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August 2017; 3 (4) ArticleOpen Access

Functionally pathogenic EARS2 variants in vitro may not manifest a phenotype in vivo

Nathan McNeill, Alessia Nasca, Aurelio Reyes, Benjamin Lemoine, Brandi Cantarel, Adeline Vanderver, Raphael Schiffmann, Daniele Ghezzi
First published July 14, 2017, DOI: https://doi.org/10.1212/NXG.0000000000000162
Nathan McNeill
From the Baylor Research Institute (N.M., B.L., R.S.), Baylor Scott and White Health, Dallas, TX; Unit of Molecular Neurogenetics (A.N., D.G.), Foundation IRCCS Institute of Neurology “Besta,” Milan, Italy; Mitochondrial Biology Unit (A.R.), Medical Research Council, Cambridge, United Kingdom; Department of Bioinformatics (B.C.), University of Texas Southwestern Medical Center, Dallas; and Department of Neurology (A.V.), George Washington University School of Medicine, Children's National Health, DC.
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Alessia Nasca
From the Baylor Research Institute (N.M., B.L., R.S.), Baylor Scott and White Health, Dallas, TX; Unit of Molecular Neurogenetics (A.N., D.G.), Foundation IRCCS Institute of Neurology “Besta,” Milan, Italy; Mitochondrial Biology Unit (A.R.), Medical Research Council, Cambridge, United Kingdom; Department of Bioinformatics (B.C.), University of Texas Southwestern Medical Center, Dallas; and Department of Neurology (A.V.), George Washington University School of Medicine, Children's National Health, DC.
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Aurelio Reyes
From the Baylor Research Institute (N.M., B.L., R.S.), Baylor Scott and White Health, Dallas, TX; Unit of Molecular Neurogenetics (A.N., D.G.), Foundation IRCCS Institute of Neurology “Besta,” Milan, Italy; Mitochondrial Biology Unit (A.R.), Medical Research Council, Cambridge, United Kingdom; Department of Bioinformatics (B.C.), University of Texas Southwestern Medical Center, Dallas; and Department of Neurology (A.V.), George Washington University School of Medicine, Children's National Health, DC.
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Benjamin Lemoine
From the Baylor Research Institute (N.M., B.L., R.S.), Baylor Scott and White Health, Dallas, TX; Unit of Molecular Neurogenetics (A.N., D.G.), Foundation IRCCS Institute of Neurology “Besta,” Milan, Italy; Mitochondrial Biology Unit (A.R.), Medical Research Council, Cambridge, United Kingdom; Department of Bioinformatics (B.C.), University of Texas Southwestern Medical Center, Dallas; and Department of Neurology (A.V.), George Washington University School of Medicine, Children's National Health, DC.
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Brandi Cantarel
From the Baylor Research Institute (N.M., B.L., R.S.), Baylor Scott and White Health, Dallas, TX; Unit of Molecular Neurogenetics (A.N., D.G.), Foundation IRCCS Institute of Neurology “Besta,” Milan, Italy; Mitochondrial Biology Unit (A.R.), Medical Research Council, Cambridge, United Kingdom; Department of Bioinformatics (B.C.), University of Texas Southwestern Medical Center, Dallas; and Department of Neurology (A.V.), George Washington University School of Medicine, Children's National Health, DC.
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Adeline Vanderver
From the Baylor Research Institute (N.M., B.L., R.S.), Baylor Scott and White Health, Dallas, TX; Unit of Molecular Neurogenetics (A.N., D.G.), Foundation IRCCS Institute of Neurology “Besta,” Milan, Italy; Mitochondrial Biology Unit (A.R.), Medical Research Council, Cambridge, United Kingdom; Department of Bioinformatics (B.C.), University of Texas Southwestern Medical Center, Dallas; and Department of Neurology (A.V.), George Washington University School of Medicine, Children's National Health, DC.
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Raphael Schiffmann
From the Baylor Research Institute (N.M., B.L., R.S.), Baylor Scott and White Health, Dallas, TX; Unit of Molecular Neurogenetics (A.N., D.G.), Foundation IRCCS Institute of Neurology “Besta,” Milan, Italy; Mitochondrial Biology Unit (A.R.), Medical Research Council, Cambridge, United Kingdom; Department of Bioinformatics (B.C.), University of Texas Southwestern Medical Center, Dallas; and Department of Neurology (A.V.), George Washington University School of Medicine, Children's National Health, DC.
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Daniele Ghezzi
From the Baylor Research Institute (N.M., B.L., R.S.), Baylor Scott and White Health, Dallas, TX; Unit of Molecular Neurogenetics (A.N., D.G.), Foundation IRCCS Institute of Neurology “Besta,” Milan, Italy; Mitochondrial Biology Unit (A.R.), Medical Research Council, Cambridge, United Kingdom; Department of Bioinformatics (B.C.), University of Texas Southwestern Medical Center, Dallas; and Department of Neurology (A.V.), George Washington University School of Medicine, Children's National Health, DC.
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Citation
Functionally pathogenic EARS2 variants in vitro may not manifest a phenotype in vivo
Nathan McNeill, Alessia Nasca, Aurelio Reyes, Benjamin Lemoine, Brandi Cantarel, Adeline Vanderver, Raphael Schiffmann, Daniele Ghezzi
Neurol Genet Aug 2017, 3 (4) e162; DOI: 10.1212/NXG.0000000000000162

