Mitochondrial Combined Oxidative Phosphorylation Deficiency via the MTFMT Gene
- Summary and Pricing
- Clinical Features and Genetics
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In a cohort of 350 patients who presented with a suspected mitochondrial disorder and either isolated or combined oxidative phosphorylation deficiencies, Haack and colleagues identified causative MTFMT variants in 4 patients (~1%) (Haack et al. 2014).
Combined oxidative phosphorylation (OXPHOS) deficiency is a multi-systemic disorder characterized by reduced activity of two or more mitochondrial respiratory chain enzyme complexes. Combined OXPHOS deficiency accounts for roughly one-quarter to one-third of all oxidative phosphorylation disorders (Skladal et al. 2003; Scaglia et al. 2004).
Patients with MTFMT-associated oxidative phosphorylation deficiency generally present within the first year of life, although clinical presentation may range from mild (with survival into adulthood and eventual apparent clinical stability) to severe (resulting in death within the first few years of life). Although many MTFMT-deficient patients show combined oxidative phosphorylation defects in muscle tissue upon biochemical analysis, a subset of patients may present with an isolated complex I deficiency (Haack et al. 2014). Overall, affected individuals exhibit a primarily encephalomyopathic phenotype, with clinical symptoms such as lactic acidosis, hypotonia, microcephaly, developmental delays, cognitive impairment, optic atrophy, dysarthria, convulsions, ataxia and spasticity at later disease stages, stroke-like episodes, and/or acute respiratory insufficiency (Haack et al. 2014; Pena et al. 2016; Neeve et al. 2013; Tucker et al. 2011). In the majority of patients, MRI analysis often leads to a diagnosis of classical Leigh syndrome, a severe, progressive encephalopathy characterized by bilateral symmetrical lesions in the brainstem and basal ganglia; psychomotor delay or regression; isolated or combined mitochondrial complex deficiencies; elevated levels of lactate in the blood and/or cerebral spinal fluid; and neurologic manifestations such as hypotonia or ataxia (Haack et al. 2014; Rahman and Thorburn 2015; Lake et al. 2015).
Combined oxidative phosphorylation (OXPHOS) deficiency may be an autosomal recessive, X-linked, or maternally-inherited disease. Pathogenic variants in over 30 different nuclear and mitochondrial genes have been reported as causative for this disorder; the majority of these genes encode for components of the mitochondrial translation machinery.
Nuclear genes associated with autosomal recessive inheritance of combined OXPHOS deficiency include: AARS2, ATP5A1, BOLA3, C12orf65, EARS2, ELAC2, FARS2, GFER, GFM1, GTPBP3, ISCU, LYRM4, MARS2, MRPL3, MRPL44, MRPS16, MRPS22, MTFMT, MTO1, NARS2, NFU1, PARS2, PNPT1, PUS1, RMND1, SERAC1, SFXN4, TARS2, TRMT5, TSFM, TUFM, VARS2, and YARS2. AIFM1 is associated with X-linked recessive inheritance of this disease. Pathogenic defects in any of the mitochondrial-encoded tRNA genes (22 total) or rRNA genes (2 total) are expected to result in maternally-inherited combined oxidative phosphorylation deficiency (Smits et al. 2010).
Additionally, defects in the mitochondrial depletion/deletion syndrome genes (see Test #1399) or coenzyme Q10 deficiency genes (see Test #4529) may result in a combined OXPHOS deficiency in conjunction with coenzyme Q10 deficiency, quantitative mitochondrial genome depletion, or a large deletion(s) of the mitochondrial genome.
The MTFMT gene encodes for the mitochondrial methionyl-tRNA formyltransferase, responsible for formylation of the initiator Met-tRNA (Haack et al. 2014). Approximately 15 causative variants have been reported in this gene to date, including several missense and nonsense variants, one splicing variant, and several small deletions resulting in frameshifts (Human Gene Mutation Database). One particular missense change (p.Ser209Leu) appears to be prevalent among affected individuals (Haack et al. 2014).
Full gene sequencing of MTFMT is performed, with bidirectional Sanger sequencing of exons 1-9. The full coding region of each exon plus ~20 bp of flanking non-coding DNA on either side are sequenced. We will also sequence any single exon (Test #100) or pair of exons (Test #200) in family members of patients with known mutations or to confirm research results.
