Gulati, Ashima

Key Points The growing knowledge of single-gene causes of pediatric-onset kidney diseases necessitates a structured application of genetic testing in practice. The clinical application of a combined nephrogenetics approach for management of kidney diseases is not well described in pediatric settings. Real-world application of a kidney genetics workflow highlights clinical value and challenges to be addressed for its successful implementation. Background The expanding knowledge of identifiable genetic contributions to pediatric inherited kidney diseases, and the increasing availability of genetic testing resources necessitates a combined nephrogenetics clinical approach. Although such models are described for adults, the effect of a structured nephrogenetics workflow on children with inherited kidney disease has not been rigorously evaluated. Methods Clinical and genetic data of patients aged younger than 1–21 years over a 10-year period between 2014 and 2024 from a single-center pediatric inherited kidney disease outpatient program were evaluated. Genetic variants were classified as pathogenic/likely pathogenic and variants of uncertain significance (VUS). Patients were grouped into “informative” or “uninformative” groups based on the effect of genetic test results on disease management and outcomes. Results Of the N =356 patients evaluated for a known or suspected inherited kidney disease, N =188 received clinical genetic testing. Of these, N =147 had an “informative” genetic test affecting at least one positive clinical outcome. Patients with an “informative” genetic test mostly harbored a pathogenic/likely pathogenic variant ( N =122). An additional N =25 had a VUS reclassified as a “VUS-of-interest” affecting a positive outcome measure. Genetic test results led to change in clinical diagnosis (reverse phenotyping, 46%), informed specific diagnosis-based treatment (46%), avoided unnecessary immunosuppression (27%) or kidney biopsy (18%), and guided extrarenal evaluation (72%) in patients with an informative test. Patients with a glomerular (odds ratio [OR]=5.23; 95% confidence interval [CI], 1.96 to 13.96) or a tubular functional disease (OR=2.17; 95% CI, 1.31 to 5.59) were more likely and those with a structural kidney disease (OR=0.39; 95% CI, 0.25 to 0.60) were less likely to receive a genetic test when compared with all other disease categories combined. Conclusions This workflow integrated multidisciplinary care for children with inherited kidney disease and describes a model for actionable clinical care plans after genetic testing. Informative genetic tests were associated with positive outcomes, and notable challenges include access to combined nephrology and genetics expertise for informed testing and an effective result return including VUS interpretation.

Genetic testing in nephrology is becoming increasingly important to diagnose patients and to provide appropriate care. This is especially true for autosomal dominant polycystic kidney disease (ADPKD) because this is a common cause of kidney failure and genetically complex. In addition to the major genes, PKD1 and PKD2 , there are at least six minor loci, and phenotypic, and in some cases, genetic overlap with other cystic disorders. Targeted next-generation sequencing, a low-cost, high-throughput technique, has made routine genetic testing viable in nephrology clinics. Appropriate pre- and post-testing genetic counseling is essential to the testing process. Carefully assessing variants is also critical, with the genetic report classifying variants in accordance with American College of Medical Genetics and Genomics guidelines. However, variant of uncertain significance (VUSs) may pose a significant challenge for the ordering clinician. In ADPKD, and particularly within PKD1 , there is high allelic heterogeneity; no single variant is present in more than 2% of families. The Mayo/Polycystic Kidney Disease Foundation variant database, a research tool, is the best current database of PKD1 and PKD2 variants containing over 2300 variants identified in individuals with polycystic kidney disease, but novel variants are often identified. In patients with a high pretest probability of ADPKD on the basis of clinical criteria, but no finding of a pathogenic (P) or likely pathogenic (LP) variant in a cystic kidney gene, additional evaluation of cystic gene VUS can be helpful. In this case-based review, we propose an algorithm for the assessment of such variants in a clinical setting and show how some can be reassigned to a diagnostic grouping. When assessing the relevance of a VUS, we consider both patient/family-specific and allele-related factors using population and variant databases and available prediction tools, as well as genetic expertise. This analysis plus further family studies can aid in making a genetic diagnosis.

Significance Statement Dominantly inherited polycystic kidney and liver phenotypes occur when epithelial cells in these organs have reduction of polycystin-1 functional dosage. In a cohort of genetically unresolved polycystic liver and kidney disease, the authors identified heterozygous loss of function mutations in ALG9 . ALG9 encodes an endoplasmic reticulum enzyme that builds N -glycans, and the authors show that Alg9 inactivation results in impaired polycystin-1 maturation. Using a novel ‘genotype-first’ approach to ascertain individuals based strictly on their ALG9 genotype from a large cohort of exome-sequenced individuals, the authors find that 7/8 (88%) of ALG9 mutation carriers over age 50 have multiple kidney cysts. Together, these findings identify ALG9 as a novel human polycystic kidney and liver disease gene and support the utility of a genotype-driven approach to candidate disease gene validation and genotype-phenotype correlation. Background Mutations in PKD1 or PKD2 cause typical autosomal dominant polycystic kidney disease (ADPKD), the most common monogenic kidney disease. Dominantly inherited polycystic kidney and liver diseases on the ADPKD spectrum are also caused by mutations in at least six other genes required for protein biogenesis in the endoplasmic reticulum, the loss of which results in defective production of the PKD1 gene product, the membrane protein polycystin-1 (PC1). Methods We used whole-exome sequencing in a cohort of 122 patients with genetically unresolved clinical diagnosis of ADPKD or polycystic liver disease to identify a candidate gene, ALG9 , and in vitro cell-based assays of PC1 protein maturation to functionally validate it. For further validation, we identified carriers of ALG9 loss-of-function mutations and noncarrier matched controls in a large exome-sequenced population-based cohort and evaluated the occurrence of polycystic phenotypes in both groups. Results Two patients in the clinically defined cohort had rare loss-of-function variants in ALG9 , which encodes a protein required for addition of specific mannose molecules to the assembling N-glycan precursors in the endoplasmic reticulum lumen. In vitro assays showed that inactivation of Alg9 results in impaired maturation and defective glycosylation of PC1. Seven of the eight (88%) cases selected from the population-based cohort based on ALG9 mutation carrier state who had abdominal imaging after age 50; seven (88%) had at least four kidney cysts, compared with none in matched controls without ALG9 mutations. Conclusions ALG9 is a novel disease gene in the genetically heterogeneous ADPKD spectrum. This study supports the utility of phenotype characterization in genetically-defined cohorts to validate novel disease genes, and provide much-needed genotype-phenotype correlations.