Early-onset SLC7A9-related cystinuria presenting as a giant bladder stone in a 29-month-old boy: a case report and family genetic analysis

Cystinuria is an inherited disorder of cystine and dibasic amino acid transport caused by pathogenic variants in SLC3A1 or SLC7A9. Symptomatic disease in early childhood, particularly with a giant bladder stone, is rare. A 29-month-old Korean boy presented with intermittent straining during urination and urinary particulate material since 12 months of age. Imaging revealed a solitary 3.7-cm bladder stone, bilateral upper urinary tract dilatation and perfusion abnormalities, and bladder-wall thickening. Stone analysis after surgical removal detected cystine, calcium, and uric acid. Urinary amino acid analysis showed marked elevations of cystine, ornithine, lysine, and arginine, confirming cystinuria. Whole-genome sequencing identified compound heterozygous SLC7A9 variants: a paternally inherited deletion involving the SLC7A9 locus at 19q13.11 and a maternally inherited c.225C>T (p.Leu75=) variant known to cause aberrant splicing. Urine alkalinization and cystine-binding thiol therapy were initiated. Nevertheless, a recurrent bladder stone and a prostatic urethral stone developed within 2 months, requiring treatment intensification. Family screening demonstrated variable dibasic aminoaciduria among heterozygous relatives. Cystinuria should be considered in young children with bladder stones or persistent voiding symptoms. Early stone analysis, quantitative urinary amino acid testing, genomic evaluation, and close biochemical and imaging surveillance are essential for diagnosis and management.