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Abstract

Objective: To investigate the genetic etiology of a patient diagnosed with leukoencephalopathy, brain calcifications, and cysts (LCC).

Methods: Whole-exome sequencing was performed on a patient with LCC and his unaffected family members. The variants were subject to in silico and in vitro functional testing to determine pathogenicity.

Results: Whole-exome sequencing uncovered compound heterozygous mutations in EARS2, c.328G>A (p.G110S), and c.1045G>A (p.E349K). This gene has previously been implicated in the autosomal recessive leukoencephalopathy with thalamus and brainstem involvement and high lactate (LTBL). The p.G110S mutation has been found in multiple patients with LTBL. In silico analysis supported pathogenicity in the second variant. In vitro functional testing showed a significant mitochondrial dysfunction demonstrated by an ∼11% decrease in the oxygen consumption rate and ∼43% decrease in the maximum respiratory rate in the patient's skin fibroblasts compared with the control. EARS2 protein levels were reduced to 30% of normal controls in the patient's fibroblasts. These deficiencies were corrected by the expression of the wild-type EARS2 protein. However, a further unrelated genetic investigation of our patient revealed the presence of biallelic variants in a small nucleolar RNA (SNORD118) responsible for LCC.

Conclusions: Here, we report seemingly pathogenic EARS2 mutations in a single patient with LCC with no biochemical or neuroimaging presentations of LTBL. This patient illustrates that variants with demonstrated impact on protein function should not necessarily be considered clinically relevant.

ClinicalTrials.gov identifier: NCT00001671.

GLOSSARY

LCC=
leukoencephalopathy, brain calcifications, and cysts;
LTBL=
leukoencephalopathy with thalamus and brainstem involvement and high lactate;
MAF=
minor allele frequency;
MRR=
maximum respiratory rate;
OCR=
oxygen consumption rate

Footnotes

  • ↵* These authors contributed equally to this work.

  • Funding information and disclosures are provided at the end of the article. Go to Neurology.org/ng for full disclosure forms. The Article Processing Charge was funded by the authors.

  • Supplemental data at Neurology.org/ng

  • See editorial

  • Received February 13, 2017.
  • Accepted in final form April 18, 2017.
  • Copyright © 2017 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of the American Academy of Neurology

This is an open access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND), which permits downloading and sharing the work provided it is properly cited. The work cannot be changed in any way or used commercially without permission from the journal.

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