LILRB4

leukocyte immunoglobulin like receptor B4, the group of CD molecules|Inhibitory leukocyte immunoglobulin like receptors

Basic information

Region (hg38): 19:54643889-54670359

Links

ENSG00000186818 ∙ NCBI:11006 ∙ OMIM:604821 ∙ HGNC:6608 ∙ Uniprot:Q8NHJ6 ∙ 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 LILRB4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LILRB4 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				3		3
missense				1		1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	4	0

Variants in LILRB4

This is a list of pathogenic ClinVar variants found in the LILRB4 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-54663051-G-A			Likely benign (Nov 01, 2022)
19-54666737-A-G			Likely benign (Nov 01, 2022)
19-54667658-C-G			Likely benign (Mar 01, 2023)
19-54667725-C-T			Likely benign (Nov 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LILRB4	protein_coding	protein_coding	ENST00000391736	12	26471

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.71e-13	0.0521	125723	0	23	125746	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.43	314	250	1.25	0.0000133	2843
Missense in Polyphen		46	42.633	1.079		541
Synonymous	-1.19	116	101	1.15	0.00000570	910
Loss of Function	0.347	20	21.7	0.920	9.25e-7	252

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000269	0.000268
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000436	0.000435
Finnish	0.00	0.00
European (Non-Finnish)	0.0000548	0.0000527
Middle Eastern	0.000436	0.000435
South Asian	0.00	0.00
Other	0.00	0.00

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, e.g. towards transplants. Interferes with TNFRSF5- signaling and NF-kappa-B up-regulation. Inhibits receptor-mediated phosphorylation of cellular proteins and mobilization of intracellular calcium ions. {ECO:0000269|PubMed:11875462, ECO:0000269|PubMed:9151699}.
• 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: 0.991
• rvis_EVS: 4.54
• rvis_percentile_EVS: 99.75

Haploinsufficiency Scores

• pHI: 0.0723
• hipred: N
• hipred_score: 0.252
• ghis: 0.484

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.150

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lilrb4a
• Phenotype: normal phenotype; hematopoietic system phenotype; respiratory system phenotype; immune system phenotype; cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: adaptive immune response;signal transduction;positive regulation of regulatory T cell differentiation;negative regulation of osteoclast differentiation;negative regulation of T cell receptor signaling pathway;negative regulation of protein localization to nucleus;negative regulation of pri-miRNA transcription by RNA polymerase II
• Cellular component: plasma membrane;integral component of membrane;extracellular exosome
• Molecular function: antigen binding;protein binding;signaling receptor activity