A recurring NFS1 pathogenic variant causes a mitochondrial disorder with variable intra-familial patient outcomes

Abstract

Iron‑sulfur clusters (FeSCs) are vital components of a variety of essential proteins, most prominently within mitochondrial respiratory chain complexes I-III; Fe-S assembly and distribution is performed via multi-step pathways. Variants affecting several proteins in these pathways have been described in genetic disorders, including severe mitochondrial disease. Here we describe a Christian Arab kindred with two infants that died due to mitochondrial disorder involving Fe-S containing respiratory chain complexes and a third sibling who survived the initial crisis. A homozygous missense variant in NFS1: c.215G>A; p.Arg72Gln was detected by whole exome sequencing. The NFS1 gene encodes a cysteine desulfurase, which, in complex with ISD11 and ACP, initiates the first step of Fe-S formation. Arginine at position 72 plays a role in NFS1-ISD11 complex formation; therefore, its substitution with glutamine is expected to affect complex stability and function. Interestingly, this is the only pathogenic variant ever reported in the NFS1 gene, previously described once in an Old Order Mennonite family presenting a similar phenotype with intra-familial variability in patient outcomes. Analysis of datasets from both populations did not show a common haplotype, suggesting this variant is a recurrent de novo variant. Our report of the second case of NFS1-related mitochondrial disease corroborates the pathogenicity of this recurring variant and implicates it as a hot-spot variant. While the genetic resolution allows for prenatal diagnosis for the family, it also raises critical clinical questions regarding follow-up and possible treatment options of severely affected and healthy homozygous individuals with mitochondrial co-factor therapy or cysteine supplementation.

Keywords: Hot-spot variant; Intra-familial variability; Iron‑sulfur clusters; Mitochondrial disease; NFS1.

Fig. 1

The NFS1 c.215G>A; p.Arg72Gln variant in a family with a mitochondrial disorder. (A) The cysteine desulfurase NFS1 works in complex with ISD11 and ACP and initiates the first step of iron-sulfur cluster (FeSC) formation. NFS1 catalyzes cysteine to provide the inorganic sulfur, which binds to cysteine ligands supplied by the ISCU scaffold protein. The FeSCs are then transferred to recepient proteins; (B) Family pedigree and segregation of the NFS1 variant; (C) Sanger sequencing chromatograms displaying the c.215G>A variant in homozygous (left) and heterozygous (right) states; (D) schematic representation of the NFS1 protein. The p.Arg72Gln variant is highlighted; (E) Model of the NFS1 protein within the heterohexameric complex with ACP, ISD11 and ISCU. Arg72 of NFS1 interacts with Tyr31 of ISD11, so that the substitution of Arg with Gln at this position is predicted to hinder complex formation and proper function.

Fig. 2

Urine organic acids analysis. Typical urine organic acids profile for Patient II-2 using gas chromatography–mass spectrometry of affected individual, (A) during acute crises showing increased excretion of lactic acid, 3-hydroxybutyric acid, 3-hydroxyisovaleric acid, aetoacetic acid, 3-methylglutaconic acid, adipic acid, 3-Hydroxy-3 methylglutaric acid, suberic acid and 3-hydroxysebasic acid, and (B) during an intercrisis interval urinary organic acids could be almost normal. IS1, internal standard 1 (2-phenylbutyric acid); IS2, internal standard 2 (tropic acid); IS3, internal standard 3 (margaric acid).

Fig. 3

Mitochondrial respiratory chain activities in muscle and liver. Enzymatic activities were measured in Patient II-2 (A,C) quadriceps muscle mitochondria (CI-CV), and in Patient II-2 (B,D) liver homogenate (CI-CIV). Absolute activities in patient (Pt) and controls (Cont) ± SD are depicted in A and D and ratios to CIV in C and D.