Novel Compound Heterozygous Variants of ETHE1 Causing Ethylmalonic Encephalopathy in a Chinese Patient: A Case Report

Abstract

Ethylmalonic encephalopathy (EE) is a very rare autosomal recessive metabolic disorder that primarily affects children. Less than one hundred EE patients have been diagnosed worldwide. The clinical manifestations include chronic diarrhea, petechiae, orthostatic acrocyanosis, psychomotor delay and regression, seizures, and hypotonia. The ETHE1 gene has been shown to be associated with EE, and genetic sequencing provides concrete evidence for diagnosis. To date, only 37 variants of ETHE1 have been reported as disease-causing in EE patients. We identified two novel ETHE1 variants, i.e., c.595+1G>T at the canonical splice site and the missense variant c.586G>C (p. D196H), in a 3-year-old Chinese boy with EE. The patient had mild symptoms with only chronic diarrhea. The typical symptoms, including spontaneous petechiae, acrocyanosis, and hypotonia, were all absent. Herein, we report on the clinical, biochemical, and genetic findings of our patient and review the phenotypes and genotypes of all patients with EE caused by ETHE1 variants with available information. This study supports the early assessment and diagnosis of EE.

Keywords: ETHE1; chronic diarrhea; elevated ethylmalonic acid; ethylmalonic encephalopathy; genetic sequencing.

FIGURE 1

(a) Results based on the Gesell Developmental Schedules. Chronological age is 29 months. Developmental quotient<75 indicates developmental delay. (b) Brain MRI. The red arrow indicates shadows in the temporal horn of the left lateral ventricle. (c) Petechiae on the skin caused by falling appeared on the patient.

FIGURE 2

Whole-exome sequencing and Sanger sequencing results. (a) Two variants of ETHE1, c.586G>C and c.595+1G>T, were identified. (b) Sanger sequencing of ETHE1 performed to verify the variants in the proband. Sanger sequencing confirmed that the c.595+1G>T variant was inherited from the father and that c.586G>C (p. D196H) was of maternal origin. (c) Multiple alignment of the ETHE1 protein sequence across several species. Variant site Asp196 is labeled by a red circle. * in the last row indicates “highly conserved.” (d) Nineteen missense variants, 8 insertions/deletions, 5 splicing variants and 1 variant in the noncoding region are labeled in blue (two variants leading to p. M1?). Our case shows c.586G>C (p. D196H) in exon 5 and c.595+1G>T at the canonical splicing site (red). The upper panel is the ETHE1 protein sequence (exon n indicates the exon n-encoding region). The bottom panel shows the ETHE1 gene sequence, including the exons, introns, and noncoding regions.

FIGURE 3

Molecular model of the human ETHE1 protein. (a) The active form of the ETHE1 protein is a dimer, including chains A and B. α-helices and β-sheets are labeled in light blue and cornflower blue, respectively. The active site (catalytic histidine cluster) is the iron-binding region. The residue affected in the missense variant, Asp196, is shown in red. (b) Interactions between Asp196 and surrounding residues. Yellow lines show interactions between labeled residues in ETHE1. (c) Wild-type Asp196 and Phe200. (d) Mutant His196 and Phe200. Powerful repulsions between two residues are labeled in the black square. Three-dimensional structures were generated based on the data from Pettinati et al. (2015) by the UCSF Chimera (Pettersen et al., 2004).