Characterization of a Splice Variant in FLNA Associated With Periventricular Nodular Heterotopia

Periventricular nodular heterotopia (PNH) is a neuronal migration disorder caused by the failure of neurons to migrate properly to the cerebral cortex, characterized predominantly by epilepsy. Most PNH cases are associated with variants in FLNA, which is inherited in an X-linked pattern and exhibits a female predominance. Affected male patients typically experience prenatal or early postnatal lethality; only those with distal truncating or mosaic variants have been reported to survive. In this study, we aimed to characterize the clinical and genetic features of a Chinese pedigree with PNH.

Whole-exome sequencing (WES) was performed on genomic DNA isolated from the peripheral blood. Mosaicism levels were quantified using droplet digital PCR (ddPCR), transcriptomic alterations were analyzed by RNA sequencing (RNA-seq), and splicing defects were investigated via a minigene splicing assay.

WES analysis identified a novel splicing variant (NM_001110556.2: c.4599-2A > G) in the FLNA gene of the proband. Sanger sequencing revealed a double peak at the same site in her father. Droplet digital PCR confirmed paternal somatic mosaicism, with variant allele frequencies of 65.98% in the blood, 60.38% in the sperm, and 28.95% in the buccal mucosa. RNA-seq and minigene assays detected an aberrant transcript containing a 10 bp deletion at the 5' end of exon 28. The minigene assay further revealed 2 mutant transcripts: one with the same 10 bp deletion and another with complete skipping of exon 28.

This study expands the phenotypic and genetics spectrum of PNH and demonstrates a dual PNH phenotype with a bi-transcript mechanism. It also provides clinical evidence of mosaic inheritance and tissue-specific mosaicism, offering valuable implications for genetic counseling and prenatal diagnosis.