Structural Modelling and Clinical Interpretation of CDKN1B and CDKN2C Variants in Patients with MEN-like Phenotypes: A Case Series

BACKGROUND: Multiple endocrine neoplasia (MEN) syndromes involve tumors in multiple endocrine organs. Distinguishing MEN1 from rarer MEN-like syndromes, including MEN4 caused by pathogenic germline CDKN1B variants, can be challenging. METHODS: We describe four individuals from two families, integrating clinical, biochemical and imaging findings with germline whole-exome sequencing, evolutionary conservation, in silico variant-effect prediction, structural modeling and molecular dynamics. Tumor tissue was unavailable for somatic sequencing or loss-of-heterozygosity analysis. RESULTS: Proband 1, initially suspected of MEN1 because of a nonfunctioning pituitary microadenoma, bilateral adrenal hyperplasia and primary hyperparathyroidism, carried a pathogenic germline CDKN1B frameshift variant, p.Lys96GlnfsTer29. Proband 2 carried the CDKN2C p.Leu107Val variant, classified as a variant of uncertain significance, and had hyperthyroidism, primary hyperaldosteronism, nephrolithiasis, primary hyperparathyroidism, a nonfunctioning pituitary microadenoma and a pancreatic mucinous cystic neoplasm. The variants showed distinct predicted mechanisms. The CDKN1B frameshift preserves the kinase-inhibitory domain but removes the C-terminal regulatory region of p27Kip1 and is predicted to trigger nonsense-mediated decay. In contrast, CDKN2C Leu107 is evolutionarily invariant and buried within the hydrophobic core of ankyrin repeat 4; substitution by valine reduced local hydrophobic packing, consistent with partial destabilization rather than protein loss. The two variant-positive sons of Proband 2 were asymptomatic, and no variant-positive individual carried a MEN1 mutation. CONCLUSIONS: These findings support CDKN1B testing in MEN1-negative patients with MEN features and highlight CDKN2C as a candidate contributor to MEN-like phenotypes. Integrated clinical, genetic, conservation and structural data may support future re-evaluation of p.Leu107Val while preserving its current VUS classification.