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

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.

Late-onset leukoencephalopathy in a patient with recessive EARS2 mutations

“…In addition, in a recent report, McNeill et al found 2 functionally deleterious EARS2 variants in a patient affected by leukoencephalopathy with calcifications and cysts, a phenotype completely explained by the presence of biallelic SNORD118 mutations, raising some doubts on the pathogenicity of EARS2 variants in cases without a classic LTBL phenotype. 5 , 6 However, it should be pointed out that the patient described there, carrying both EARS2 and SNORD118 mutations, died prematurely (age 16 years), keeping open the possibility of the subsequent development of EARS2 -related late-onset disease, as in the case reported here.…”

Corpus Callosum Agenesis: An Insight into the Etiology and Spectrum of Symptoms

“…Interestingly, according to the American College of Medical Genetics and Genomics (ACMG), the EARS2 variant found in this subject is considered pathogenic and should result in the phenotype typical of COXPD12. It demonstrates that the results of in vitro sequencing do not necessarily reflect the expected phenotype in vivo, as the possible influence of genetic or epigenetic factors in some cases remains unknown [ 42 ].…”

Alteration of mitochondrial membrane inner potential in three Italian patients with megaconial congenital muscular dystrophy carrying new mutations in CHKB gene

“…Fibroblasts from skin biopsies and myoblasts from quadriceps muscular biopsies of patients and healthy controls were grown following standard laboratory procedures (9,10). DNA was extracted from peripheral blood of PI and PII and from fibroblasts pellet from PIII, using standard methods (11).…”