Mitochondrial Complex V Deficiency via the ATPAF2 Gene
- Summary and Pricing
- Clinical Features and Genetics
|Test Code||Test Copy Genes||Individual Gene Price||CPT Code Copy CPT Codes|
For ordering targeted known variants, please proceed to our Targeted Variants landing page.
The great majority of tests are completed within 18 days.
ATPAF2-associated mitochondrial complex V deficiency has been described in only one patient to date (De Meirleir et al. 2004). Although we cannot precisely estimate clinical sensitivity at this time, defects in ATPAF2 appear to be a rare cause of mitochondrial complex V deficiency. In contrast, defects in TMEM70 appear to be the most frequent cause of this disorder (Human Gene Mutation Database; http://www.hgmd.cf.ac.uk/ac/index.php).
Mitochondrial complex V deficiency is considered the rarest oxidative phosphorylation (OXPHOS) complex disorder, accounting for approximately one percent of all OXPHOS disease (Rodenburg 2011). Although patients with this disorder share a similar biochemical phenotype, with a significant decrease in the activity of mitochondrial complex V, the phenotypic disease spectrum can be broad (Hejzlarová et al. 2004; Jonckheere et al. 2012). Defects in complex V-associated nuclear genes often result in a severe, neonatal-onset mitochondrial encephalopathy and/or cardiomyopathy.
To date, only a single patient has been described with ATPAF2-associated mitochondrial complex V deficiency (De Meirleir et al. 2014; Meulemans et al. 2009). The affected individual presented as a neonate with degenerative encephalopathy, dysmorphic features, lactic acidosis, developmental delay, and seizures.
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 the mitochondrial ATP synthase, variants in only six of these genes (ATP5A1, ATP5E, ATPAF2, TMEM70, MT-ATP6, and MT-ATP8) are currently associated with 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 (ATP5A1, ATP5E, 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.
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). To date, only one pathogenic variant, a homozygous missense change, has been documented as a cause of ATPAF2-associated mitochondrial complex V deficiency (De Meirleir et al. 2004; Meulemans et al. 2010).
Full gene sequencing of ATPAF2 is performed, with bidirectional sequencing of exons 1-8. The full coding region of each exon plus ~20 base pairs 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
ATPAF2 sequencing should be considered in patients with a family history of mitochondrial complex V deficiency, or patients who present with symptoms consistent with the disease. We will also sequence the ATPAF2 gene to determine carrier status.
|Official Gene Symbol||OMIM ID|
|Mitochondrial Complex V (ATP Synthase) Deficiency, Nuclear Type 1||AR||604273|
- Genetic Counselor Team - firstname.lastname@example.org
- Kym Bliven, PhD - email@example.com
- Ackerman S.H. 2002. Biochimica et Biophysica Acta. 1555:101-5. PubMed ID: 12206899
- De Meirleir L. et al. 2004. Journal of Medical Genetics. 41:120-4. PubMed ID: 14757859
- Hejzlarova K. et al. 2014. Physiological Research. 63:S57-1. PubMed ID: 24564666
- Human Gene Mutation Database (Bio-base).
- Jonckheere A.I. et al. 2012. Journal of Inherited Metabolic Disease. 35:211-25. PubMed ID: 21874297
- Meulemans A. et al. 2010. Journal of Biological Chemistry. 285:4099-109. PubMed ID: 19933271
- Rodenburg R.J. 2011. Journal of Inherited Metabolic Disease. 34:283-92. PubMed ID: 20440652
- Wang Z.G. et al. 2001. Journal of Biological Chemistry. 276:30773-8. PubMed ID: 11410595
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.
myPrevent - Online Ordering
- The test can be added to your online orders in the Summary and Pricing section.
- Once the test has been added log in to myPrevent to fill out an online requisition form.
- A completed requisition form must accompany all specimens.
- Billing information along with specimen and shipping instructions are within the requisition form.
- All testing must be ordered by a qualified healthcare provider.
(Delivery accepted Monday - Saturday)
- Collect 3 ml -5 ml (5 ml preferred) of whole blood in EDTA (purple top tube) or ACD (yellow top tube). For Test #500-DNA Banking only, collect 10 ml -20 ml of whole blood.
- For small babies, we require a minimum of 1 ml of blood.
- Only one blood tube is required for multiple tests.
- Ship blood tubes at room temperature in an insulated container. Do not freeze blood.
- During hot weather, include a frozen ice pack in the shipping container. Place a paper towel or other thin material between the ice pack and the blood tube.
- In cold weather, include an unfrozen ice pack in the shipping container as insulation.
- At room temperature, blood specimen is stable for up to 48 hours.
- If refrigerated, blood specimen is stable for up to one week.
- Label the tube with the patient name, date of birth and/or ID number.
(Delivery accepted Monday - Saturday)
- Send in screw cap tube at least 5 µg -10 µg of purified DNA at a concentration of at least 20 µg/ml for NGS and Sanger tests and at least 5 µg of purified DNA at a concentration of at least 100 µg/ml for gene-centric aCGH, MLPA, and CMA tests, minimum 2 µg for limited specimens.
- For requests requiring more than one test, send an additional 5 µg DNA per test ordered when possible.
- DNA may be shipped at room temperature.
- Label the tube with the composition of the solute, DNA concentration as well as the patient’s name, date of birth, and/or ID number.
- We only accept genomic DNA for testing. We do NOT accept products of whole genome amplification reactions or other amplification reactions.
(Delivery preferred Monday - Thursday)
- PreventionGenetics should be notified in advance of arrival of a cell culture.
- Culture and send at least two T25 flasks of confluent cells.
- Some panels may require additional flasks (dependent on size of genes, amount of Sanger sequencing required, etc.). Multiple test requests may also require additional flasks. Please contact us for details.
- Send specimens in insulated, shatterproof container overnight.
- Cell cultures may be shipped at room temperature or refrigerated.
- Label the flasks with the patient name, date of birth, and/or ID number.
- We strongly recommend maintaining a local back-up culture. We do not culture cells.