LAIR1
leukocyte associated immunoglobulin like receptor 1, the group of Immunoglobulin like domain containing|CD molecules
Basic information
Region (hg38): 19:54351383-54370558
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
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:
| 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:
- 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