LILRB5

protein-coding

leukocyte immunoglobulin like receptor B5, the group of CD molecules|Inhibitory leukocyte immunoglobulin like receptors

Gene summary

This gene is a member of the leukocyte immunoglobulin-like receptor (LIR) family, which is found in a gene cluster at chromosomal region 19q13.4. The encoded protein belongs to the subfamily B class of LIR receptors which contain two or four extracellular immunoglobulin domains, a transmembrane domain, and two to four cytoplasmic immunoreceptor tyrosine-based inhibitory motifs (ITIMs). Several other LIR subfamily B receptors are expressed on immune cells where they bind to MHC class I molecules on antigen-presenting cells and inhibit stimulation of an immune response. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

MANE transcript

NM_001081442.3

Inheritance

—

ClinVar variants

U:114B:12

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.07

Max pathogenic AF

—

Genomic locus

chr19:54,249,421-54,257,301

External References & Databases

Ensembl (ENSG00000105609)

Transcript & Mutation Effects

hg38 • Region Span ~7.9 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LILRB5 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 112

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001081442.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	5 clinvar		6
missense			110 clinvar	7 clinvar		117
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	114	12	0	126

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001081442.3	RefSeq	NP_001074911.2	13	MANE Select
ENST00000449561.3	Ensembl	ENSP00000406478.1	13	MANE Select
NM_001081443.3	RefSeq	NP_001074912.2	12	Standard
NM_001304457.3	RefSeq	NP_001291386.2	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Osteoclast differentiation - Homo sapiens (human)
Immune System
Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
Adaptive Immune System

Biological Process

adaptive immune response
defense response
cell surface receptor signaling pathway

Molecular Function

transmembrane signaling receptor activity

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000449561
Coding exons: 13
Length: 6902
Individuals with no LoFs: 125630
Homozygous LoFs: 0
Heterozygous LoFs: 118
Defined: 125748
p: 0.000469

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.999	398	346	1.15	0.0000195	3711
Missense (PolyPhen)		87	75.313	1.1552		918
Synonymous	-1.99	182	151	1.21	0.00000902	1259
Loss of Function	-0.354	33	30.9	1.07	0.00000157	332

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00017	0.00012	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00026	0.00017	rare
South Asian	0.0040	0.0030	notable
Other	0.00065	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May act as receptor for class I MHC antigens.;

Recessive Scores

pRec: 0.0683

Intolerance Scores

LoFtool: 0.952
RVIS EVS: 0.79
RVIS percentile EVS: 87.29

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0318

Gene Damage Prediction

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