LILRB3

leukocyte immunoglobulin like receptor B3, the group of CD molecules|Inhibitory leukocyte immunoglobulin like receptors

Basic information

Region (hg38): 19:54216278-54223506

Links

ENSG00000204577 ∙ NCBI:11025 ∙ OMIM:604820 ∙ HGNC:6607 ∙ Uniprot:O75022 ∙ 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 LILRB3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LILRB3 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				2		2
missense			44	5		49
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	45	7	0

Variants in LILRB3

This is a list of pathogenic ClinVar variants found in the LILRB3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-54217101-T-C		not specified	Uncertain significance (Dec 12, 2023)
19-54217143-C-T		not specified	Uncertain significance (Sep 29, 2023)
19-54217175-C-G		not specified	Uncertain significance (Apr 20, 2023)
19-54217186-C-A		not specified	Uncertain significance (Oct 24, 2024)
19-54217199-T-C		not specified	Uncertain significance (Oct 24, 2024)
19-54217323-G-C		not specified	Uncertain significance (Aug 04, 2023)
19-54217324-T-C		not specified	Uncertain significance (Aug 02, 2021)
19-54217335-C-T		not specified	Uncertain significance (Sep 08, 2024)
19-54217358-C-G		not specified	Uncertain significance (Sep 26, 2024)
19-54218362-T-C		not specified	Uncertain significance (Dec 05, 2022)
19-54218365-C-G		not specified	Uncertain significance (Dec 05, 2022)
19-54218372-G-T		not specified	Uncertain significance (Dec 05, 2022)
19-54218382-G-C		not specified	Likely benign (Feb 21, 2024)
19-54218663-C-T		not specified	Likely benign (Apr 13, 2022)
19-54218669-C-G		not specified	Uncertain significance (Dec 08, 2023)
19-54218681-A-G		not specified	Uncertain significance (Aug 04, 2024)
19-54218815-G-A		not specified	Uncertain significance (May 26, 2022)
19-54218829-T-G		not specified	Uncertain significance (Sep 14, 2022)
19-54219161-A-T		not specified	Uncertain significance (Jun 05, 2023)
19-54219180-G-C		not specified	Uncertain significance (Sep 11, 2024)
19-54219198-C-T		not specified	Likely benign (Feb 06, 2024)
19-54219209-G-A		not specified	Uncertain significance (Jul 30, 2024)
19-54220169-G-A		not specified	Uncertain significance (Oct 04, 2024)
19-54220564-A-T		not specified	Uncertain significance (Jun 24, 2022)
19-54220578-T-A		not specified	Uncertain significance (Oct 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LILRB3	protein_coding	protein_coding	ENST00000245620	13	26456

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000311	0.986	125652	0	95	125747	0.000378

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.01	345	296	1.17	0.0000157	3915
Missense in Polyphen		105	100.53	1.0444		1540
Synonymous	-1.85	151	125	1.21	0.00000719	1271
Loss of Function	2.22	13	25.0	0.520	0.00000114	334

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00252	0.00236
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000354	0.000352
Middle Eastern	0.000109	0.000109
South Asian	0.0000328	0.0000327
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as receptor for class I MHC antigens. Becomes activated upon coligation of LILRB3 and immune receptors, such as FCGR2B and the B-cell receptor. Down-regulates antigen-induced B- cell activation by recruiting phosphatases to its immunoreceptor tyrosine-based inhibitor motifs (ITIM). {ECO:0000250|UniProtKB:P97484}.
• Pathway: B cell receptor signaling pathway - Homo sapiens (human);Osteoclast differentiation - Homo sapiens (human);Spinal Cord Injury;Neutrophil degranulation;Innate Immune System;Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System (Consensus)

Intolerance Scores

• loftool: 0.928
• rvis_EVS: 1.76
• rvis_percentile_EVS: 96.71

Haploinsufficiency Scores

• pHI: 0.0709
• hipred: N
• hipred_score: 0.332
• ghis: 0.514

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0411

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Pirb
• Phenotype: cellular phenotype; immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hematopoietic system phenotype

Gene ontology

• Biological process: adaptive immune response;defense response;cell surface receptor signaling pathway;neutrophil degranulation;negative regulation of osteoclast differentiation
• Cellular component: plasma membrane;integral component of plasma membrane;secretory granule membrane
• Molecular function: amyloid-beta binding;transmembrane signaling receptor activity;protein binding;signaling receptor activity