Identification of Rare LRP5 Variants in a Cohort of Males with Impaired Bone Mass

Abstract

Osteoporosis is the most common bone disease characterized by reduced bone mass and increased bone fragility. Genetic contribution is one of the main causes of primary osteoporosis; therefore, both genders are affected by this skeletal disorder. Nonetheless, osteoporosis in men has received little attention, thus being underestimated and undertreated. The aim of this study was to identify novel genetic variants in a cohort of 128 males with idiopathic low bone mass using a next-generation sequencing (NGS) panel including genes whose mutations could result in reduced bone mineral density (BMD). Genetic analysis detected in eleven patients ten rare heterozygous variants within the LRP5 gene, which were categorized as VUS (variant of uncertain significance), likely pathogenic and benign variants according to American College of Medical Genetics and Genomics (ACMG) guidelines. Protein structural and Bayesian analysis performed on identified LRP5 variants pointed out p.R1036Q and p.R1135C as pathogenic, therefore suggesting the likely association of these two variants with the low bone mass phenotype. In conclusion, this study expands our understanding on the importance of a functional LRP5 protein in bone formation and highlights the necessity to sequence this gene in subjects with idiopathic low BMD.

Keywords: BMD; LRP5; NGS panel; computational study; impaired bone microstructure.

Figure 1

3D-model prediction of LRP5 repeats domains and self-analysis of repeated units. (A) Cartoon representation of β-Propeller domains I–IV with repeated units colored by localization. Residues found mutated are presented as green spheres. Sequence insertions are presented in yellow; (B) auto-alignment of β-Propeller domains highlighting the internal evolutive conservation of each unit; (C) heat-map showing the conservation score calculated by self-alignment of LRP5 protein sequence; (D) superimposition of structural units forming the β-Propeller domains I–IV.

Figure 2

Molecular dynamics simulations of LRP5. (A) Cartoon representation of the wild-type β-Propeller IV after 250 ns of simulation. Roman numbers are for different blades forming the propeller. Variants are presented as spheres. (B) The same domain harboring the p.R1036Q substitution. Secondary structure elements lost after 250 ns of simulation are colored in red. (C) Transparent surface representation showing the solvent-accessible C1135.

Figure 3

Schematic presentation of the protein structure and domain organization of LRP5.