The T allele of lysyl oxidase-like 1 rs41435250 is a novel risk factor for pseudoexfoliation syndrome and pseudoexfoliation glaucoma independently and through intragenic epistatic interaction

PURPOSE: Two coding single nucleotide polymorphisms (SNPs) in lysyl oxidase-like 1 (LOXL1) are major genetic risk factors for pseudoexfoliation syndrome (XFS) and pseudoexfoliation glaucoma (XFG) in diverse populations. However, recent conflicting results suggest that the currently known disease-associated missense variants R141L and G153D are not causal and that they may be proxies for other unknown functional LOXL1 variants. The purpose of this study was to investigate the possible association of XFS/XFG with a novel LOXL1 exonic variant. METHODS: Genotypes of the synonymous coding LOXL1 SNP rs41435250 (p.A310A) were identified with direct sequencing. A case-control study was conducted with 115 unrelated Mexican patients with XFS/XFG (43 XFS/72 XFG) as well as 130 control subjects. Allele frequencies, genotype frequencies, and Hardy–Weinberg equilibrium were assessed with the HaploView software. A probable intragenic epistasis effect was assessed by comparing the frequencies of the rs41435250 alleles among a subset of 51 patients with XFS/XFG without the high-risk TT genotype at LOXL1 intronic rs2165241 and the control group. RESULTS: The T allele of the exonic SNP rs41435250 was more frequent in patients with XFS/XFG than in controls (odds ratios [95% confidence intervals]=2.0 [1.1–3.6]; p=0.01). Interestingly, the strength of association with the rs41435250 T allele was strongly increased (odds ratio [95% confidence intervals]=4.9 [2.7–9.1]; p=0.00000005) in the subgroup of subjects without the risk genotype at rs2165241. CONCLUSIONS: Our results indicate that allele T of rs41435250 is a novel risk genetic factor for XFS/XFG development in our population and points toward the possibility of a LOXL1 intragenic epistatic effect between rs41435250 and rs2165241. Functional studies are needed to investigate if the synonymous p.A310A mutation could affect messenger ribonucleic acid stability and thus LOXL1 enzymatic activity.