Mitochondrial Complex V Deficiency Panel (Nuclear Genes)

Mitochondrial complex V deficiency is considered the rarest oxidative phosphorylation (OXPHOS) complex disorder, accounting for approximately one percent of all OXPHOS disease (Rodenburg 2011). Patients share a similar biochemical phenotype, with a significant decrease in the activity of mitochondrial complex V, mitochondrial adenosine triphosphate (ATP) synthase.

Severe neonatal-onset mitochondrial encephalopathy and/or cardiomyopathy are the most common clinical phenotypes associated with complex V nuclear gene defects. The majority of patients present with severe lactic acidosis and 3-methylglutaconic aciduria (Hejzlarová et al. 2014; Jonckheere et al. 2012). Additional clinical symptoms may include respiratory distress, hypotonia, ataxia, dysmorphism, and psychomotor delay or regression.

Mitochondrial complex V deficiency is caused by defects in the mitochondrial adenosine triphosphate (ATP) synthase, the fifth multi-subunit oxidative phosphorylation (OXPHOS) complex (Jonckheere et al. 2012; Hejzlarová et al. 2014). Although over 20 genes have been implicated in the assembly, structure, and function of this complex, variants in only six of these genes (ATP5F1A, ATP5F1E, ATPAF2, TMEM70, MT-ATP6, and MT-ATP8) have been linked to disease. Depending on the cellular localization of the affected gene, this disorder may have an autosomal recessive or maternal mode of inheritance. Causative variants in the nuclear genes (ATP5F1A, ATP5F1E, ATPAF2, and TMEM70) are inherited in an autosomal recessive manner. In contrast, causative variants in the MT-ATP6 or MT-ATP8 genes, which are encoded by the mitochondrial genome, are inherited in a maternal manner.

This NextGen Panel covers the four nuclear genes (ATP5F1A, ATP5F1E, ATPAF2, and TMEM70) that have been associated with mitochondrial complex V deficiency. This panel does not cover MT-ATP6 or MT-ATP8.

TMEM70: Defects in the TMEM70 gene appear to be the most frequent cause of mitochondrial complex V deficiency, with approximately 50 cases described to date (Hejzlarová et al. 2014). TMEM70 is required to maintain normal expression levels of complex V, although the exact function of this mitochondrial transmembrane protein is unknown (Cizková et al. 2008). Approximately 15 pathogenic variants have been reported in the TMEM70 gene, the majority of which are missense or nonsense (Human Gene Mutation Database). However, several small deletions and insertions, splicing variants, and gross deletions have also been documented.

ATP5F1A: The ATP5A1 gene encodes for subunit α of the F₁ catalytic complex in the mitochondrial ATP synthase. Two pathogenic missense variants have been identified in this gene (Jonckheere et al. 2013; Lieber et al. 2013).

ATP5F1E: The ATP5F1E gene encodes subunit ε of the F₁ catalytic complex in the mitochondrial ATP synthase. Although the exact function of this protein is still unclear, ATP5E may play a role in F₁ complex assembly (Havlíčková et al. 2010). Only one pathogenic variant, a homozygous missense change, has been reported in ATP5F1E (Mayr et al. 2010).

ATPAF2: The ATPAF2 gene (also referred to as Atp12p in the literature) encodes a chaperone protein thought to prevent aggregation of the F₁ alpha subunit prior to its integration into the mitochondrial ATP synthase complex (Wang et al. 2001; Ackerman 2002). Only one pathogenic variant, a homozygous missense change, has been documented in this gene (De Meirleir et al. 2004; Meulemans et al. 2010).

Pathogenic variants in TMEM70 appear to be the most frequent cause of mitochondrial complex V deficiency associated with nuclear gene defects. In one cohort of nine complex V-deficient patients who tested negative for pathogenic variants in mtDNA, all nine patients (100%) carried homozygous or compound heterozygous pathogenic variants in TMEM70 (Diodato et al. 2015). Clinical sensitivities for ATP5F1A, ATP5F1E, and ATPAF2 are difficult to estimate, as only a few affected individuals have been described with defects in these genes.

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

This panel provides 100% coverage of all coding exons of the genes plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define full coverage as >20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Due to sequence similarity with other genomic sites, the entire coding region of ATP5F1A (12 exons), in addition to ~10 bp of adjacent noncoding sequence of each exon, is bi-directionally sequenced using Sanger sequencing technology.

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).