Nanopore-based haplotype-resolved X chromosome inactivation for severity assessment in X-linked disorders: An AIFM1 study with a mosaic PDHA1 carrier.

X chromosome inactivation (XCI) modifies disease severity in females with X-linked variants, but clinically applicable high-resolution assessment remains limited. We report a family with an apoptosis-inducing factor, mitochondria-associated 1 (AIFM1) variant that shows marked intrafamilial phenotypic variability and evaluated whether haplotype-resolved nanopore sequencing can inform clinical interpretation. Targeted long-read sequencing was performed in a severely affected hemizygous male, his asymptomatic heterozygous mother, and a severely affected heterozygous sibling. In the hemizygous male, the sample served as a technical control, with all reads mapping to a single haplotype, consistent with a hemizygous X chromosome. Among heterozygous carriers with the identical variant (c.506C>T [p.Pro169Leu]), XCI correlated with severity: the affected sibling showed 84% skew favoring activation of the pathogenic allele, whereas the mother showed preferential inactivation (20%). This family-based study shows that using nanopore sequencing for haplotype-resolved XCI analysis may provide a practical framework for selected X-linked disorders with variable expressivity.