LILRA5

leukocyte immunoglobulin like receptor A5, the group of CD molecules|Activating leukocyte immunoglobulin like receptors

Basic information

Region (hg38): 19:54307070-54313166

Previous symbols: [ "LILRB7" ]

Links

ENSG00000187116 ∙ NCBI:353514 ∙ OMIM:606047 ∙ HGNC:16309 ∙ Uniprot:A6NI73 ∙ 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 LILRA5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LILRA5 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				1		1
missense			21	1		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	2	0

Variants in LILRA5

This is a list of pathogenic ClinVar variants found in the LILRA5 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-54307423-G-A		not specified	Uncertain significance (Dec 11, 2023)
19-54307535-C-G		not specified	Uncertain significance (Nov 08, 2022)
19-54307742-G-A		not specified	Uncertain significance (Oct 29, 2021)
19-54311454-T-C			Likely benign (Aug 01, 2022)
19-54311518-G-C		not specified	Uncertain significance (Feb 05, 2024)
19-54311561-G-T		not specified	Uncertain significance (Dec 28, 2022)
19-54311632-C-A		not specified	Uncertain significance (Mar 28, 2023)
19-54311888-C-T		not specified	Uncertain significance (May 05, 2023)
19-54311912-G-A		not specified	Uncertain significance (May 18, 2023)
19-54311924-A-G		not specified	Uncertain significance (May 18, 2023)
19-54312043-C-T		not specified	Uncertain significance (Sep 15, 2021)
19-54312046-T-G		not specified	Uncertain significance (May 06, 2022)
19-54312056-C-T		not specified	Uncertain significance (Aug 02, 2022)
19-54312070-T-C		not specified	Uncertain significance (Jan 04, 2024)
19-54312076-C-T		not specified	Uncertain significance (Dec 20, 2021)
19-54312077-G-A		not specified	Likely benign (Oct 04, 2022)
19-54312079-A-C		not specified	Uncertain significance (Aug 16, 2022)
19-54312106-A-G		not specified	Uncertain significance (Sep 27, 2021)
19-54312144-G-T		not specified	Uncertain significance (Aug 12, 2021)
19-54312344-C-G		not specified	Uncertain significance (Mar 23, 2022)
19-54312346-T-C		not specified	Uncertain significance (Nov 29, 2023)
19-54312552-C-T		not specified	Uncertain significance (Aug 12, 2021)
19-54312584-A-G		not specified	Uncertain significance (Oct 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LILRA5	protein_coding	protein_coding	ENST00000301219	7	6057

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.25e-9	0.149	125677	0	71	125748	0.000282

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.151	173	168	1.03	0.00000947	1912
Missense in Polyphen		28	30.178	0.92783		414
Synonymous	-2.01	88	67.0	1.31	0.00000372	618
Loss of Function	0.214	13	13.9	0.938	6.07e-7	160

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000158	0.000158
Middle Eastern	0.000272	0.000272
South Asian	0.00150	0.00150
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in triggering innate immune responses. Does not seem to play a role for any class I MHC antigen recognition. {ECO:0000269|PubMed:16675463}.
• 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: 0.0705

Intolerance Scores

• loftool: 0.930
• rvis_EVS: -0.85
• rvis_percentile_EVS: 11.06

Haploinsufficiency Scores

• pHI: 0.0738
• hipred: N
• hipred_score: 0.112
• ghis: 0.475

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0142

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lilra5

Gene ontology

• Biological process: positive regulation of MAPK cascade;innate immune response;positive regulation of interleukin-1 beta secretion;positive regulation of inflammatory response;positive regulation of cell activation;positive regulation of calcium ion transport;positive regulation of protein tyrosine kinase activity;positive regulation of tumor necrosis factor secretion;negative regulation of interleukin-13 secretion;positive regulation of interleukin-6 secretion;positive regulation of interleukin-10 secretion;negative regulation of interleukin-12 secretion
• Cellular component: extracellular region;plasma membrane;cell surface;integral component of membrane