OLR1

Chr 12

oxidized low density lipoprotein receptor 1

Also known as: CLEC8A, LOX1, LOXIN, SCARE1, SLOX1

NCBI Gene: 4973 ENSG00000173391 UniProt: P78380 OMIM: 602601

The protein functions as a scavenger receptor that binds, internalizes and degrades oxidized low-density lipoprotein and also serves as a receptor for heat shock proteins, advanced glycation end products, and bacterial components. Mutations cause susceptibility to myocardial infarction and may modify risk for atherosclerosis and Alzheimer's disease. The gene shows low constraint to loss-of-function mutations, and inheritance pattern information is not available from the provided data.

OMIM ResearchSummary from RefSeq, OMIM, UniProt

This gene encodes a low density lipoprotein receptor that belongs to the C-type lectin superfamily. This gene is regulated through the cyclic AMP signaling pathway. The encoded protein binds, internalizes and degrades oxidized low-density lipoprotein. This protein may be involved in the regulation of Fas-induced apoptosis. This protein may play a role as a scavenger receptor. Mutations of this gene have been associated with atherosclerosis, risk of myocardial infarction, and may modify the risk of Alzheimer's disease. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Feb 2010]

OMIM ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

{Myocardial infarction, susceptibility to}MIM #608446

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.80

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.80LOEUF

pLI 0.007

Z-score 2.13

OE 0.40 (0.22–0.80)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.55Z-score

OE missense 0.87 (0.75–1.01)

123 obs / 141.4 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.40 (0.22–0.80)

0≤0.351.4

Missense OE?0.87 (0.75–1.01)

0≤0.61.4

Synonymous OE?1.04

0≤1.21.6

LoF obs/exp: 6 / 14.9Missense obs/exp: 123 / 141.4Syn Z: -0.25

Background carrier burden — how many people carry a rare variant somewhere in OLR1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 340

321 rare PASS variants

Rare truncating (LoF)

1 in 3,100

52 rare PASS variants

Rare synonymous (reference)

1 in 900

102 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for OLR1. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 470	1 in 2,800
South Asian	~43k	1 in 200	1 in 4,800
Remaining (unassigned)	~30k	1 in 200	1 in 6,000
European (Finnish)	~27k	1 in 550	≈ 1 in 13,000
Admixed American	~22k	1 in 340	1 in 2,200
African / African American	~21k	1 in 190	≈ 1 in 4,400
East Asian	~20k	1 in 200	≈ 1 in 4,900
Ashkenazi Jewish	~13k	1 in 900	none seen
Middle Eastern	~2,884	1 in 170	none seen

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): All 6 coding exons well covered in gnomAD exomes and genomes.? see exons ↓