LILRA1

leukocyte immunoglobulin like receptor A1, the group of CD molecules|Activating leukocyte immunoglobulin like receptors

Basic information

Region (hg38): 19:54593582-54602381

Links

ENSG00000104974 ∙ NCBI:11024 ∙ OMIM:604810 ∙ HGNC:6602 ∙ Uniprot:O75019 ∙ 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 LILRA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LILRA1 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	5		38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	5	0

Variants in LILRA1

This is a list of pathogenic ClinVar variants found in the LILRA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-54594261-C-A		not specified	Uncertain significance (Apr 17, 2024)
19-54594272-T-G		not specified	Uncertain significance (Apr 25, 2023)
19-54594453-G-A		not specified	Uncertain significance (Feb 07, 2023)
19-54594462-C-T		not specified	Uncertain significance (Oct 31, 2022)
19-54594764-A-G		not specified	Uncertain significance (May 16, 2024)
19-54594808-C-T		not specified	Uncertain significance (Apr 12, 2024)
19-54594818-A-G		not specified	Uncertain significance (Nov 15, 2021)
19-54594844-C-T		not specified	Likely benign (Dec 16, 2022)
19-54594901-C-T		not specified	Uncertain significance (Sep 06, 2022)
19-54594932-C-T		not specified	Uncertain significance (Feb 13, 2024)
19-54595129-C-A		not specified	Uncertain significance (Nov 18, 2022)
19-54595162-G-A		not specified	Uncertain significance (Sep 17, 2021)
19-54595256-C-T		not specified	Uncertain significance (Jun 02, 2023)
19-54595261-A-G		not specified	Uncertain significance (Mar 16, 2022)
19-54595271-G-T		not specified	Uncertain significance (Dec 11, 2023)
19-54595351-T-C		not specified	Uncertain significance (Sep 22, 2022)
19-54595357-C-T		not specified	Likely benign (Dec 08, 2023)
19-54595648-A-G		not specified	Likely benign (Jul 05, 2023)
19-54595699-G-T		not specified	Uncertain significance (Apr 08, 2024)
19-54595726-T-C		not specified	Uncertain significance (Mar 03, 2022)
19-54595864-G-C		not specified	Uncertain significance (Jun 10, 2024)
19-54595865-A-T		not specified	Uncertain significance (Oct 04, 2022)
19-54595870-C-A		not specified	Likely benign (Aug 10, 2021)
19-54595872-G-T		not specified	Uncertain significance (Dec 21, 2022)
19-54595888-C-T		not specified	Uncertain significance (Mar 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LILRA1	protein_coding	protein_coding	ENST00000251372	9	8509

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.39e-20	0.000513	125719	0	29	125748	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.17	381	279	1.36	0.0000165	3075
Missense in Polyphen		86	70.514	1.2196		946
Synonymous	-5.43	192	117	1.64	0.00000714	1027
Loss of Function	-0.757	27	23.1	1.17	0.00000100	260

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000514	0.000514
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.0000796	0.0000791
Middle Eastern	0.000218	0.000217
South Asian	0.0000654	0.0000653
Other	0.00	0.00

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)

Intolerance Scores

• loftool: 0.919
• rvis_EVS: 2.54
• rvis_percentile_EVS: 98.72

Haploinsufficiency Scores

• pHI: 0.0381
• hipred: N
• hipred_score: 0.112
• ghis: 0.522

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.140

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;regulation of immune response
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: antigen binding;transmembrane signaling receptor activity