OLR1

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

Basic information

Region (hg38): 12:10158300-10172138

Links

ENSG00000173391 ∙ NCBI:4973 ∙ OMIM:602601 ∙ HGNC:8133 ∙ Uniprot:P78380 ∙ 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 OLR1 gene.

• Inborn genetic diseases (9 variants)
• not provided (2 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.

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				1		1
missense			8	1		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	8	2	1

Variants in OLR1

This is a list of pathogenic ClinVar variants found in the OLR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-10159692-A-A		Myocardial infarction, susceptibility to	risk factor (Dec 01, 2003)
12-10159944-G-A		not specified	Uncertain significance (Nov 29, 2023)
12-10159988-G-A		OLR1-related disorder	Likely benign (Jul 01, 2023)
12-10160350-T-C		not specified	Uncertain significance (Oct 03, 2022)
12-10160445-T-A		OLR1-related disorder	Likely benign (Feb 20, 2019)
12-10160535-G-A			Benign (Feb 24, 2021)
12-10160849-C-G		Myocardial infarction, susceptibility to • OLR1-related disorder	Benign (Nov 25, 2019)
12-10160860-T-C		not specified	Uncertain significance (Jan 04, 2022)
12-10160922-G-A		not specified	Uncertain significance (May 17, 2023)
12-10166703-T-C		OLR1-related disorder	Likely benign (Jun 19, 2019)
12-10166733-T-C		not specified	Uncertain significance (Jan 30, 2024)
12-10166795-T-C		not specified	Uncertain significance (Jun 23, 2021)
12-10166819-A-G		not specified	Uncertain significance (Mar 21, 2023)
12-10166826-C-T		not specified	Uncertain significance (May 23, 2023)
12-10166829-T-C		not specified	Uncertain significance (Dec 18, 2023)
12-10166876-G-A		not specified	Uncertain significance (Dec 13, 2022)
12-10169157-G-C		not specified	Uncertain significance (Jan 03, 2024)
12-10169169-T-C		not specified	Likely benign (Jan 11, 2023)
12-10172034-G-A		not specified	Uncertain significance (Dec 03, 2021)

GnomAD

Source: gnomAD

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: 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

	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