LILRA2

leukocyte immunoglobulin like receptor A2, the group of CD molecules|Activating leukocyte immunoglobulin like receptors

Basic information

Region (hg38): 19:54572920-54590287

Links

ENSG00000239998 ∙ NCBI:11027 ∙ OMIM:604812 ∙ HGNC:6603 ∙ Uniprot:Q8N149 ∙ 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 LILRA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LILRA2 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						0
missense			55	3		58
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	55	3	0

Variants in LILRA2

This is a list of pathogenic ClinVar variants found in the LILRA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-54573895-C-T		not specified	Uncertain significance (Oct 27, 2021)
19-54573906-T-C		not specified	Uncertain significance (Nov 07, 2022)
19-54573909-C-T		not specified	Uncertain significance (Aug 10, 2021)
19-54574087-G-A		not specified	Uncertain significance (Jul 26, 2021)
19-54574091-C-T		not specified	Uncertain significance (Aug 14, 2023)
19-54574102-G-A		not specified	Uncertain significance (May 10, 2023)
19-54574102-G-C		not specified	Uncertain significance (Sep 23, 2023)
19-54574304-A-C		not specified	Uncertain significance (Dec 20, 2023)
19-54574372-A-G		not specified	Uncertain significance (May 17, 2023)
19-54574385-G-C		not specified	Likely benign (Aug 22, 2023)
19-54574406-A-G		not specified	Likely benign (Mar 20, 2024)
19-54574444-C-T		not specified	Uncertain significance (Jun 03, 2022)
19-54574451-A-C		not specified	Uncertain significance (Feb 28, 2024)
19-54574453-G-A		not specified	Uncertain significance (Mar 22, 2023)
19-54574511-G-A		not specified	Uncertain significance (Mar 13, 2023)
19-54574523-A-C		not specified	Uncertain significance (Feb 10, 2023)
19-54574547-C-T		not specified	Uncertain significance (Apr 10, 2023)
19-54574745-C-T		not specified	Uncertain significance (Apr 29, 2024)
19-54574768-C-A		not specified	Uncertain significance (Jun 07, 2023)
19-54574797-C-T		not specified	Uncertain significance (Jun 24, 2022)
19-54574815-A-G		not specified	Uncertain significance (Jan 17, 2024)
19-54574854-A-C		not specified	Uncertain significance (Oct 10, 2023)
19-54574855-A-T		not specified	Uncertain significance (Jun 09, 2022)
19-54574872-G-A		not specified	Uncertain significance (Dec 16, 2021)
19-54574885-T-G		not specified	Likely benign (Apr 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LILRA2	protein_coding	protein_coding	ENST00000251377	8	14641

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.91e-20	0.000256	125734	0	13	125747	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.70	389	265	1.47	0.0000151	3024
Missense in Polyphen		112	83.523	1.341		1056
Synonymous	-2.99	154	113	1.36	0.00000655	999
Loss of Function	-1.16	26	20.3	1.28	8.87e-7	240

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000127	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000441	0.0000439
Middle Eastern	0.000109	0.000109
South Asian	0.0000654	0.0000653
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Part of the innate immune responses against microbial infection (PubMed:12529506, PubMed:27572839). Specifically recognizes a set of N-terminally truncated immunoglobulins that are produced via cleavage by proteases from a range of pathogenic bacteria and fungi, including L.pneumophila, M.hyorhinis, S.pneumoniae, S.aureus and C.albicans (PubMed:27572839). Recognizes epitopes that are in part in the variable region of the immunoglobulin light chains, but requires also the constant region for signaling (PubMed:27572839). Binds to a subset of cleaved IgM, IgG3 and IgG4 molecules, but does not bind cleaved IgA1 (PubMed:27572839). Binding of N-terminally truncated immunoglobulins mediates activation of neutrophils (PubMed:27572839). In monocytes, activation leads to the release of CSF2, CF3, IL6, CXCL8 and CCL3 and down-regulates responses to bacterial lipopolysaccharide (LPS), possibly via down-regulation of TLR4 expression and reduced signaling via TLR4 (PubMed:22479404). In eosinophils, activation by ligand binding leads to the release of RNASE2, IL4 and leukotriene C4 (PubMed:12529506). Does not bind class I MHC antigens (PubMed:19230061). {ECO:0000269|PubMed:12529506, ECO:0000269|PubMed:19230061, ECO:0000269|PubMed:22479404, ECO:0000269|PubMed:27572839}.
• 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: 0.899
• rvis_EVS: 3.23
• rvis_percentile_EVS: 99.37

Haploinsufficiency Scores

• pHI: 0.217
• hipred: N
• hipred_score: 0.112
• ghis: 0.521

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.142

Gene Damage Prediction

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

Gene ontology

• Biological process: innate immune response activating cell surface receptor signaling pathway;neutrophil activation involved in immune response;defense response;signal transduction;negative regulation of lipopolysaccharide-mediated signaling pathway;granulocyte macrophage colony-stimulating factor production;interleukin-6 production;interleukin-8 production;negative regulation of toll-like receptor 4 signaling pathway;innate immune response;positive regulation of interleukin-1 beta secretion;positive regulation of cell activation;positive regulation of calcium ion transport;granulocyte colony-stimulating factor production;positive regulation of tumor necrosis factor secretion;positive regulation of interleukin-6 secretion
• Cellular component: extracellular region;integral component of plasma membrane
• Molecular function: IgM binding;antigen binding;signaling receptor activity