Neonatal Niemann–Pick type C: a case series integrating clinical findings, structural modeling and ACMG-based variant interpretation

Abstract Background Niemann–Pick disease type C (NPC) is a rare autosomal recessive lysosomal storage disorder that can present in the neonatal period with cholestasis and hepatosplenomegaly, making early diagnosis challenging. We report a case series of three neonates evaluated for NPC in the neonatal period -two with a molecularly confirmed diagnosis and one in whom the clinical and biochemical findings were highly suggestive of NPC but molecular confirmation is pending -and use in silico structural modeling as an exploratory adjunct to support American College of Medical Genetics and Genomics (ACMG) interpretation of NPC1 and NPC2 variants. Clinical, biochemical, imaging, and histopathologic data were collected from three neonates born to consanguineous parents who presented with cholestatic jaundice. Lysosphingolipid profiling, including lysosphingomyelin-509 (Lyso-SM-509), was performed as a biochemical screen. Molecular diagnosis was based on clinical exome sequencing, allowing evaluation of a broad panel of cholestasis- and metabolic-disease genes prior to focused analysis of NPC1 and NPC2, with variant annotation and ACMG/AMP classification. Homology models based on AlphaFold and the NPC1 – NPC2 co-crystal structure were generated, complemented by DeepTMHMM transmembrane topology prediction and protein expression analysis using the Human Protein Atlas. Results All patients showed elevated Lyso-SM-509 and hepatomegaly; two had generalized hypotonia. We identified one truncating NPC1 variant (c.852del; p.Phe284Leufs*26), one in-frame NPC2 deletion (c.420_422del; p.Cys140del), and one novel NPC1 missense variant (c.2693A>C; p.Asp898Ala), all in the homozygous state. Structural modeling indicated loss of sterol-sensing and transmembrane architecture for p.Phe284Leufs*26, disruption of a stabilizing disulfide bridge and the NPC1 interface for p.Cys140del, and allosteric perturbation of the C-terminal domain for p.Asp898Ala. Under ACMG/AMP criteria, the variants were classified as pathogenic (NPC1 p.Phe284Leufs*26), likely pathogenic (NPC2 p.Cys140del), and of uncertain significance (NPC1 p.Asp898Ala), the last of these remaining unresolved by calibrated computational predictors. Case 3 is therefore reported as clinically and biochemically highly suggestive of NPC, carrying a homozygous NPC1 variant of uncertain significance, pending functional confirmation. Conclusions In these three neonates - two with molecularly confirmed NPC and one with a homozygous NPC1 variant of uncertain significance pending functional confirmation - integrating lysosphingolipid biomarkers with structure-based in silico analyses provided a supportive, hypothesis-generating adjunct to ACMG/AMP interpretation of NPC1 and NPC2 variants. In silico modeling does not replace functional assays and should be regarded as an exploratory tool to prioritize variants for confirmatory studies, particularly when functional testing is unavailable in the neonatal period.