MT-ATP6 mitochondrial disease variants: Phenotypic and biochemical features analysis in 218 published cases and cohort of 14 new cases

Abstract

Mitochondrial complex V (CV) generates cellular energy as adenosine triphosphate (ATP). Mitochondrial disease caused by the m.8993T>G pathogenic variant in the CV subunit gene MT-ATP6 was among the first described human mitochondrial DNA diseases. Due to a lack of clinically available functional assays, validating the definitive pathogenicity of additional MT-ATP6 variants remains challenging. We reviewed all reportedMT-ATP6 disease cases ( n = 218) to date, to assess for MT-ATP6 variants, heteroplasmy levels, and inheritance correlation with clinical presentation and biochemical findings. We further describe the clinical and biochemical features of a new cohort of 14 kindreds with MT-ATP6 variants of uncertain significance. Despite extensive overlap in the heteroplasmy levels of MT-ATP6 variant carriers with and without a wide range of clinical symptoms, previously reported symptomatic subjects had significantly higher heteroplasmy load (p = 2.2 x 10^-16 ). Pathogenic MT-ATP6 variants resulted in diverse biochemical features. The most common findings were reduced ATP synthesis rate, preserved ATP hydrolysis capacity, and abnormally increased mitochondrial membrane potential. However, no single biochemical feature was universally observed. Extensive heterogeneity exists among both clinical and biochemical features of distinct MT-ATP6 variants. Improved mechanistic understanding and development of consistent biochemical diagnostic analyses are needed to permit accurate pathogenicity assessment of variants of uncertain significance in MT-ATP6.

Keywords: Leigh syndrome; genotype-phenotype correlation; heteroplasmy; mitochondria; neurogenic ataxia and retinitis pigmentosa.

Figure 1.. MT-ATP6 Heteroplasmy Level Analysis.

A. Average tissue heteroplasmy (averaged across all tissues analyzed) among symptomatic patients (red) and their asymptomatic relatives (blue) across all shows that there is a significantly higher heteroplasmy level in affected patients (p< 2.2e-16 by Mann-Whitney U test) B. Average tissue heteroplasmy (averaged across all tissues analyzed) among symptomatic patients (red) and their asymptomatic relatives (blue) by variant site. (*=p< 0.05; **** = p<0.00001). Heteroplasmy level is significantly higher in Leigh Syndrome compared to NARP patients across all pathogenic MT-ATP6 variants (p= 5.989e-06 by Mann-Whitney U nonparametric analysis). D. Heteroplasmy level shows a significant negative association with patient age at presentation (Pearson correlation coefficient=−0.37, p=1.6E-07).

Figure 2.. Variant map of variants in MT-ATP6 mapped by protein domain

A. Reported pathogenic variants in MT-ATP6 mapped across its five transmembrane domains. The area of each circle is proportional to the number of reported patients. B. Reported MT-ATP6 variants in a new cohort reported in this publication (n=16). White circles represent variants re-classified as benign, yellow circles represent variants re-classified as likely benign, orange circles represent VUS, and red circles represent variants re-classified as likely pathogenic. C: List of all mutations including protein changes and classification.