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.

not_specified (83 variants)
not_provided (1 variants)

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. These statistics are base on transcript: NM_000012276.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			72 clinvar	11 clinvar		83
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	72	12	0

Loading clinvar variants...

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