A Novel Intronic Variant in FRMPD4 Disrupts Splicing: Case Report of an X-Linked Neurodevelopmental Disorder

FRMPD4, a gene on the X-chromosome, encodes a neuronal scaffold protein, and six variants in this gene have been associated with X-linked neurodevelopmental disorder. We identified a novel intronic hemizygous variant (NM_014728.3:c.1198-6C>A) in FRMPD4 in a 2-year-old male patient with moderate developmental delay inherited from his asymptomatic heterozygous mother. Minigene assays in different cell lines demonstrated that this variant led to the consistent skipping of in-frame exon 12, which encodes 30 amino acids within the FERM domain. We speculated that this splicing defect may be due to the impaired recruitment of essential splicing factor U2AF2, as this C>A intronic variant is positioned at the center of the uridine-rich polypyrimidine tract, adjacent to the 3'-splice site. Structural modeling predicted that the loss of this region would disrupt the integrity of the FERM domain. Given that FRMPD4 mediates metabotropic glutamate receptor signaling via its FERM domain, we conclude that this intronic variant is likely pathogenic.