Indications for Test
MTFMT sequencing could be considered for patients who present with symptoms consistent with combined oxidative phosphorylation deficiency or for individuals with a family history of this disorder. We will also sequence the MTFMT gene to determine carrier status.
|Official Gene Symbol||OMIM ID|
|Autism Spectrum Disorders and Intellectual Disability (ASD-ID) Comprehensive Panel|
|Mitochondrial Complex I Deficiency Sequencing Panel (Nuclear Genes)|
- Genetic Counselor Team - email@example.com
- Kym Bliven, PhD - firstname.lastname@example.org
- Haack T.B. et al. 2014. Molecular Genetics and Metabolism. 111:342-52. PubMed ID: 24461907
- Human Gene Mutation Database (Bio-base).
- Lake N.J. et al. 2015. Journal of Neuropathology & Experimental Neurology. 74:482-92. PubMed ID: 25978847
- Neeve V.C. et al. 2013. Mitochondrion. 13:743-8. PubMed ID: 23499752
- Pena J.A. et al. 2016. Journal of Child Neurology. 31:215-9. PubMed ID: 26060307
- Rahman S, Thorburn D. 2015. Nuclear Gene-Encoded Leigh Syndrome Overview. In: Pagon RA, Adam MP, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews (®), Seattle (WA): University of Washington, Seattle. PubMed ID: 26425749
- Scaglia F. et al. 2004. Pediatrics. 114:925-31. PubMed ID: 15466086
- Skladal D. et al. 2003. Brain: A Journal of Neurology. 126:1905-12. PubMed ID: 12805096
- Smits P. et al. 2010. Journal of Biomedicine and Biotechnology. 2010:737385. PubMed ID: 20396601
- Tucker E.J. et al. 2011. Cell Metabolism. 14:428-34. PubMed ID: 21907147
Bi-Directional Sanger Sequencing
Nomenclature for sequence variants was from the Human Genome Variation Society (http://www.hgvs.org). As required, DNA is extracted from the patient specimen. PCR is used to amplify the indicated exons plus additional flanking non-coding sequence. After cleaning of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit. Products are resolved by electrophoresis on an ABI 3730xl capillary sequencer. In most cases, sequencing is performed in both forward and reverse directions; in some cases, sequencing is performed twice in either the forward or reverse directions. In nearly all cases, the full coding region of each exon as well as 20 bases of non-coding DNA flanking the exon are sequenced.
As of March 2016, we compared 17.37 Mb of Sanger DNA sequence generated at PreventionGenetics to NextGen sequence generated in other labs. We detected only 4 errors in our Sanger sequences, and these were all due to allele dropout during PCR. For Proficiency Testing, both external and internal, in the 12 years of our lab operation we have Sanger sequenced roughly 8,800 PCR amplicons. Only one error has been identified, and this was due to sequence analysis error.
Our Sanger sequencing is capable of detecting virtually all nucleotide substitutions within the PCR amplicons. Similarly, we detect essentially all heterozygous or homozygous deletions within the amplicons. Homozygous deletions which overlap one or more PCR primer annealing sites are detectable as PCR failure. Heterozygous deletions which overlap one or more PCR primer annealing sites are usually not detected (see Analytical Limitations). All heterozygous insertions within the amplicons up to about 100 nucleotides in length appear to be detectable. Larger heterozygous insertions may not be detected. All homozygous insertions within the amplicons up to about 300 nucleotides in length appear to be detectable. Larger homozygous insertions may masquerade as homozygous deletions (PCR failure).
In exons where our sequencing did not reveal any variation between the two alleles, we cannot be certain that we were able to PCR amplify both of the patient’s alleles. Occasionally, a patient may carry an allele which does not amplify, due for example to a deletion or a large insertion. In these cases, the report contains no information about the second allele.
Similarly, our sequencing tests have almost no power to detect duplications, triplications, etc. of the gene sequences.
In most cases, only the indicated exons and roughly 20 bp of flanking non-coding sequence on each side are analyzed. Test reports contain little or no information about other portions of the gene, including many regulatory regions.
In nearly all cases, we are unable to determine the phase of sequence variants. In particular, when we find two likely causative mutations for recessive disorders, we cannot be certain that the mutations are on different alleles.
Our ability to detect minor sequence variants, due for example to somatic mosaicism is limited. Sequence variants that are present in less than 50% of the patient’s nucleated cells may not be detected.
Runs of mononucleotide repeats (eg (A)n or (T)n) with n >8 in the reference sequence are generally not analyzed because of strand slippage during PCR and cycle sequencing.
Unless otherwise indicated, the sequence data that we report are based on DNA isolated from a specific tissue (usually leukocytes). Test reports contain no information about gene sequences in other tissues.
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- Culture and send at least two T25 flasks of confluent cells.
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