Rare LOXL1 variants associated with exfoliation syndrome and secondary glaucoma risk in US cohorts

Purpose: Common LOXL1 protein-altering variants are significant genetic risk factors for exfoliation syndrome (XFS) and the related secondary glaucoma (XFG). A rare LOXL1 missense allele was associated with protective effects in a Japanese cohort, suggesting that other rare alleles may also exhibit protective effects. The goal of this study is to assess the contributions of rare LOXL1 variants to XFS/XFG risk in cases and controls from the United States (US). Methods: LOXL1 rare variants (minor allele frequency (MAF) < 1%) were identified from Human exome BeadArray (Illumina) data for 1118 XFS/XFG cases and 3661 controls (Mass Eye and Ear (MEE) cohort) and from exome sequence data for 284 cases and 37,499 controls in All of Us (AoU) The distribution of rare variants, haplotypes, and diplotypes was examined using Fisher exact test. Results: Four rare LOXL1 missense alleles, more common in controls, were identified in MEE, P= 7.6E-4), and 456 variants identified in AoU were found only in controls (P=0.045). The rare protective alleles were preferentially located (P= 5.8E-45) in a LOXL1 intrinsic disordered region (IDR) potentially involved in LOXL1 aggregation. Haplotypes that included the rare or minor variants were more common in controls compared to cases in both MEE (Odds Ratio (OR)= 0.21 (95% Confidence interval (CI): 0.19-0.24), P=1.7E-173) and AoU (OR=0.28 (95% CI: 0.23-0.34), P=4.4E-41), and heterozygous diplotypes were also significantly associated with reduced risk overall in both MEE (OR= 0.45 (95% CI: 0.52-0.39), P= 1.7E-89) and AoU (OR=0.26 (95% CI: 0.18-0.33, P=7.6E-28). Diplotypes comprised of only homozygous genotypes were associated with increased disease risk in both MEE and AoU (OR= 4.16 (95% CI: 3.60-4.76), P= 4.2E-89 and 5.26 (95% CI: 4.12-6.73), P=1.87E-42, respectively) and excess homozygosity and decreased heterozygosity was correlated with disease risk for common LOXL1 variants across multi-ethnic populations (P=1.0E-6). Conclusions: Using exome array and exome sequence data from XFS/XFG cases and controls from the United States, we identified rare protective LOXL1 missense variants and show that the distribution of the corresponding haplotypes and diplotypes was associated with lower risk of XFS/XFG. Diplotype results also demonstrated that LOXL1 allelic heterozygosity was inversely associated, while homozygosity was associated with increased disease risk. These results suggest that LOXL1 MAF variation among populations, with corresponding variation in genotype heterozygosity and homozygosity, determines the XFS/XFG association.