Synonymous BTK variant activating a non-canonical cryptic splice site in X-linked agammaglobulinemia with catastrophic CNS demyelination

X-linked agammaglobulinemia (XLA) is a rare inborn error of immunity caused by pathogenic variants in the BTK gene, characterised by a profound B cell deficiency and markedly reduced or absent antibody production, typically presenting with recurrent sinopulmonary and gastrointestinal infections. Central nervous system complications are uncommon and usually infectious. We report a preschool-aged male with near-fatal acute haemorrhagic leukoencephalopathy, a subtype of acute disseminated encephalomyelitis, who harboured a hemizygous synonymous BTK variant NM_000061.3:c.942A>G; p.(Lys314=). Despite low to moderate in silico splicing disruption predictions, RNA analysis revealed 95% aberrantly spliced BTK transcripts. Minigene assays with engineered U1 small nuclear RNAs (snRNAs) in HeLa cells demonstrated that the variant enhanced U1 snRNA binding to a cryptic GC donor splice site, thereby inhibiting the use of the authentic splice site and disrupting normal splicing. This case uncovers a novel splicing pathomechanism driven by altered U1 snRNA recognition and documents an exceptionally rare clinical presentation of XLA with important diagnostic implications. Our findings underscore that silent exonic variants, even when not creating a de novo splice site, may exert unexpected effects on splicing and should not be dismissed as benign without functional validation.