High detection rate for disease-causing variants in a cohort of 30 Iranian pediatric steroid resistant nephrotic syndrome cases

Abstract

Background: Steroid resistant nephrotic syndrome (SRNS) represents a significant renal disease burden in childhood and adolescence. In contrast to steroid sensitive nephrotic syndrome (SSNS), renal outcomes are significantly poorer in SRNS. Over the past decade, extensive genetic heterogeneity has become evident while disease-causing variants are still only identified in 30% of cases in previously reported studies with proportion and type of variants identified differing depending on the age of onset and ethnical background of probands. A genetic diagnosis however can have implications regarding clinical management, including kidney transplantation, extrarenal disease manifestations, and, in some cases, even causal therapy. Genetic diagnostics therefore play an important role for the clinical care of SRNS affected individuals.

Methodology and results: Here, we performed NPHS2 Sanger sequencing and subsequent exome sequencing in 30 consanguineous Iranian families with a child affected by SRNS with a mean age of onset of 16 months. We identified disease-causing variants and one variant of uncertain significance in 22 families (73%), including variants in NPHS1 (30%), followed by NPHS2 (20%), WT1 (7%) as well as in NUP205, COQ6, ARHGDIA, SGPL1, and NPHP1 in single cases. Eight of these variants have not previously been reported as disease-causing, including four NPHS1 variants and one variant in NPHS2, ARHGDIA, SGPL1, and NPHP1 each.

Conclusion: In line with previous studies in non-Iranian subjects, we most frequently identified disease-causing variants in NPHS1 and NPHS2. While Sanger sequencing of NPHS2 can be considered as first diagnostic step in non-congenital cases, the genetic heterogeneity underlying SRNS renders next-generation sequencing based diagnostics as the most efficient genetic screening method. In accordance with the mainly autosomal recessive inheritance pattern, diagnostic yield can be significantly higher in consanguineous than in outbred populations.

Keywords: ARHGDIA; COQ6; Iran; NUP205; SGPL1; SRNS; nephrotic syndrome.

Figure 1

Summary of genetic findings. (A) Gene-specific distribution of identified disease-causing variants and one variant of uncertain significance; unsolved cases are shown in gray. (B) Variant type distribution. Alleles not previously reported are marked as novel alleles.

Figure 2

Location of disease-causing variants in COQ6, NUP205, ARHGDIA, and SGPL1 on protein level. (A) COQ6, (B) NUP205, (C) ARHDIA, and (D) SGPL1 variants. Previously reported variants are shown in blue, variants first reported in this publication marked in red.

Figure 3

Podocyte subcellular localization of proteins encoded for by genes found to carry disease alleles in this study. While WT1 functions as a transcription factor in the nucleus, NUP205 functions within the nuclear pore complex, enabling transport between the nucleus and the cytoplasm. SGPL1 represents an endoplasmic reticulum based enzyme catalyzing sphingolipid breakdown resulting in cleavage of the lipid-signaling molecule sphingosine-1-phosphate. COQ6 represents a flavin-dependent monooxygenase essential for biosynthesis of coenzyme Q10 which serves as a redox carrier in the mitochondrial respiratory chain as well as an antioxidant protecting cells from reactive oxygen damage. ARHGDIA sequesters Rho-GTPases in an inactive state in the cytosol, controlling RhoA, Rac1, and Cdc42 levels and influencing actin dynamics. NPHS1 and NPHS2 localize to the podocyte foot process membrane, enabling proper function of the glomerular slit diaphragm.