Mitochondrial Complex I Deficiency Panel (Nuclear Genes)

Mitochondrial complex I (CI) deficiency is characterized by a primary deficiency of the first and largest oxidative phosphorylation complex (Fassone and Rahman 2012). Primary mitochondrial CI deficiency accounts for roughly one-third of all oxidative phosphorylation disorders and is the most frequently reported childhood-onset mitochondrial disease (Skladal et al. 2003; Scaglia et al. 2004).

The majority of CI-deficient patients present within the first year of life (Distelmaier et al. 2009). Respiratory infections, gastrointestinal disease, or long periods of fasting may trigger the initial symptoms of this disorder and stimulate additional episodes, leading to rapid deterioration of the patient’s condition. Similar to other OXPHOS disorders, recurrent lactic acidosis is a prevalent finding in patients with CI deficiency. Additional clinical symptoms, which can involve single or multiple organ systems, may be highly heterogeneous. The most common clinical presentations in patients with nuclear-encoded CI deficiency include Leigh/Leigh-like syndrome (LS/LLS), leukoencephalopathy with macrocephaly, fatal infantile lactic acidosis, hypertrophic cardiomyopathy, and hepatopathy with renal tubulopathy (Fassone and Rahman 2012; Distelmaier et al. 2009). LS is a severe, progressive encephalopathy characterized by psychomotor delay or regression, isolated or combined mitochondrial complex deficiencies, elevated levels of lactate in the blood and/or cerebral spinal fluid, bilateral symmetrical lesions in the brainstem and basal ganglia, and neurologic manifestations such as hypotonia or ataxia (Rahman and Thorburn 2015; Lake et al. 2015).

At the present time, although over 30 genes have been linked to CI deficiency to date (see ‘Genetics,’ below), clear genotype-phenotype correlations are lacking.

The mitochondrial respiratory chain complex I (nicotinamide adenine dinucleotide (NADH):ubiquinone oxidoreductase) is composed of at least 45 structural subunits (Fassone and Rahman 2012). 38 of these subunits are encoded by nuclear DNA, and 7 (MT-ND1, MT-ND2, MT-ND3, MT-ND4, MT-ND4L, MT-ND5, and MT-ND6) are encoded by mitochondrial DNA. The resulting holoenzyme complex plays a critical role in redox-driven proton translocation, which ultimately results in synthesis of adenosine triphosphate (ATP). Due to the many structural and accessory subunits required to support the assembly and function of complex I, mitochondrial CI deficiency is a genetically heterogeneous disorder. At least 33 genes have been linked to this disease to date. Causative variants in the nuclear genes are predominantly inherited in an autosomal recessive manner with the exception of NDUFA1, which has an X-linked recessive mode of inheritance. In contrast, causative variants in mitochondrial-encoded genes are inherited in a maternal manner.

This NextGen Panel covers 29 nuclear genes (ACAD9, FOXRED1, MTFMT, NDUFA1, NDUFA10, NDUFA11, NDUFA12, NDUFA13, NDUFA2, NDUFA9, NDUFAF1, NDUFAF2, NDUFAF3, NDUFAF4, NDUFAF5, NDUFAF6, NDUFB3, NDUFB9, NDUFS1, NDUFS2, NDUFS3, NDUFS4, NDUFS6, NDUFS7, NDUFS8, NDUFV1, NDUFV2, NUBPL, and POLG) that have been associated with primary mitochondrial complex I deficiency. This panel does not cover the mitochondrial-encoded genes known to be associated with this disorder (MT-ND1, MT-ND2, MT-ND3, MT-ND4, MT-ND4L, MT-ND5, and MT-ND6).

NDUFA1, NDUFA10, NDUFA11, NDUFA12, NDUFA13, NDUFA2, NDUFA9, NDUFB3, NDUFB9, NDUFS1, NDUFS2, NDUFS3, NDUFS4, NDUFS6, NDUFS7, NDUFS8, NDUFV1, and NDUFV2 encode for subunits of CI, while NDUFAF1, NDUFAF2, NDUFAF3, NDUFAF4, NDUFAF5, NDUFAF6, ACAD9, and FOXRED1 encode assembly factors of the complex (Fassone and Rahman 2012). The NUBPL gene encodes for an additional assembly protein that plays a role in CI incorporation of the eight iron-sulfur clusters necessary for electron transfer activity.

Although pathogenic variants in POLG or MTFMT more commonly result in a combined oxidative phosphorylation deficiency, several patients with defects in these genes presented with a primary CI defect (Swalwell et al. 2011; Haack et al. 2012). Therefore, POLG and MTFMT have also been included in this panel. POLG encodes for the catalytic subunit of DNA polymerase gamma, while MTFMT encodes for the mitochondrial methionyl-tRNA formyltransferase.

See individual gene test descriptions for information on molecular biology of gene products.

Approximately 25% of CI-deficient cases have defects in nuclear-encoded genes, while another ~25% carry a pathogenic variant in a mitochondrial-encoded gene (Fassone and Rahman 2012). In patients with a molecular diagnosis, ~60% have defects in genes that encode core subunits of CI, while the remaining ~40% have defects in genes that encode accessory subunits.

Causative variants in many of the genes in this NextGen Panel have only been documented in one or two families to date, making clinical sensitivity difficult to estimate. No large cohort studies have been reported. In a small cohort of ten unrelated individuals with complex I deficiency, exome sequencing revealed probable causative variants in NDUFS3, ACAD9, NDUFS8, NDUFB3, or MTFMT in seven of the ten patients (70%; Haack et al. 2012).

Large deletions/duplications have been reported in NDUFAF2, NDUFS1, NDUFS4, NDUFS6, NUBPL, and POLG (Human Gene Mutation Database). Although we cannot estimate precisely clinical sensitivity at this time, large deletions and duplications in these genes appear to be a rare cause of CI deficiency.

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

This panel typically provides 99.9% 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 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).

Two intronic variants are also covered in this test: c.17-1167C>G in the NDUFS7 gene and c.815-27T>C in the NUBPL gene (Lebon et al. 2007; Tucker et al. 2012).

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).