CLEC2D
protein-codingC-type lectin domain family 2 member D, the group of C-type lectin domain containing
Gene summary
This gene encodes a member of the natural killer cell receptor C-type lectin family. The encoded protein inhibits osteoclast formation and contains a transmembrane domain near the N-terminus as well as the C-type lectin-like extracellular domain. Several alternatively spliced transcript variants have been identified for this gene. [provided by RefSeq, Oct 2010]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~34.6 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 CLEC2D variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_013269.6. 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 | 13 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 14 | 0 | 0 | 14 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_037401.1 | 5 | MANE Select | |
| Ensembl | ENSP00000290855.6 | 5 | MANE Select | |
| RefSeq | NP_001004419.1 | 6 | Standard | |
| RefSeq | NP_001184246.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Immune System
- Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
- Adaptive Immune System
Biological Process
- cell surface receptor signaling pathway
- regulation of immune response
Molecular Function
- transmembrane signaling receptor activity
- carbohydrate binding
Cellular Component
- endoplasmic reticulum
- plasma membrane
- integral component of plasma membrane
- cell surface
- membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000261340
- Coding exons
- 6
- Length
- 30849
- Individuals with no LoFs
- 125025
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 2
- Defined
- 125027
- p
- 0.00000800
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.514 | 85 | 99.4 | 0.855 | 0.00000449 | 1280 |
| Missense (PolyPhen) | 14 | 21.66 | 0.64636 | 315 | ||
| Synonymous | -1.03 | 39 | 31.6 | 1.23 | 0.00000136 | 333 |
| Loss of Function | 2.34 | 3 | 11.6 | 0.259 | 4.91e-7 | 140 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000057 | 0.000055 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Receptor for KLRB1 that protects target cells against natural killer cell-mediated lysis (PubMed:20843815, PubMed:16339513). Inhibits osteoclast formation (PubMed:14753741, PubMed:15123656). Inhibits bone resorption (PubMed:14753741). Modulates the release of interferon-gamma (PubMed:15104121). Binds high molecular weight sulfated glycosaminoglycans (PubMed:15123656). {ECO:0000269|PubMed:14753741, ECO:0000269|PubMed:15104121, ECO:0000269|PubMed:15123656, ECO:0000269|PubMed:16339513, ECO:0000269|PubMed:20843815}.;
Recessive Scores
- pRec
- 0.0869
Intolerance Scores
- LoFtool
- 0.391
- RVIS EVS
- 0.86
- RVIS percentile EVS
- 88.62
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.222
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |