Novel compound-heterozygous variants in PYCR1 broaden the mutation spectrum of autosomal-recessive cutis laxa

Background and Objectives: Autosomal recessive cutis laxa (ARCL) is a rare genetically heterogeneous connective tissue disorder characterized by loose, inelastic skin and variable multisystem involvement, including developmental delay and neurologic abnormalities. Pathogenic variants in PYCR1 are an established cause of ARCL, but the spectrum and functional consequences of previously unreported variants remain incompletely defined. The primary objective of this study was to determine the pathogenicity of 2 novel compound-heterozygous PYCR1 variants through segregation and functional validation. Secondary objectives were to characterize the associated neurodevelopmental phenotype and to contextualize PYCR1 expression during human neurodevelopment using public multi-omics datasets. Methods: We investigated a patient with ARCL-like features and his family using copy number variation sequencing and whole-exome sequencing. Candidate variants were validated by Sanger sequencing. Functional effects were assessed using an in vivo splicing assay for the splice-site variant and in vitro expression studies for the frameshift variant. Neuroimaging, EEG spectral analysis, and developmental single-cell multi-omics data were integrated to evaluate PYCR1-related neurodevelopmental abnormalities. Results: The study included 1 proband and available family members for segregation analysis. The proband presented with intellectual and motor developmental delay, generalized loose wrinkled skin with prominent subcutaneous veins, joint hyperlaxity, facial dysmorphism, and reduced muscle bulk. Genetic testing identified 2 previously unreported compound-heterozygous PYCR1 variants: a maternally inherited splice-site variant, c.139-1G>A, and a paternally inherited frameshift variant, c.724_725del (p.L242Afs*31). Functional studies showed that c.139-1G>A caused exon 3 skipping, whereas c.724_725del markedly reduced PYCR1 protein expression. Together, these findings provided functional evidence supporting reclassification of both variants as likely pathogenic. Brain MRI demonstrated corpus callosum abnormalities, and EEG spectral analysis showed abnormal bilateral symmetry patterns. Public multi-omics analyses demonstrated dynamic PYCR1 expression during neurodevelopment, with enrichment in early neural progenitors. Discussion: These findings expand the pathogenic variant spectrum of PYCR1 and provide functional evidence supporting the pathogenicity of 2 previously unreported variants associated with ARCL. The integrated genetic, functional, neuroimaging, electrophysiologic, and developmental multi-omics data also strengthen interpretation of the associated neurodevelopmental phenotype. This work may improve molecular diagnosis, support variant interpretation in PYCR1 -related ARCL, and inform genetic counseling for affected families.