LOXL1 rs1048664: Understanding the Genetic Link to Eye Health
The rs1048664 variant is a genetic marker located within the LOXL1 gene, which plays a critical role in the structure of the eye's extracellular matrix. Research has identified this variant as being associated with an increased risk of developing pseudoexfoliation syndrome and related secondary open-angle glaucoma.
What each genotype means
Typical risk profile
You carry two copies of the common C allele at rs1048664 in the LOXL1 gene. Research suggests this genotype is not typically linked to increased risk for pseudoexfoliation syndrome or secondary open-angle glaucoma compared to carrying the alternative variant. Because eye health is shaped by many genes and lifestyle factors, routine comprehensive eye exams remain an important part of preventive healthcare.
Carried by approximately 60% to 75% of individuals across European and Asian populations.
Moderately elevated susceptibility
You have one copy of the T allele and one copy of the C allele at rs1048664 in LOXL1. Genetic association studies have linked this missense variant to a modestly increased relative risk for pseudoexfoliation syndrome and subsequent glaucoma in certain populations, though findings remain complex and evidence is limited. Carrying this allele is not a diagnosis, and most individuals with this variant never develop ocular issues.
Found in approximately 25% to 35% of people of European and Asian descent.
Elevated susceptibility profile
You carry two copies of the T allele (encoding the Asp153 amino acid variant) in the LOXL1 gene. Published studies have observed statistical associations between this genotype and higher susceptibility to pseudoexfoliation syndrome and secondary open-angle glaucoma, particularly in specific ancestral cohorts. However, the variant is neither necessary nor sufficient to cause the condition on its own, and standard eye examinations provide the clearest picture of actual ocular health.
Carried by roughly 2% to 6% of European and Asian populations.
What is the rs1048664 Variant?
The rs1048664 variant is a single nucleotide polymorphism (SNP) found within the LOXL1 gene, which is located on chromosome 15. In genetics, a SNP represents a variation at a single position in the DNA sequence among individuals. This specific variant is categorized as a missense mutation, meaning the change in the DNA sequence results in a different amino acid being incorporated into the protein structure. Specifically, it involves a change from glycine to aspartic acid (p.Gly153Asp). Because this variant is located in a region of the gene that may influence protein function or regulation, researchers have studied it extensively to determine how it contributes to the development of certain eye conditions. It is important to note that while this variant is a well-studied marker, it is just one of many factors that contribute to the complex biological processes involved in maintaining ocular health.
The Role of the LOXL1 Gene
The LOXL1 gene provides instructions for making the lysyl oxidase-like 1 protein. This protein is essential for the formation and maintenance of elastic fibers in the body's connective tissues, including those found in the eye. Elastic fibers provide strength and flexibility to various structures, such as the lens capsule and the drainage system of the eye. When the LOXL1 protein does not function optimally, or when its expression is altered, it can lead to the accumulation of abnormal fibrillar material in the eye. This accumulation is the hallmark of pseudoexfoliation syndrome. By studying how variants like rs1048664 affect the production or stability of the LOXL1 protein, scientists aim to better understand the underlying mechanisms that lead to the breakdown of these critical ocular tissues, which can eventually increase intraocular pressure and lead to glaucoma.
Research and Evidence Strength
The association between LOXL1 variants and pseudoexfoliation syndrome is well-documented in scientific literature, though the evidence is considered limited in terms of clinical predictability for individuals. Numerous genome-wide association studies have confirmed that specific SNPs in this gene are strongly linked to the risk of developing the syndrome across various populations. However, the strength and direction of these associations can be highly dependent on ancestry. For example, risk alleles identified in European populations have sometimes shown different or even reversed effects in Asian populations. Because pseudoexfoliation syndrome is a complex, multifactorial condition, having a specific genotype does not guarantee that an individual will develop the disease. Current research focuses on how these genetic markers interact with environmental factors and other genes to influence disease progression. As such, this information is primarily used for population-level research rather than individual diagnostic screening.
Population Frequency
The frequency of the rs1048664 variant varies significantly across different global populations. Data indicates that the minor allele frequency (MAF) typically ranges between 0.15 and 0.25 in European and Asian populations. These frequency differences are a key area of study, as they help researchers understand why the prevalence of pseudoexfoliation syndrome differs between ethnic groups. Because the variant is relatively common in many populations, it is considered a widespread genetic marker rather than a rare mutation. Understanding these frequency patterns is essential for researchers to account for ancestry-based differences when conducting large-scale genetic studies, ensuring that findings are interpreted accurately within the context of a person's genetic background.
What This Information Means for You
Genetic information regarding the rs1048664 variant is intended for educational purposes and should not be used to diagnose or predict personal health outcomes. While the variant is associated with a higher statistical risk for pseudoexfoliation syndrome, many people with the risk genotype never develop the condition. Conversely, individuals without the variant can still be affected. If you are concerned about your eye health or have a family history of glaucoma, the most effective step is to consult with an ophthalmologist or a qualified eye care professional. They can perform clinical examinations, such as checking intraocular pressure and inspecting the lens, which are the standard methods for monitoring eye health. Never use genetic data to make medical decisions or alter your healthcare routine without professional guidance. Genetic testing provides a piece of the puzzle, but it does not replace the comprehensive care provided by your doctor.
How common is this variant?
The rs1048664 variant is common, with a minor allele frequency typically ranging from 0.15 to 0.25 in European and Asian populations.
Frequently asked questions
Does having the rs1048664 variant mean I will get glaucoma?
No. While this variant is associated with an increased statistical risk for pseudoexfoliation syndrome and related glaucoma, it is not a diagnostic test. Many factors, including age and environment, influence your actual risk.
Should I get tested for LOXL1 variants?
Genetic testing for this variant is generally not recommended for clinical diagnosis. Regular eye exams with an ophthalmologist are the most effective way to monitor your eye health and detect signs of glaucoma early.
Why do the risk associations differ between populations?
Genetic associations can vary due to differences in genetic background and the presence of other modifying genes. Researchers have observed that the risk alleles for LOXL1 can differ significantly between European and Asian populations.
What is pseudoexfoliation syndrome?
Pseudoexfoliation syndrome is an age-related condition where abnormal protein material accumulates in the eye. This can block the eye's drainage system, potentially leading to increased pressure and glaucoma.
Sources & further reading
Educational information only, last refreshed 10/19/2026. Not medical advice — these associations describe population statistics, not individual predictions.
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This LOXL1 variant is associated with exfoliation syndrome (XFS) and exfoliation glaucoma (XFG), though recent evidence suggests it may act as a proxy for other functional variants in the locus rather than being directly causative.
Common missense variant (Arg141Leu) in LOXL1 historically associated with pseudoexfoliation syndrome; recent evidence suggests these variants may be proxies for other causative regulatory variants.
Missense variant in LOXL1 associated with pseudoexfoliation syndrome and glaucoma.
Exonic missense variant (p.Gly153Asp) in LOXL1 conferring major risk for pseudoexfoliation syndrome and secondary glaucoma.
Missense variant in LOXL1 strongly associated with pseudoexfoliation syndrome and secondary glaucoma.
Common missense variant (Arg141Leu) in LOXL1; strongly associated with exfoliation syndrome and glaucoma.