LILRA2
leukocyte immunoglobulin like receptor A2, the group of CD molecules|Activating leukocyte immunoglobulin like receptors
Basic information
Region (hg38): 19:54572920-54590287
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (102 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the LILRA2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001130917.3. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | |||||
| missense | 92 | 10 | 102 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 92 | 12 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LILRA2 | protein_coding | protein_coding | ENST00000251377 | 8 | 14641 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 6.91e-20 | 0.000256 | 125734 | 0 | 13 | 125747 | 0.0000517 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -2.70 | 389 | 265 | 1.47 | 0.0000151 | 3024 |
| Missense in Polyphen | 112 | 83.523 | 1.341 | 1056 | ||
| Synonymous | -2.99 | 154 | 113 | 1.36 | 0.00000655 | 999 |
| Loss of Function | -1.16 | 26 | 20.3 | 1.28 | 8.87e-7 | 240 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000127 | 0.000123 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000441 | 0.0000439 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.0000654 | 0.0000653 |
| Other | 0.000329 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Part of the innate immune responses against microbial infection (PubMed:12529506, PubMed:27572839). Specifically recognizes a set of N-terminally truncated immunoglobulins that are produced via cleavage by proteases from a range of pathogenic bacteria and fungi, including L.pneumophila, M.hyorhinis, S.pneumoniae, S.aureus and C.albicans (PubMed:27572839). Recognizes epitopes that are in part in the variable region of the immunoglobulin light chains, but requires also the constant region for signaling (PubMed:27572839). Binds to a subset of cleaved IgM, IgG3 and IgG4 molecules, but does not bind cleaved IgA1 (PubMed:27572839). Binding of N-terminally truncated immunoglobulins mediates activation of neutrophils (PubMed:27572839). In monocytes, activation leads to the release of CSF2, CF3, IL6, CXCL8 and CCL3 and down-regulates responses to bacterial lipopolysaccharide (LPS), possibly via down-regulation of TLR4 expression and reduced signaling via TLR4 (PubMed:22479404). In eosinophils, activation by ligand binding leads to the release of RNASE2, IL4 and leukotriene C4 (PubMed:12529506). Does not bind class I MHC antigens (PubMed:19230061). {ECO:0000269|PubMed:12529506, ECO:0000269|PubMed:19230061, ECO:0000269|PubMed:22479404, ECO:0000269|PubMed:27572839}.;
- Pathway
- Osteoclast differentiation - Homo sapiens (human);Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System
(Consensus)
Intolerance Scores
- loftool
- 0.899
- rvis_EVS
- 3.23
- rvis_percentile_EVS
- 99.37
Haploinsufficiency Scores
- pHI
- 0.217
- hipred
- N
- hipred_score
- 0.112
- ghis
- 0.521
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.142
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Gene ontology
- Biological process
- innate immune response activating cell surface receptor signaling pathway;neutrophil activation involved in immune response;defense response;signal transduction;negative regulation of lipopolysaccharide-mediated signaling pathway;granulocyte macrophage colony-stimulating factor production;interleukin-6 production;interleukin-8 production;negative regulation of toll-like receptor 4 signaling pathway;innate immune response;positive regulation of interleukin-1 beta secretion;positive regulation of cell activation;positive regulation of calcium ion transport;granulocyte colony-stimulating factor production;positive regulation of tumor necrosis factor secretion;positive regulation of interleukin-6 secretion
- Cellular component
- extracellular region;integral component of plasma membrane
- Molecular function
- IgM binding;antigen binding;signaling receptor activity