OLR1

oxidized low density lipoprotein receptor 1, the group of Scavenger receptors|C-type lectin domain containing

Basic information

Region (hg38): 12:10158301-10172138

Links

ENSG00000173391NCBI:4973OMIM:602601HGNC:8133Uniprot:P78380AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the OLR1 gene.

  • 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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
2
missense
25
clinvar
3
clinvar
28
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 25 5 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
OLR1protein_codingprotein_codingENST00000309539 613836
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.007200.978125738091257470.0000358
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.5501231410.8700.000007191774
Missense in Polyphen2736.0480.74901440
Synonymous-0.2525754.61.040.00000293509
Loss of Function2.13614.90.4036.40e-7171

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001170.000117
Ashkenazi Jewish0.000.00
East Asian0.0001690.000163
Finnish0.000.00
European (Non-Finnish)0.00001770.0000176
Middle Eastern0.0001690.000163
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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