OLR1
Basic information
Region (hg38): 12:10158301-10172138
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (28 variants)
- OLR1-related_disorder (3 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the OLR1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002543.4. Only rare variants are included in the table.
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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 2 | |||||
missense | 25 | 28 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 25 | 5 | 0 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
OLR1 | protein_coding | protein_coding | ENST00000309539 | 6 | 13836 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00720 | 0.978 | 125738 | 0 | 9 | 125747 | 0.0000358 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.550 | 123 | 141 | 0.870 | 0.00000719 | 1774 |
Missense in Polyphen | 27 | 36.048 | 0.74901 | 440 | ||
Synonymous | -0.252 | 57 | 54.6 | 1.04 | 0.00000293 | 509 |
Loss of Function | 2.13 | 6 | 14.9 | 0.403 | 6.40e-7 | 171 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000117 | 0.000117 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000169 | 0.000163 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000177 | 0.0000176 |
Middle Eastern | 0.000169 | 0.000163 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Receptor that mediates the recognition, internalization and degradation of oxidatively modified low density lipoprotein (oxLDL) by vascular endothelial cells. OxLDL is a marker of atherosclerosis that induces vascular endothelial cell activation and dysfunction, resulting in pro-inflammatory responses, pro- oxidative conditions and apoptosis. Its association with oxLDL induces the activation of NF-kappa-B through an increased production of intracellular reactive oxygen and a variety of pro- atherogenic cellular responses including a reduction of nitric oxide (NO) release, monocyte adhesion and apoptosis. In addition to binding oxLDL, it acts as a receptor for the HSP70 protein involved in antigen cross-presentation to naive T-cells in dendritic cells, thereby participating in cell-mediated antigen cross-presentation. Also involved in inflammatory process, by acting as a leukocyte-adhesion molecule at the vascular interface in endotoxin-induced inflammation. Also acts as a receptor for advanced glycation end (AGE) products, activated platelets, monocytes, apoptotic cells and both Gram-negative and Gram- positive bacteria. {ECO:0000269|PubMed:11821063, ECO:0000269|PubMed:12354387, ECO:0000269|PubMed:9052782}.;
- Disease
- DISEASE: Note=Independent association genetic studies have implicated OLR1 gene variants in myocardial infarction susceptibility.; DISEASE: Note=OLR1 may be involved in Alzheimer disease (AD). Involvement in AD is however unclear: according to some authors (PubMed:12354387, PubMed:12810610 and PubMed:15976314), variations in OLR1 modify the risk of AD, while according to other (PubMed:15000751 and PubMed:15060104) they do not. {ECO:0000269|PubMed:12384789, ECO:0000269|PubMed:12807963, ECO:0000269|PubMed:15860461}.;
- Pathway
- Phagosome - Homo sapiens (human);PPAR signaling pathway - Homo sapiens (human);PPAR signaling pathway;Neutrophil degranulation;Innate Immune System;Immune System;Cell surface interactions at the vascular wall;Hemostasis
(Consensus)
Recessive Scores
- pRec
- 0.347
Intolerance Scores
- loftool
- 0.374
- rvis_EVS
- -0.12
- rvis_percentile_EVS
- 44.89
Haploinsufficiency Scores
- pHI
- 0.101
- hipred
- N
- hipred_score
- 0.369
- ghis
- 0.452
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.451
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Olr1
- Phenotype
- homeostasis/metabolism phenotype; muscle phenotype; immune system phenotype; normal phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan);
Gene ontology
- Biological process
- proteolysis;inflammatory response;cell adhesion;blood circulation;neutrophil degranulation;leukocyte migration
- Cellular component
- extracellular region;nucleoplasm;plasma membrane;integral component of plasma membrane;membrane;specific granule membrane;intracellular membrane-bounded organelle;receptor complex;membrane raft;tertiary granule membrane
- Molecular function
- protein binding;carbohydrate binding;identical protein binding