LAIR1

leukocyte associated immunoglobulin like receptor 1, the group of Immunoglobulin like domain containing|CD molecules

Basic information

Region (hg38): 19:54351384-54370558

Links

ENSG00000167613 ∙ NCBI:3903 ∙ OMIM:602992 ∙ HGNC:6477 ∙ Uniprot:Q6GTX8 ∙ 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 LAIR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LAIR1 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	0

Variants in LAIR1

This is a list of pathogenic ClinVar variants found in the LAIR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-54355318-T-C		not specified	Uncertain significance (Feb 27, 2024)
19-54355344-G-A		not specified	Uncertain significance (May 13, 2024)
19-54355974-C-T		not specified	Uncertain significance (May 25, 2022)
19-54356238-C-T		not specified	Uncertain significance (Apr 15, 2024)
19-54356244-A-G		not specified	Uncertain significance (Oct 17, 2023)
19-54356253-A-G		not specified	Uncertain significance (Dec 27, 2023)
19-54356511-C-T		not specified	Uncertain significance (Dec 27, 2023)
19-54356529-A-G		not specified	Uncertain significance (Mar 04, 2024)
19-54356584-G-T		not specified	Uncertain significance (Oct 06, 2021)
19-54360034-C-T		not specified	Uncertain significance (Jun 10, 2024)
19-54360981-C-G		not specified	Uncertain significance (Feb 28, 2024)
19-54361021-G-A		not specified	Uncertain significance (May 09, 2022)
19-54361156-C-T		not specified	Uncertain significance (Apr 07, 2023)
19-54361162-G-T		not specified	Uncertain significance (Dec 06, 2021)
19-54361182-G-A		not specified	Uncertain significance (Sep 16, 2021)
19-54364315-T-C		not specified	Uncertain significance (Jun 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LAIR1	protein_coding	protein_coding	ENST00000391742	10	16804

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.26e-7	0.556	125689	0	59	125748	0.000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.314	181	170	1.07	0.0000101	1823
Missense in Polyphen		91	78.965	1.1524		867
Synonymous	-1.82	92	72.3	1.27	0.00000463	592
Loss of Function	0.945	12	16.1	0.746	7.84e-7	180

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00121	0.00121
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000109
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000248	0.000246
Middle Eastern	0.000111	0.000109
South Asian	0.0000327	0.0000327
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as an inhibitory receptor that plays a constitutive negative regulatory role on cytolytic function of natural killer (NK) cells, B-cells and T-cells. Activation by Tyr phosphorylation results in recruitment and activation of the phosphatases PTPN6 and PTPN11. It also reduces the increase of intracellular calcium evoked by B-cell receptor ligation. May also play its inhibitory role independently of SH2-containing phosphatases. Modulates cytokine production in CD4+ T-cells, down- regulating IL2 and IFNG production while inducing secretion of transforming growth factor beta. Down-regulates also IgG and IgE production in B-cells as well as IL8, IL10 and TNF secretion. Inhibits proliferation and induces apoptosis in myeloid leukemia cell lines as well as prevents nuclear translocation of NF-kappa-B p65 subunit/RELA and phosphorylation of I-kappa-B alpha/CHUK in these cells. Inhibits the differentiation of peripheral blood precursors towards dendritic cells. {ECO:0000269|PubMed:10229813, ECO:0000269|PubMed:10764762, ECO:0000269|PubMed:11069054, ECO:0000269|PubMed:11160222, ECO:0000269|PubMed:12072189, ECO:0000269|PubMed:15939744, ECO:0000269|PubMed:15950745, ECO:0000269|PubMed:16380958, ECO:0000269|PubMed:9285412, ECO:0000269|PubMed:9692876}.
• Pathway: Neutrophil degranulation;Innate Immune System;Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System (Consensus)

Recessive Scores

• pRec: 0.0715

Intolerance Scores

• loftool: 0.842
• rvis_EVS: 1.53
• rvis_percentile_EVS: 95.53

Haploinsufficiency Scores

• pHI: 0.0353
• hipred: N
• hipred_score: 0.252
• ghis: 0.498

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.341

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lair1
• Phenotype: immune system phenotype; normal phenotype; hematopoietic system phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: adaptive immune response;neutrophil degranulation;regulation of immune response
• Cellular component: plasma membrane;integral component of membrane;specific granule membrane;tertiary granule membrane
• Molecular function: protein binding