Mitochondrial Complex II Deficiency Panel

Isolated mitochondrial complex II (CII) deficiency, a deficit of one of the five oxidative phosphorylation complexes of the mitochondrial respiratory chain, has been associated with a diverse spectrum of clinical disease (Hoekstra and Bayley 2013). In all patients, enzymatic activity of the mitochondrial CII (also referred to as succinate dehydrogenase) is severely reduced in muscle biopsies and cultured fibroblasts.

Leigh syndrome, isolated cardiomyopathy, and infantile leukoencephalopathy are early-onset phenotypes commonly associated with isolated mitochondrial CII deficiency. Patients generally present in infancy or childhood. Leigh syndrome, also known as subacute necrotizing encephalopathy, is characterized by elevated levels of lactate in blood and cerebral spinal fluid; bilateral symmetric necrotic lesions in the basal ganglia, brain stem, thalamus, and/or spinal cord; psychomotor delay or regression; and neurologic manifestations such as hypotonia or ataxia (Wedatilake et al. 2013; Leigh 1951). Alternatively, a small subset of patients present with isolated cardiomyopathy accompanied by mild increases in lactate (Hoekstra and Bayley 2013; Levitas et al. 2010). Finally, defects in mitochondrial CII genes may result in an infantile leukoencephalopathy phenotype, with mild to severe lactic acidosis (Helman et al. 2016; Ghezzi et al. 2009).

Loss of mitochondrial CII activity may also contribute to tumor development, and CII deficiency has been linked to hereditary paraganglioma-pheochromocytoma, gastrointestinal stromal tumor (GIST) development, and renal cell carcinoma (Hoekstra and Bayley 2013; Rutter et al. 2010). For more information regarding hereditary paraganglioma-pheochromocytoma syndrome, see the Hereditary Paraganglioma-Pheochromocytoma Syndrome Sequencing Panel test.

Mitochondrial complex II deficiency is the result of defects in the assembly or function of the succinate dehydrogenase (complex II) of the mitochondrial respiratory chain (Hoekstra and Bayley 2013). Complex II (CII) consists of four structural subunits (SDHA, SDHB, SDHC, and SDHD), while at least two accessory factors (SDHAF1 and SDHAF2) play roles in complex II assembly. Two additional accessory factors (SDHAF3 and SDHAF4) may also contribute to complex maturation, although their respective roles in this process have been less well defined (Na et al. 2014; Van Vranken et al. 2014).

This panel covers four nuclear-encoded genes that have been linked to mitochondrial CII deficiency to date (SDHA, SDHB, SDHD, and SDHAF1). SDHC and SDHAF2, which have only been associated with hereditary paraganglioma, are not included in this panel but are available either as single gene tests or via the Hereditary Paraganglioma-Pheochromocytoma Syndrome Sequencing Panel.

While disorders such as Leigh syndrome, cardiomyopathy, and infantile leukoencephalopathy are inherited in an autosomal recessive manner, familial paraganglioma may be inherited in an autosomal dominant manner with variable expressivity and age-related penetrance (Hoekstra and Bayley 2013).

SDHA: The 15-exon SDHA gene encodes for the flavoprotein subunit of the mitochondrial CII. Over 40 pathogenic variants have been reported in the SDHA gene to date (Human Gene Mutation Database). The majority of these variants are missense changes, although nonsense and splicing variants have been described, as well as a number of small deletions or insertions and one large deletion.

SDHB: The eight-exon SDHB gene encodes for the iron-sulfur cluster subunit of the mitochondrial CII. Over 200 pathogenic variants have been described in this gene to date, the majority of which are missense variants or deletions (HGMD).

SDHD: The four-exon SDHD gene encodes for an integral membrane structural subunit of the mitochondrial CII. Over 150 pathogenic variants, primarily missense changes, nonsense variants, and deletions, have been reported in this gene (HGMD).

SDHAF1: The single-exon SDHAF1 gene encodes for an LYR-family assembly factor that mediates maturation of SDHB, the iron-sulfur cluster subunit of mitochondrial CII (Na et al. 2014; Maio et al. 2016). Four pathogenic variants have been reported in the SDHAF1 gene, including three missense changes and one nonsense change (Ghezzi et al. 2009; Ohlenbusch et al. 2012).

Isolated complex II deficiency is considered a rare form of mitochondrial disease, accounting for approximately 2-23% of all respiratory chain deficiencies (Parfait et al. 2000; Vladutiu and Heffner 2000). Clinical sensitivity for this test is difficult to estimate, however, as no large cohort studies have been reported.

Clinical testing for large deletions and duplications is difficult to predict as no large cohort studies are available.

Only one gross deletion has been described in SDHA to date (Helman et al. 2016).

In a cohort of 24 paraganglioma patients, large deletions in SDHB were reported in 3 individuals (~12%) who previously tested negative for point mutations in paraganglioma-related genes (Cascón et al. 2006).

At the present time, gross deletion/insertion frequencies for the SDHD gene are unknown, although approximately 15 large deletions and one complex rearrangement have been reported in the SDHD gene to date (Human Gene Mutation Database).

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 homology issues, the entire coding region of SDHA (exons 1-15), in addition to ~10 bp of adjacent noncoding sequence of each exon, is bi-directionally sequenced using Sanger sequencing technology. Exon 4 of SDHD is also covered 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).