Mitochondrial Genome Maintenance/Integrity Nuclear Genes Panel

Abnormalities in the maintenance of the mitochondrial genome integrity represent a group of clinically and genetically heterogeneous disorders including mitochondrial DNA (mtDNA) depletion syndromes and disorders with multiple mtDNA deletions. These disorders are caused by defects in nuclear-encoded genes responsible for mtDNA maintenance.

Mitochondrial DNA depletion syndromes (MDS) are characterized by a quantitative abnormality of the mitochondrial genome, leading to impaired energy production in a single or multiple organs (Suomalainen et al. 2010; El-Hattab et al. 2013). MDS is clinically and genetically heterogeneous; and it is usually classified into four forms: myopathic (onset at infancy to early childhood; caused by mutations in TK2, RRM2B and AGK), encephalomyopathic (onset at neonatal to infancy; caused by SUCLA2, SUCLG1, RRM2B and possibly SUCLG2), hepatocerebral (onset at neonatal to childhood, caused by mutations in DGUOK, MPV17, POLG and TWNK/C10orf2) and neurogastrointestinal (onset at late childhood to adolescence; caused by mutations in TYMP). More detailed clinical features are presented in each individual gene’s test description.

The accumulation of multiple mtDNA deletions represents the other major abnormality in the maintenance of the mitochondrial genome integrity. It is typically seen in skeletal muscle of patients affected by adult-onset progressive external ophthalmoplegia (PEO), which is accompanied by ptosis and mitochondrial myopathy (see for example Fratter et al. 2010; more information can be found at Test #1255 for the TWNK gene). The autosomal recessive mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) disease is also associated with multiple mtDNA deletions (Nishino et al. 1999; more information can be found at Test #1242 for the TYMP gene).

Mitochondrial DNA depletion syndromes (MDS) are autosomal recessive disorders due to defects in nuclear genes responsible for mtDNA maintenance that function in either mitochondrial nucleotide synthesis (TK2, SUCLA2, SUCLG1, SUCLG2, RRM2B, DGUOK and TYMP) or mtDNA replication (POLG, TWNK and MGME1) or other activities (MPV17, FBXL4 and AGK).

Disorders with multiple mtDNA deletions can be autosomal dominant or recessive. In adults, the accumulation of multiple mtDNA deletions in postmitotic tissues (such as skeletal muscle) results from defects in proteins involved in mtDNA replication (POLG, POLG2, TWNK and DNA2), deoxyribonucleotide metabolism (TK2, TYMP, SLC25A4 and RRM2B), and mitochondrial fusion (OPA1, OPA3, MFN2 and SPG7).

Of the 22 genes in the panel, 16 are also currently available at our Sanger sequencing test menu: TK2 (Test# 1245), SUCLA2 (Test# 1251), SUCLG1 (Test# 1249), RRM2B (Test# 1246), DGUOK (Test# 1243), MPV17 (Test# 1247), POLG (Test# 1241), TWNK (Test# 1255), TYMP (Test# 1242); POLG2 (Test# 1248), DNA2 (Test# 1253), MFN2 (Test# 1254), OPA1 (Test# 566), OPA3 (Test# 567), SLC25A3 (Test# 1252), SLC25A4 (Test# 1250). Please find more information under each individual test description. Sanger tests for the remaining genes in the panel may be offered at a later date.

The SUCLG2 gene (11 coding exons) encodes a GTP-specific beta-subunit of succinyl-CoA synthetase, which catalyzes the reversible conversion of succinyl-CoA and ADP or GDP to succinate and ATP or GTP. No SUCLG2 mutations have been reported in human diseases. However, defects in genes encoding other subunits of succinyl-CoA synthetase (SUCLA2 and SUCLG1) have been reported to cause the encephalomyopathic form of MDS. Therefore, the SUCLG2 gene is included in this panel.

