Prevalence of hereditary tubulointerstitial kidney diseases in the German Chronic Kidney Disease study

Popp B, Ekici AB, Knaup K, Schneider K, Uebe S, Park J, Bafna V, Meiselbach H, Eckardt KU, Schiffer M, Wiesmann da Silva Reis A, Kraus C, Wiesener M (2022)

Publication Type: Journal article

Publication year: 2022

Journal

European Journal of Human Genetics Nature Publishing Group: Open Access Hybrid Model Option B

DOI: 10.1038/s41431-022-01177-9

Abstract

Hereditary chronic kidney disease (CKD) appears to be more frequent than the clinical perception. Exome sequencing (ES) studies in CKD cohorts could identify pathogenic variants in similar to 10% of individuals. Tubulointerstitial kidney diseases, showing no typical clinical/histologic finding but tubulointerstitial fibrosis, are particularly difficult to diagnose. We used a targeted panel (29 genes) and MUC1-SNaPshot to sequence 271 DNAs, selected in defined disease entities and age cutoffs from 5217 individuals in the German Chronic Kidney Disease cohort. We identified 33 pathogenic variants. Of these 27 (81.8%) were in COL4A3/4/5, the largest group being 15 COL4A5 variants with nine unrelated individuals carrying c.1871G>A, p.(Gly624Asp). We found three cysteine variants in UMOD, a novel missense and a novel splice variant in HNF1B and the homoplastic MTTF variant m.616T>C. Copy-number analysis identified a heterozygous COL4A5 deletion, and a HNF1B duplication/deletion, respectively. Overall, pathogenic variants were present in 12.5% (34/271) and variants of unknown significance in 9.6% (26/271) of selected individuals. Bioinformatic predictions paired with gold standard diagnostics for MUC1 (SNaPshot) could not identify the typical cytosine duplication ("c.428dupC") in any individual, implying that ADTKD-MUC1 is rare. Our study shows that >10% of selected individuals carry disease-causing variants in genes partly associated with tubulointerstitial kidney diseases. COL4A3/4/5 genes constitute the largest fraction, implying they are regularly overlooked using clinical Alport syndrome criteria and displaying the existence of phenocopies. We identified variants easily missed by some ES pipelines. The clinical filtering criteria applied enriched for an underlying genetic disorder.

Authors with CRIS profile

Bernt Popp Institute of Human Genetics Arif Bülent Ekici Institute of Human Genetics Karl Knaup Department of Medicine 4 – Nephrology and Hypertension Steffen Uebe Institute of Human Genetics Heike Meiselbach Department of Medicine 4 – Nephrology and Hypertension Kai-Uwe Eckardt Department of Medicine 4 – Nephrology and Hypertension Mario Schiffer Lehrstuhl für Innere Medizin IV André Wiesmann da Silva Reis Lehrstuhl für Humangenetik Cornelia Kraus Institute of Human Genetics Michael Wiesener Professur für Innere Medizin (Nephrologie)

Involved external institutions

University of California, San Diego US United States (USA) (US)

How to cite

APA:

Popp, B., Ekici, A.B., Knaup, K., Schneider, K., Uebe, S., Park, J.,... Wiesener, M. (2022). Prevalence of hereditary tubulointerstitial kidney diseases in the German Chronic Kidney Disease study. European Journal of Human Genetics. https://doi.org/10.1038/s41431-022-01177-9

MLA:

Popp, Bernt, et al. "Prevalence of hereditary tubulointerstitial kidney diseases in the German Chronic Kidney Disease study." European Journal of Human Genetics (2022).

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