BackgroundPeriventricular nodular heterotopia (PNH), associated withFLNAmutations, is a rare clinical condition potentially associated with multiple systemic conditions, including cardiac, pulmonary, skeletal, and cutaneous diseases. However, due to a paucity of information in the literature, accurate prognostic advice cannot be provided to patients with the disease.Case presentationWe report a 2-year-old female whose PNH was associated with a nonsense mutation in the q28 region of the X chromosome, in exon 31 ofFLNA(c.5159dupA). The patient is currently seizure-free and has no congenital heart disease, lung disease or skeletal or joint issues, and her development is normal.ConclusionsFLNA-associated PNH is a genetically-heterogeneous disease, and theFLNAmutation, c.5159dupA (p.Tyr1720*) is a newly identified pathogenic variant.FLNAcharacterization will help the clinical diagnosis and treatment of PNH and provide individualized genetic counseling for patients.