LILRB1
leukocyte immunoglobulin like receptor B1, the group of CD molecules|Inhibitory leukocyte immunoglobulin like receptors
Basic information
Region (hg38): 19:54617158-54638022
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (142 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the LILRB1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001081637.3. 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 | 0 | |||||
| missense | 131 | 11 | 142 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 131 | 11 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LILRB1 | protein_coding | protein_coding | ENST00000324602 | 14 | 63634 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 5.65e-14 | 0.342 | 125717 | 0 | 28 | 125745 | 0.000111 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -1.91 | 472 | 369 | 1.28 | 0.0000218 | 4095 |
| Missense in Polyphen | 40 | 37.776 | 1.0589 | 507 | ||
| Synonymous | -3.53 | 217 | 160 | 1.35 | 0.0000101 | 1348 |
| Loss of Function | 1.30 | 25 | 33.1 | 0.755 | 0.00000158 | 358 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000244 | 0.000242 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000538 | 0.0000527 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.000464 | 0.000457 |
| Other | 0.000164 | 0.000163 |
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. Receptor for H301/UL18, a human cytomegalovirus class I MHC homolog. Ligand binding results in inhibitory signals and down-regulation of the immune response. Engagement of LILRB1 present on natural killer cells or T-cells by class I MHC molecules protects the target cells from lysis. Interaction with HLA-B or HLA-E leads to inhibition of the signal triggered by FCER1A and inhibits serotonin release. Inhibits FCGR1A-mediated phosphorylation of cellular proteins and mobilization of intracellular calcium ions. {ECO:0000269|PubMed:11907092, ECO:0000269|PubMed:9285411, ECO:0000269|PubMed:9842885}.;
- 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
- 0.869
- rvis_EVS
- 2.75
- rvis_percentile_EVS
- 98.98
Haploinsufficiency Scores
- pHI
- 0.104
- hipred
- N
- hipred_score
- 0.327
- ghis
- 0.526
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.700
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Gene ontology
- Biological process
- negative regulation of T cell mediated cytotoxicity;positive regulation of defense response to virus by host;adaptive immune response;T cell proliferation involved in immune response;negative regulation of cytokine secretion involved in immune response;immune response-inhibiting cell surface receptor signaling pathway;Fc receptor mediated inhibitory signaling pathway;signal transduction;response to virus;positive regulation of gene expression;negative regulation of serotonin secretion;receptor internalization;interferon-gamma production;negative regulation of interferon-gamma production;negative regulation of mononuclear cell proliferation;negative regulation of interferon-beta secretion;negative regulation of T cell proliferation;negative regulation of tumor necrosis factor biosynthetic process;positive regulation of apoptotic process;negative regulation of interferon-gamma biosynthetic process;negative regulation of cell cycle;negative regulation of endocytosis;positive regulation of cytolysis;positive regulation of transcription by RNA polymerase II;negative regulation of natural killer cell mediated cytotoxicity;negative regulation of alpha-beta T cell activation;regulation of immune response;defense response to virus;negative regulation of calcium ion transport;positive regulation of macrophage cytokine production;cellular response to lipopolysaccharide;interferon-gamma secretion;dendritic cell differentiation;negative regulation of dendritic cell apoptotic process;negative regulation of interleukin-10 secretion;negative regulation of interleukin-12 secretion;negative regulation of CD8-positive, alpha-beta T cell activation;negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell;positive regulation of gamma-delta T cell activation involved in immune response;negative regulation of dendritic cell differentiation;negative regulation of transforming growth factor-beta secretion;negative regulation of osteoclast development
- Cellular component
- extracellular region;cytoplasm;plasma membrane;external side of plasma membrane;integral component of membrane
- Molecular function
- amyloid-beta binding;protein binding;protein phosphatase 1 binding;HLA-A specific inhibitory MHC class I receptor activity;HLA-B specific inhibitory MHC class I receptor activity;MHC class I receptor activity;MHC class Ib receptor activity;SH2 domain binding;MHC class I protein binding;protein homodimerization activity