Phenotypic diversity of FLNA-related periventricular nodular heterotopia and cardiovascular defects associated with allelic dosage and distinct mutation types

FLNA gene defects disrupt cytoskeletal dynamics and mechanotransduction, resulting in a broad phenotypic spectrum that includes cardiovascular malformations, periventricular nodular heterotopia, skeletal abnormalities, connective tissue disorders, gastrointestinal manifestations, and neurological dysfunction. However, the relationship between distinct FLNA mutation genotypes and phenotypic variability remains incompletely defined. In particular, the pathogenic contribution of skewed X-chromosome inactivation (XCI), synonymous variants, and small deletion-induced frameshift mutations is rarely explored. To investigate genotype–phenotype correlation in FLNA-related disorders, with particular emphasis on allelic dosage effects, pathogenic synonymous mutations, and frameshift variants. Clinical and genetic data were collected from four patients across three unrelated families with suspected FLNA -associated disorders. Whole-exome sequencing was performed to identify candidate pathogenic variants, validated by Sanger sequencing. X-chromosome haplotype analysis combined with next-generation sequencing-based ultra-deep targeted RNA sequencing was applied to assess XCI status to explain marked phenotypic discordance between two related individuals carrying the same mutation. The functional impact of the synonymous mutation c.5184C>T was evaluated using an in vitro minigene splicing assay. Additionally, a literature review of FLNA mutations associated with cardiovascular and neurological abnormalities published over the past three years was performed. Three FLNA mutations were identified in four patients: (1) c.1087C>T (p. Gln363*), a truncating mutation leading to premature termination of translation; differential XCI ratios were associated with distinct phenotypic severity within one family, with higher mutant allele expression correlating with more severe manifestations. (2) c.5184C>T (p. Gly1728 =), a synonymous mutation that induced aberrant splicing with 35-bp exon 31 deletion, resulting in a truncated transcript. (3) c.666delT (p. Thr223ProfsTer19), a new frameshift mutation truncating the N-terminal actin-binding domain and predicted to trigger nonsense-mediated mRNA decay. The literature review highlighted mutation-specific effects of the ROD1 and ROD2 domains, with ROD1 variants showing a potential association with cardiovascular phenotypes that warrants validation in larger cohorts. Ultra-deep RNA sequencing was effective for assessing XCI in FLNA-related disease. Distinct mutation types across different FLNA domains may drive pathogenesis through heterogeneous mechanisms, contributing to pronounced phenotypic variability. The ROD1 domain (Ig1-15) may represent a hotspot region for cardiovascular involvement in FLNA-related disorders, although larger cohorts are needed to confirm this association. Integrating genetic, transcriptomic, and clinical data may improve diagnostic accuracy and risk stratification in affected individuals.