Extrapolation of Variant Phase in Mitochondrial Short-Chain Enoyl-CoA Hydratase (ECHS1) Deficiency

Abstract

Loss-of-function and hypomorphic ECHS1 variants are associated with mitochondrial short-chain enoyl-CoA hydratase deficiency, an inborn error of valine metabolism. We report an 8-year-old boy with developmental delay, ataxia, hemiplegia, and hearing loss with abnormalities in the basal ganglia. Biochemical studies were essentially normal except for a persistent mildly elevated CSF alanine. This patient demonstrates an intermediate phenotype between a Leigh-like, early-onset presentation and paroxysmal exercise-induced dyskinesia. Two novel ECHS1 variants (c.79T>G; p.Phe27Val and c.789_790del; p.Phe263fs) were identified via exome sequencing in the proband, and pathogenicity was confirmed by enzyme assay performed on patient fibroblasts. Neither of the ECHS1 variants detected in the child were present in the mother. However, due to nearby polymorphisms, it was possible to determine that p.Phe263fs occurred de novo on the maternal chromosome and that p.Phe27Val likely derived from the paternal chromosome. Nearby polymorphisms can help set phase of variants when only a single parent is available for testing or when an identified variant occurs de novo.

Keywords: ECHS1; Exome interpretation; Mitochondrial short-chain enoyl-CoA hydratase deficiency; Phase determination.

Fig. 1

Mutational spectrum of ECHS1. (a) A gene diagram illustrating the 32 previously identified pathogenic ECHS1 variants (28 missense, 2 splicing, 1 frameshift, and 1 nonsense) as well as the novel pathogenic variants detected in this patient (in bold). (b) Protein diagram of pathogenic amino acid alterations (changes associated with splicing not shown, and the patient’s amino acid changes are in bold). Protein diagram illustrates that p.Phe27Val affects the first amino acid following the mitochondrial peptide signal and that Phe27 is predicted to be recognized and cleaved by the Icp55/XPNPEP3 aminopeptidase in order to stabilize the N-terminus of ECHS1 in mitochondria

Fig. 2

Next-generation sequencing (NGS) suggests that the ECHS1 variants identified in the patient are in trans. (a) The patient’s Caucasian mother is homozygous for the common exon 7 polymorphism rs10745295 (99.5% allele frequency in Caucasians), while the Afro-Caucasian patient is heterozygous for the polymorphism (66.6% allele frequency in Africans). (b) NGS reads demonstrate that the rs10745295 polymorphism is in cis with p.Phe263fs (example read in red box). Thus, p.Phe263fs occurred de novo on the maternal chromosome. (c) NGS data demonstrate that p.Phe27Val (0.0924% allele frequency in Africans) is in trans from the exon 1 rs10466126 polymorphism (example read in red box). (d) Both the patient’s mother and the patient are heterozygous for the rs10466126 polymorphism (allele frequency of 72.9% in non-Finnish Europeans but only 30.9% in Africans), suggesting that p.Phe27Val is likely paternally inherited and in trans from p.Phe263fs