LAIR2

leukocyte associated immunoglobulin like receptor 2, the group of CD molecules|Immunoglobulin like domain containing

Basic information

Region (hg38): 19:54497879-54510687

Links

ENSG00000167618 ∙ NCBI:3904 ∙ OMIM:602993 ∙ HGNC:6478 ∙ Uniprot:Q6ISS4 ∙ 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 LAIR2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LAIR2 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			8	2		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	2	0

Variants in LAIR2

This is a list of pathogenic ClinVar variants found in the LAIR2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-54502935-C-T		not specified	Uncertain significance (Oct 12, 2022)
19-54503727-C-T		not specified	Uncertain significance (Dec 09, 2023)
19-54507942-C-T		not specified	Likely benign (Jan 07, 2022)
19-54507968-C-T		not specified	Uncertain significance (Dec 12, 2023)
19-54507974-C-T		not specified	Uncertain significance (Dec 28, 2022)
19-54508038-A-C		not specified	Uncertain significance (Nov 13, 2023)
19-54508055-C-A		not specified	Uncertain significance (Dec 05, 2024)
19-54508100-G-A		not specified	Uncertain significance (Oct 22, 2021)
19-54508128-A-G		not specified	Uncertain significance (Apr 11, 2023)
19-54509047-G-A		not specified	Likely benign (Dec 21, 2022)
19-54509083-C-G		not specified	Uncertain significance (Dec 02, 2024)
19-54510541-C-G		not specified	Uncertain significance (Apr 23, 2024)
19-54510552-G-A		not specified	Uncertain significance (Dec 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LAIR2	protein_coding	protein_coding	ENST00000301202	5	12798

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.60e-7	0.0912	125648	1	96	125745	0.000386

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.423	102	90.7	1.13	0.00000517	955
Missense in Polyphen		25	26.654	0.93795		272
Synonymous	-0.528	43	38.8	1.11	0.00000232	322
Loss of Function	-0.664	9	7.09	1.27	2.98e-7	89

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000242	0.000242
Ashkenazi Jewish	0.00	0.00
East Asian	0.00446	0.00441
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.00446	0.00441
South Asian	0.000164	0.000163
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Pathway: Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System (Consensus)

Intolerance Scores

• loftool: 0.903
• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.12

Haploinsufficiency Scores

• pHI: 0.0702
• hipred: N
• hipred_score: 0.112
• ghis: 0.406

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.105

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of immune response
• Cellular component: extracellular region
• Molecular function: protein binding