Reclassification of PAPSS2 Missense Variants in Turkish Patients with Brachyolmia Type 4: Multi-Modal Computational and Structural Biology Evidence for APS-Kinase Domain Dysfunction.

Background and Objectives: PAPSS2 loss-of-function variants cause autosomal recessive brachyolmia type 4 with skeletal dysplasia. Despite over 90 documented cases, molecular characterization remains incomplete, with many variants classified as uncertain significance (VUS). Materials and Methods: We performed integrated multi-modal in silico analysis of two novel and rare homozygous missense variants [c.227T>A p.(Leu76Gln) and c.143C>G p.(Thr48Arg)] identified via whole-exome sequencing in two unrelated Turkish girls. Analysis incorporated AlphaMissense (0.92, 0.96), REVEL (0.85), CADD Phred (28.8-29.1), evolutionary conservation across seven vertebrate species (100% identity), and AlphaFold2 structural modeling. Variant reclassification followed 2015 ACMG/AMP guidelines. Results: Both variants fulfilled criteria for VUS-to-Likely Pathogenic reclassification: PS3 (functional loss), PM1 (critical APS-kinase domain localization), PM2 (population rarity), and PP3 (computational consensus). Structurally, p.(Leu76Gln) disrupts hydrophobic core stability (Grantham score 113), while p.(Thr48Arg) causes active-site steric hindrance. Both probands presented with platyspondyly, short stature, and profound DHEA-sulfate depletion (3.15 and 1.79 µg/dL). Although identical variants were reported in a 14.5-year-old with PCOS-like androgen excess, our prepubertal cases (ages 5-6 years) exhibited normal androgens, suggesting PAPSS2 loss-of-function is necessary but insufficient for androgen excess. Conclusions: Multi-modal computational analysis supports likely pathogenic reclassification of these PAPSS2 variants, enabling precision genetic counseling and advancing understanding of skeletal and endocrine heterogeneity. These findings expand the PAPSS2 variant registry to over 92 cases across 18 countries.