Rare heterozygous variants in paediatric steroid resistant nephrotic syndrome – a population-based analysis of their significance

• Published in: Scientific reports Vol. 14; no. 1; pp. 18568 - 11
• Main Authors: Platt, C. J., Bierzynska, A., Ding, W., Saleem, S. A., Koziell, A., Saleem, M. A.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group 10.08.2024; Nature Publishing Group UK; Nature Portfolio
• Subjects: Diagnosis; Gene frequency; Genes; Genetic analysis; Genetic screening; Genetics; Kidney diseases; Nephrotic syndrome; Pathogenicity; Pathogens; Patients; Pediatrics; Population genetics; Statistical analysis; Steroids; Whole genome sequencing
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-024-68837-2

Abstract Genetic testing in nephrotic syndrome may identify heterozygous predicted-pathogenic variants (HPPVs) in autosomal recessive (AR) genes that are known to cause disease in the homozygous or compound heterozygous state. In such cases, it can be difficult to define the variant’s true significance and questions remain about whether a second pathogenic variant has been missed during analysis or whether the variant is an incidental finding. There are now known to be over 70 genes associated with nephrotic syndrome, the majority inherited as an AR trait. Knowledge of whether such HPPVs occur with equal frequency in patients compared to the general population would assist interpretation of their significance. Exome sequencing was performed on 187 Steroid-Resistant Nephrotic Syndrome (SRNS) paediatric patients recruited to a UK rare disease registry plus originating from clinics at Evelina, London. 59 AR podocytopathy linked genes were analysed in each patient and a list of HPPVs created. We compared the frequency of detected HPPVs with a ‘control’ population from the gnomAD database containing exome data from approximately 50,000 individuals. A bespoke filtering process was used for both patients and controls to predict ‘likely pathogenicity’ of variants. In total 130 Caucasian SRNS patients were screened across 59 AR genes and 201 rare heterozygous variants were identified. 17/201 (8.5%) were assigned as ‘likely pathogenic’ (HPPV) using our bespoke filtering method. Comparing each gene in turn, for SRNS patients with a confirmed genetic diagnosis, in 57 of the 59 genes we found no statistically significant difference in the frequency of these HPPVs between patients and controls (In genes ARHGDIA and TP53RK , we identified a significantly higher number of HPPVs in the control population compared with the patients when filtering was performed with ‘high stringency’ settings only). In the SRNS patients without a genetics diagnosis confirmed, there was no statistically significant difference identified in any gene between patient and control. In children with SRNS, we propose that identification of HPPV in AR podocytopathy linked genes is not necessarily representative of pathogenicity, given that the frequency is similar to that seen in controls for the majority. Whilst this may not exclude the presence of genetic kidney disease, this type of heterozygous variant is unlikely to be causal and each result must be interpreted in its clinical context.