LILRA4

leukocyte immunoglobulin like receptor A4, the group of CD molecules|Activating leukocyte immunoglobulin like receptors

Basic information

Region (hg38): 19:54333185-54339162

Links

ENSG00000239961 ∙ NCBI:23547 ∙ OMIM:607517 ∙ HGNC:15503 ∙ Uniprot:P59901 ∙ 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 LILRA4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LILRA4 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			33	4		37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	33	4	0

Variants in LILRA4

This is a list of pathogenic ClinVar variants found in the LILRA4 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-54333583-C-T		not specified	Uncertain significance (May 10, 2023)
19-54333589-G-C		not specified	Uncertain significance (Oct 29, 2021)
19-54333601-T-C		not specified	Uncertain significance (Dec 03, 2021)
19-54333649-G-C		not specified	Uncertain significance (Nov 01, 2022)
19-54333724-T-C		not specified	Uncertain significance (Apr 20, 2023)
19-54333726-C-T		not specified	Uncertain significance (Nov 10, 2022)
19-54333765-G-A		not specified	Uncertain significance (Jun 06, 2023)
19-54336847-C-T		not specified	Uncertain significance (Aug 17, 2022)
19-54336877-A-T		not specified	Uncertain significance (Sep 06, 2022)
19-54336890-G-T		not specified	Uncertain significance (Jun 06, 2023)
19-54336892-T-C		not specified	Likely benign (Jul 08, 2022)
19-54336982-C-T		not specified	Likely benign (Nov 18, 2023)
19-54336992-T-G		not specified	Uncertain significance (Oct 20, 2023)
19-54337098-G-A		not specified	Uncertain significance (Sep 26, 2022)
19-54337138-T-C		not specified	Uncertain significance (Jan 31, 2024)
19-54337143-C-T		not specified	Uncertain significance (Jan 03, 2024)
19-54337459-G-A		not specified	Uncertain significance (Dec 16, 2023)
19-54337463-C-T		not specified	Uncertain significance (May 15, 2023)
19-54337487-A-G		not specified	Likely benign (Dec 07, 2023)
19-54337492-C-G		not specified	Uncertain significance (Mar 06, 2023)
19-54337505-T-A		not specified	Uncertain significance (May 12, 2024)
19-54337505-T-C		not specified	Likely benign (Oct 06, 2021)
19-54337546-C-T		not specified	Likely benign (Apr 20, 2024)
19-54337594-T-C		not specified	Uncertain significance (May 18, 2023)
19-54337643-C-T		not specified	Uncertain significance (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LILRA4	protein_coding	protein_coding	ENST00000291759	8	5966

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.90e-16	0.00811	125698	1	22	125721	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.498	314	290	1.08	0.0000167	3162
Missense in Polyphen		64	79.097	0.80913		960
Synonymous	-1.25	147	129	1.14	0.00000798	1042
Loss of Function	-0.0984	23	22.5	1.02	0.00000105	246

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.000871	0.000816
Finnish	0.00	0.00
European (Non-Finnish)	0.0000447	0.0000440
Middle Eastern	0.000871	0.000816
South Asian	0.0000659	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions coreceptor to limit the innate immune responses to viral infections; signaling occurs via FCER1G (PubMed:16735691, PubMed:19564354). Down-regulates the production of IFNA1, IFNA2, IFNA4, IFNB1 and TNF by plasmacytoid dendritic cells that have been exposed to influenza virus or cytidine- phosphate-guanosine (CpG) dinucleotides, indicating it functions as negative regulator of TLR7 and TLR9 signaling cascades (PubMed:16735691, PubMed:19564354, PubMed:24586760). Down- regulates interferon production in response to interaction with BST2 on HIV-1 infected cells (PubMed:26172439). Activates a signaling cascade in complex with FCER1G that results in phosphorylation of Src family and Syk kinases and thereby triggers mobilization of intracellular Ca(2+) (PubMed:16735691, PubMed:19564354). Does not interfere with the differentiation of plasmacytoid dendritic cells into antigen-presenting cells (PubMed:24586760). {ECO:0000269|PubMed:16735691, ECO:0000269|PubMed:19564354, ECO:0000269|PubMed:24586760, ECO:0000269|PubMed:26172439}.
• 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: 0.0944

Intolerance Scores

• loftool: 0.905
• rvis_EVS: 0.54
• rvis_percentile_EVS: 81.07

Haploinsufficiency Scores

• pHI: 0.0418
• hipred: N
• hipred_score: 0.112
• ghis: 0.483

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.121

Gene Damage Prediction

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

Gene ontology

• Biological process: negative regulation of interferon-alpha production;negative regulation of tumor necrosis factor production;negative regulation of toll-like receptor 7 signaling pathway;negative regulation of toll-like receptor 9 signaling pathway;Fc-epsilon receptor signaling pathway;innate immune response
• Cellular component: integral component of plasma membrane;Fc-epsilon receptor I complex
• Molecular function: signaling receptor binding;protein binding;coreceptor activity