LILRB2
leukocyte immunoglobulin like receptor B2, the group of CD molecules|Inhibitory leukocyte immunoglobulin like receptors|Ig-like cell adhesion molecule family
Basic information
Region (hg38): 19:54273812-54281184
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (117 variants)
- not_provided (10 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the LILRB2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001080978.4. 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 | 10 | 10 | ||||
| missense | 106 | 10 | 116 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 106 | 20 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LILRB2 | protein_coding | protein_coding | ENST00000391749 | 13 | 7365 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.28e-14 | 0.158 | 125675 | 0 | 70 | 125745 | 0.000278 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -2.30 | 455 | 336 | 1.35 | 0.0000207 | 3719 |
| Missense in Polyphen | 96 | 92.747 | 1.0351 | 1177 | ||
| Synonymous | -2.10 | 178 | 146 | 1.22 | 0.00000955 | 1269 |
| Loss of Function | 1.03 | 25 | 31.2 | 0.801 | 0.00000169 | 330 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000510 | 0.000510 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.0000464 | 0.0000462 |
| European (Non-Finnish) | 0.0000537 | 0.0000527 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.00141 | 0.00141 |
| Other | 0.000330 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Receptor for class I MHC antigens. Recognizes a broad spectrum of HLA-A, HLA-B, HLA-C and HLA-G alleles. Involved in the down-regulation of the immune response and the development of tolerance. Competes with CD8A for binding to class I MHC antigens. Inhibits FCGR1A-mediated phosphorylation of cellular proteins and mobilization of intracellular calcium ions. {ECO:0000269|PubMed:11875462, ECO:0000269|PubMed:12853576, ECO:0000269|PubMed:9548455, ECO:0000269|PubMed:9842885}.;
- Pathway
- Osteoclast differentiation - Homo sapiens (human);Neutrophil degranulation;Innate Immune System;Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System
(Consensus)
Intolerance Scores
- loftool
- 0.874
- rvis_EVS
- 2.83
- rvis_percentile_EVS
- 99.09
Haploinsufficiency Scores
- pHI
- 0.318
- hipred
- N
- hipred_score
- 0.327
- ghis
- 0.491
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.344
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | High | Medium | High |
Gene ontology
- Biological process
- adaptive immune response;negative regulation of antigen processing and presentation;positive regulation of tolerance induction;positive regulation of T cell tolerance induction;immune response-inhibiting cell surface receptor signaling pathway;Fc receptor mediated inhibitory signaling pathway;immune response;cellular defense response;signal transduction;cell surface receptor signaling pathway;cell-cell signaling;learning or memory;positive regulation of interleukin-6 production;heterotypic cell-cell adhesion;positive regulation of protein dephosphorylation;positive regulation of T cell proliferation;negative regulation of T cell proliferation;neutrophil degranulation;positive regulation of regulatory T cell differentiation;regulation of immune response;negative regulation of protein metabolic process;negative regulation of calcium ion transport;cellular response to lipopolysaccharide;regulation of long-term synaptic potentiation;positive regulation of long-term synaptic depression;negative regulation of postsynaptic density organization;regulation of dendritic cell differentiation
- Cellular component
- extracellular space;cytoplasm;plasma membrane;integral component of plasma membrane;cell surface;membrane;tertiary granule membrane;ficolin-1-rich granule membrane
- Molecular function
- amyloid-beta binding;protein binding;protein phosphatase 1 binding;MHC class Ib protein binding;inhibitory MHC class I receptor activity;MHC class I protein binding;protein homodimerization activity;protein-containing complex binding;cell adhesion molecule binding