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

ENSG00000131042 ∙ ∙ OMIM:604815 ∙ HGNC:6606 ∙ Uniprot:Q8N423 ∙ 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 LILRB2 gene.

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.

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				7		7
missense			41	6		47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	13	0

Variants in LILRB2

This is a list of pathogenic ClinVar variants found in the LILRB2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-54274711-C-T		not specified	Uncertain significance (Apr 07, 2022)
19-54274723-G-A		not specified	Uncertain significance (Oct 12, 2022)
19-54274798-G-A		not specified	Uncertain significance (Jan 04, 2024)
19-54274811-G-A		not specified	Uncertain significance (Dec 27, 2023)
19-54274829-C-G		not specified	Uncertain significance (Jun 19, 2024)
19-54275975-T-C			Likely benign (May 01, 2023)
19-54276285-C-A		not specified	Uncertain significance (Mar 23, 2023)
19-54276413-C-T			Likely benign (Oct 01, 2022)
19-54276445-C-A		not specified	Uncertain significance (May 17, 2023)
19-54276450-C-G		not specified	Uncertain significance (Jul 20, 2022)
19-54276830-C-T		not specified	Uncertain significance (Apr 18, 2023)
19-54276839-C-T		not specified	Uncertain significance (May 10, 2024)
19-54276882-C-T			Likely benign (Nov 01, 2022)
19-54276907-A-C			Likely benign (May 01, 2023)
19-54276909-C-G		not specified	Uncertain significance (Apr 19, 2024)
19-54276926-A-G		not specified	Uncertain significance (Oct 27, 2022)
19-54277919-G-T		not specified	Uncertain significance (Jan 04, 2024)
19-54278269-C-T		not specified	Uncertain significance (Jan 26, 2022)
19-54278281-G-T		not specified	Uncertain significance (Jan 04, 2024)
19-54278282-C-G		not specified	Likely benign (Jan 26, 2023)
19-54278296-A-T		not specified	Likely benign (Sep 27, 2022)
19-54278298-A-G		not specified	Uncertain significance (May 24, 2023)
19-54278340-G-T		not specified	Uncertain significance (Apr 04, 2024)
19-54278358-G-A		not specified	Uncertain significance (Dec 15, 2022)
19-54278390-C-G		not specified	Uncertain significance (Oct 12, 2022)

GnomAD

Source: gnomAD

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: dbNSFP

• 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