Early-onset hereditary spastic paraplegia type 56 (SPG56): clinical-molecular correlations and functional validation of CYP2U1 variants

Hereditary spastic paraplegia type 56 (SPG56) is a rare autosomal recessive neurodegenerative disorder caused by biallelic variants in the CYP2U1 gene, which encodes a cytochrome P450 enzyme involved in fatty acid metabolism and mitochondrial function. The clinical spectrum includes progressive spasticity of the lower limbs, developmental delay or regression, cognitive impairment, and variable ophthalmological findings. Although several cases have been reported in recent years, the functional characterization of individual variants remains limited. Here we describe a male patient with early-onset SPG56 carrying two CYP2U1 missense variants, NM_183075.3:c.1376 C > T p.(Pro459Leu) and NM_183075.3:c.557G > A p.(Arg186His). Combined genomic, cellular, and in silico analyses confirmed loss of enzymatic activity and protein instability, supporting the pathogenic classification of both variants. Functional validation led to reclassification of the p.(Arg186His) variant from uncertain significance to pathogenic. Further, we link specific CYP2U1 missense changes to convergent molecular defects, thereby refining genotype–phenotype correlations. From a therapeutic perspective, we highlight the relevance of experimental interventions such as folinic acid supplementation and multimodal spasticity management, while emphasizing the future promise of gene therapy for SPG56 patients. Our findings highlight the value of integrating genomic, biochemical, and structural approaches in the diagnostic evaluation of rare neurogenetic disorders, and provide functional evidence that the identified CYP2U1 variants are damaging, consistent with the observed early-onset complex SPG56 phenotype.