LILRB1

leukocyte immunoglobulin like receptor B1, the group of CD molecules|Inhibitory leukocyte immunoglobulin like receptors

Basic information

Region (hg38): 19:54617158-54638022

Links

ENSG00000104972 ∙ NCBI:10859 ∙ OMIM:604811 ∙ HGNC:6605 ∙ Uniprot:Q8NHL6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LILRB1 gene.

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			58	6	1	65
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	58	6	2

Variants in LILRB1

This is a list of pathogenic ClinVar variants found in the LILRB1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-54631086-C-G		not specified	Uncertain significance (May 15, 2024)
19-54631530-A-G		not specified	Uncertain significance (Jun 26, 2023)
19-54631566-C-A		not specified	Uncertain significance (Nov 07, 2024)
19-54631595-C-G		not specified	Uncertain significance (Feb 28, 2024)
19-54631605-G-A		not specified	Likely benign (Dec 15, 2022)
19-54631625-A-G		not specified	Uncertain significance (Mar 01, 2023)
19-54631665-A-G		not specified	Uncertain significance (Feb 16, 2023)
19-54631695-C-T		not specified	Uncertain significance (Aug 17, 2021)
19-54631713-G-A		not specified	Likely benign (Mar 16, 2022)
19-54631962-C-T		not specified	Uncertain significance (Mar 06, 2023)
19-54631976-G-A		not specified	Uncertain significance (Dec 10, 2024)
19-54631977-T-A		not specified	Uncertain significance (Dec 15, 2022)
19-54632001-C-C			Benign (Feb 24, 2021)
19-54632003-C-A		not specified	Uncertain significance (Dec 12, 2023)
19-54632062-T-G		not specified	Uncertain significance (Aug 22, 2023)
19-54632072-C-G		not specified	Uncertain significance (Nov 25, 2024)
19-54632099-C-T		not specified	Uncertain significance (Feb 17, 2024)
19-54632100-G-A		not specified	Uncertain significance (Feb 06, 2024)
19-54632100-G-C		not specified	Uncertain significance (Dec 05, 2023)
19-54632112-G-A		not specified	Uncertain significance (Sep 01, 2021)
19-54632196-A-T		not specified	Likely benign (Oct 12, 2024)
19-54632205-T-C		not specified	Uncertain significance (Mar 12, 2024)
19-54632213-G-C		not specified	Uncertain significance (Nov 26, 2024)
19-54632505-A-G		not specified	Likely benign (Nov 07, 2022)
19-54632563-G-C		not specified	Uncertain significance (Nov 21, 2024)

GnomAD

Source: gnomAD

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: dbNSFP

• 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