The FBXL4 gene (7 coding exons) encodes an F-box protein with a possible role in maintaining mtDNA integrity and stability. Loss-of-function and splice mutations in this protein cause mitochondrial encephalopathy with a severe respiratory chain deficiency, loss of mitochondrial membrane potential, and a disturbance of the dynamic mitochondrial network in affected individuals (Bonnen et al. 2013; Gai et al. 2013).

The MGME1 gene (also known as C20orf72; 4 coding exons) encodes a mitochondrial RecB-type exonuclease belonging to the PD-(D/E)XK nuclease superfamily. Loss-of-function mutations in MGME1 impair mtDNA replication and cause a multisystemic mitochondrial syndrome characterized by external ophthalmoplegia, emaciation and respiratory failure (Kornblum et al. 2013).

The AGK gene (15 coding exons) encodes the acylglycerol kinase, which phosphorylates monoacylglycerols and diacylglycerols to lysophosphatidic acid and phosphatidic acid respectively. Frameshift and splicing mutation in the AGK gene, resulting in a deletion of a highly conserved C-terminal region, cause Sengers syndrome, also known as a subtype of myopathic form of MDS (Mayr et al. 2012; Calvo et al. 2012).

The SPG7 gene (17 coding exons) encodes the protein paraplegin, a mitochondrial metalloprotease protein, which is a member of the AAA protein family. SPG7 mutations in this gene cause autosomal recessive spastic paraplegia 7 (Casari et al. 1998). Mutations in this gene also cause chronic progressive external ophthalmoplegia due to defected mitochondrial DNA maintenance (Pfeffer et al. 2014).

The APTX gene (8 coding exons) encodes aprataxin, which is involved in mitochondrial single strand break repair (SSBR). APTX mutations cause ataxia-ocular apraxia 1 (AOA1) (Date et al. 2001; Moreira et al. 2001).

A TWNK defect is likely in autosomal dominant PEO patients (Fratter et al. 2010). Fratter et al. identified 16 different TWNK mutations within 26 (16/26; 62%) unrelated patients with adPEO from United Kingdom and Germany. POLG mutations were identified in 136 out of 2,697 unrelated individuals (5%) with clinical presentations suggestive of POLG deficiency (Tang et al. 2011). RRM2B mutations account for approximately 13% of PEO and multiple mtDNA deletions in adults (Pitceathly et al. 2012). However, RRM2B mutation detection rate in patients with encephalomyopathic form of MDS or MNGIE is uncertain because these RRM2B mutations have been only reported in individual families. In a limited number of patients, biallelic TK2 mutations were found in 20% to 46% of patients with the myopathic form of MDS (Alberio et al. 2007; Spinazzola et al. 2009). TYMP mutations were identified in 92 out of 102 unrelated individuals worldwide (~ 90%) with clinical presentations suggestive of MNGIE disease (Garone et al. 2011). Three of 90 patients (3.3%) with multiple mtDNA deletions were found via DNA sequencing to have DNA2 pathogenic mutations (Ronchi et al. 2013). In a molecular screening of 980 cases with suspected hereditary optic neuropathy, 440 patients had molecular defects. Among these 440 patients, 295 had OPA1 mutations (67%), and 14 patients (3%) had OPA3 mutations (Ferre et al. 2009). SLC25A4 mutations accounted for approximately 4% of familial adPEO cases in a study of a limited number of PEO patients (Lamantea et al. 2002). In 68 patients affected by progressive external ophthalmoplegia (PEO) and negative for the previous known causative genes, 9 (~13%) were found to have compound heterozygous SPG7 mutations and 6 (~9%) have a single heterozygous SPG7 mutation (Pfeffer et al. 2014). The mutation detection rates of other genes (POLG2, DGUOK, MPV17, SUCLA2, SUCLG1, MFN2, SLC25A3, FBXL4, MGME1, AGK and APTX) in a large cohort of patients are unknown because these mutations were only reported in a limited number of patients (families). SUCLG2 mutations have not been reported yet.

No gross deletions or duplications have been reported in SUCLG1 thus far (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 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).

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).