_001380271.1 | 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)
- GPVI-mediated activation cascade
- Platelet activation, signaling and aggregation
- Hemostasis
Biological Process
- defense response
- cell surface receptor signaling pathway
- signal transduction by protein phosphorylation
- platelet activation
- platelet formation
Molecular Function
- transmembrane signaling receptor activity
- protein binding
- carbohydrate binding
Cellular Component
- plasma membrane
- integral component of plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000298527
- Coding exons
- 6
- Length
- 27783
- Individuals with no LoFs
- 124958
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 33
- Defined
- 124991
- p
- 0.000132
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.725 | 154 | 131 | 1.18 | 0.00000730 | 1504 |
| Missense (PolyPhen) | 28 | 39.802 | 0.70348 | 453 | ||
| Synonymous | -2.56 | 67 | 45.1 | 1.49 | 0.00000233 | 403 |
| Loss of Function | 0.358 | 12 | 13.4 | 0.894 | 5.71e-7 | 157 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00032 | 0.00032 | rare |
| Latino/Admixed American | 0.00020 | 0.00020 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00028 | 0.00028 | rare |
| Finnish | 0.000047 | 0.000046 | rare |
| European (Non-Finnish) | 0.00011 | 0.00011 | rare |
| South Asian | 0.000098 | 0.000098 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: C-type lectin-like receptor that functions as a platelet receptor for the lymphatic endothelial marker, PDPN (PubMed:18215137). After ligand activation, signals via sequential activation of SRC and SYK tyrosine kinases leading to activation of PLCG2 (PubMed:18955485). {ECO:0000269|PubMed:18215137, ECO:0000269|PubMed:18955485}.; FUNCTION: (Microbial infection) Acts as an attachment factor for Human immunodeficiency virus type 1 (HIV-1) and facilitates its capture by platelets (PubMed:16940507). {ECO:0000305|PubMed:16940507}.;
Recessive Scores
- pRec
- 0.0990
Intolerance Scores
- LoFtool
- 0.763
- RVIS EVS
- 0.68
- RVIS percentile EVS
- 85.04
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.179
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |