LILRB5

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

Basic information

Region (hg38): 19:54249421-54257301

Links

ENSG00000105609 ∙ ∙ OMIM:604814 ∙ HGNC:6609 ∙ Uniprot:O75023 ∙ 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 LILRB5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LILRB5 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				4		4
missense			42	2	1	45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	6	1

Variants in LILRB5

This is a list of pathogenic ClinVar variants found in the LILRB5 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-54250806-C-T		not specified	Uncertain significance (May 09, 2023)
19-54250808-T-C		not specified	Uncertain significance (Feb 12, 2024)
19-54250852-A-C			Likely benign (Feb 01, 2024)
19-54250857-C-G		not specified	Uncertain significance (Jun 06, 2023)
19-54250868-C-G		not specified	Uncertain significance (Jan 08, 2024)
19-54250868-C-T		not specified	Uncertain significance (Apr 15, 2024)
19-54250896-C-T		not specified	Uncertain significance (Apr 07, 2022)
19-54250920-C-G		not specified	Uncertain significance (Feb 05, 2024)
19-54252058-G-T		not specified	Uncertain significance (Aug 16, 2021)
19-54252064-A-G		not specified	Uncertain significance (Sep 26, 2023)
19-54252085-T-C		not specified	Uncertain significance (Aug 08, 2022)
19-54252098-C-G		not specified	Uncertain significance (Apr 19, 2023)
19-54252385-G-A			Likely benign (Apr 01, 2022)
19-54252401-G-A		not specified	Uncertain significance (Apr 08, 2024)
19-54252522-G-A		not specified	Uncertain significance (Nov 18, 2022)
19-54252537-C-T		not specified	Uncertain significance (Jan 23, 2024)
19-54252878-C-A		not specified	Uncertain significance (Dec 14, 2023)
19-54252972-A-C		not specified	Uncertain significance (Sep 29, 2023)
19-54254382-C-G			Likely benign (Apr 01, 2022)
19-54254791-C-G		not specified	Uncertain significance (Oct 26, 2022)
19-54254809-C-T		not specified	Uncertain significance (Jan 04, 2024)
19-54254899-G-A		not specified	Uncertain significance (Jul 12, 2022)
19-54254903-G-T		not specified	Uncertain significance (May 13, 2024)
19-54254947-T-C		not specified	Uncertain significance (Apr 22, 2022)
19-54254959-C-T		not specified	Uncertain significance (Oct 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LILRB5	protein_coding	protein_coding	ENST00000449561	13	6902

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.49e-23	0.000334	125630	0	118	125748	0.000469

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.999	398	346	1.15	0.0000195	3711
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000174	0.000174
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000257	0.000167
Middle Eastern	0.0000544	0.0000544
South Asian	0.00400	0.00298
Other	0.000653	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as receptor for class I MHC antigens.
• Pathway: Osteoclast differentiation - Homo sapiens (human);Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System (Consensus)

Recessive Scores

• pRec: 0.0683

Intolerance Scores

• loftool: 0.952
• rvis_EVS: 0.79
• rvis_percentile_EVS: 87.29

Haploinsufficiency Scores

• pHI: 0.0593
• hipred: N
• hipred_score: 0.139
• ghis: 0.455

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0318

Gene Damage Prediction

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

Gene ontology

• Biological process: adaptive immune response;defense response;cell surface receptor signaling pathway
• Cellular component: integral component of membrane
• Molecular function: transmembrane signaling receptor activity