Molecular Pathology Insights into ALS Susceptibility: Exploratory Association of CYP46A1 rs754203 in Brazilian Case–Control Study

Background/Objectives: Amyotrophic lateral sclerosis (ALS) is a complex neurodegenerative disease, and alterations in cholesterol metabolism may contribute to motor neuron vulnerability. This study investigated CYP7B1 rs121908613 and CYP46A1 rs754203 in relation to ALS susceptibility in a Brazilian case–control study. Methods: The study included 115 patients with ALS and 115 controls. Both variants were genotyped using TaqMan® allelic discrimination assays. Genetic association analyses were performed under codominant, dominant, recessive, and overdominant inheritance models using Firth penalized logistic regression, with p-values adjusted for multiple testing using the Holm procedure. Sex-stratified analyses and a formal genotype-by-sex interaction test were also performed. Survival and in silico analyses were conducted as complementary exploratory analyses. Results: Genotyping of CYP7B1 rs121908613 revealed no allelic variability. Given the extremely low frequency of this variant in the general population, this finding should be interpreted as a negative result. For CYP46A1 rs754203, the overdominant model showed a nominal association with ALS (OR = 1.94, 95% CI: 1.14–3.34; nominal p = 0.015), but this association did not remain statistically significant after Holm correction (adjusted p = 0.148). In the male subgroup, the overdominant model remained significant after Holm correction (adjusted p = 0.046). However, the genotype-by-sex interaction test was not statistically significant (OR = 2.46, 95% CI: 0.84–7.32; p = 0.101), indicating insufficient evidence to support a sex-specific genetic effect. Hardy–Weinberg equilibrium (HWE) analysis revealed that the ALS group was deviated, therefore associations should be interpreted with caution. (exact p = 0.012). Survival analyses showed no statistically significant differences among CYP46A1 rs754203 genotypes. In silico analyses identified sequence-dependent structural and regulatory predictions that require experimental validation. Conclusions: CYP46A1 rs754203 showed exploratory association signals, including an overdominant effect in the male subgroup after multiple-testing correction. Additionally, the absence of a statistically significant genotype-by-sex interaction did not support sex-dependent evidence. These findings should be considered preliminary and hypothesis-generating and require replication in larger and well-characterized cohorts, together with experimental functional validation.