Rare Biallelic CTU2 Variants in an Individual With CAKUT: Clinical Characterization and Minigene Splicing Analysis

Congenital anomalies of the kidney and urinary tract (CAKUT) are clinically heterogeneous and remain genetically unexplained in many patients. Biallelic variants in CTU2 have been reported in DREAM-PL syndrome, a severe multisystem disorder characterized by dysmorphic facies, renal agenesis, ambiguous genitalia, microcephaly, polydactyly, and lissencephaly. However, to date, there have been no reports on the involvement of CTU2 in CAKUT.

Exome sequencing (ES) was performed in 200 patients with CAKUT. Candidate CTU2 variants were validated by Sanger sequencing, and segregation analysis was conducted in available family members. Variant rarity was assessed using public population databases and an in-house cohort of 200 ethnically matched kidney disease-free controls. Potential functional effects were evaluated using in silico prediction tools and minigene splicing assays.

The affected individual, who had a diagnosis of CAKUT, presented with bilateral hydronephrosis, chronic kidney disease, and focal segmental glomerulosclerosis. Genetic analysis revealed compound heterozygous CTU2 variants, NM_001012759.3: c.913C>T, p.(Arg305Trp), and c.1492C>G, p.(Gln498Glu), which were inherited from his father and mother, respectively. Both variants were rare and had not been previously reported in CTU2-related disease. In silico splicing analyses suggested that both variants may alter putative exonic splicing enhancers (ESE) motifs. Minigene splicing assays showed that c.913C>T altered pre-mRNA splicing by increasing exon 9 skipping, whereas c.1492C>G had no statistically significant effect on exon inclusion.

This study identifies two rare CTU2 variants in an individual with renal-predominant CAKUT and provides in vitro evidence that c.913C>T partially alters splicing. While these findings do not establish CTU2 as a definitive cause of isolated CAKUT, they support further case collection and kidney-relevant functional studies of CTU2 in renal developmental phenotypes.