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Mitochondrial Complex V Deficiency via the ATP5F1A (ATP5A1) Gene

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy GenesTest CPT Code Gene CPT Codes Copy CPT Codes Base Price
ATP5F1A 81479 81479,81479 $990
Test Code Test Copy Genes Test CPT Code Gene CPT Codes Copy CPT Code Base Price
8173ATP5F1A81479 81479,81479 $990 Order Options and Pricing

Pricing Comments

Our favored testing approach is exome based NextGen sequencing with CNV analysis. This will allow cost effective reflexing to PGxome or other exome based tests. However, if full gene Sanger sequencing is desired for STAT turnaround time, insurance, or other reasons, please see link below for Test Code, pricing, and turnaround time information.

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

Click here for costs to reflex to whole PGxome (if original test is on PGxome Sequencing platform).

Click here for costs to reflex to whole PGnome (if original test is on PGnome Sequencing platform).

The Sanger Sequencing method for this test is NY State approved.

For Sanger Sequencing click here.

Turnaround Time

3 weeks on average for standard orders or 2 weeks on average for STAT orders.

Please note: Once the testing process begins, an Estimated Report Date (ERD) range will be displayed in the portal. This is the most accurate prediction of when your report will be complete and may differ from the average TAT published on our website. About 85% of our tests will be reported within or before the ERD range. We will notify you of significant delays or holds which will impact the ERD. Learn more about turnaround times here.

Targeted Testing

For ordering sequencing of targeted known variants, go to our Targeted Variants page.


Genetic Counselors


  • Kym Bliven, PhD

Clinical Features and Genetics

Clinical Features

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 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. 2014; Jonckheere et al. 2012). Defects in complex V-associated nuclear genes often result in a severe, neonatal-onset mitochondrial encephalopathy and/or cardiomyopathy. In contrast, pathogenic variants in genes encoded by the mitochondrial genome (such as MT-ATP6 or MT-ATP8) may lead to NARP (neuropathy, ataxia, and retinitis pigmentosa), MILS (maternally inherited Leigh syndrome), or bilateral striatal necrosis.

To date, ATP5F1A-associated mitochondrial complex V deficiency has been documented in only four patients from two different families (Jonckheere et al. 2013; Lieber et al. 2013). Two of the affected individuals presented as neonates with isolated complex V deficiency, severe encephalopathy, intractable seizures, nystagmus, hypoplastic lungs, and renal cysts (Jonckheere et al. 2013). Clinical features of the remaining two neonates included a combined oxidative phosphorylation deficiency, mtDNA depletion, failure to thrive, microcephaly, encephalopathy, hypotonia, pulmonary hypertension, and heart failure (Leiber et al. 2013).


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 (ATP5F1A, ATP5E, ATPAF2, TMEM70, MT-ATP6, and MT-ATP8) have been linked to disease to date. 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 (ATP5F1A, 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 ATP5F1A gene encodes for subunit α of the F1 catalytic complex in the mitochondrial ATP synthase. To date, only two pathogenic missense variants have been identified as a cause of ATP5F1A-associated mitochondrial complex V deficiency (Jonckheere et al. 2013; Lieber et al. 2013).

Clinical Sensitivity - Sequencing with CNV PGxome

Defects in ATP5F1A appear to be a rare cause of mitochondrial complex V deficiency, as only four patients from two separate families have been described (Jonckheere et al. 2013; Lieber et al. 2013). In contrast, defects in TMEM70 appear to be the most frequent cause of this disorder, with over fifteen pathogenic variants reported (Human Gene Mutation Database).

Testing Strategy

This test provides full coverage of all coding exons of the ATP5F1A gene 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).

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).

Indications for Test

ATP5F1A 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 ATP5F1A gene to determine carrier status.


Official Gene Symbol OMIM ID
ATP5F1A 164360
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Related Test

Mitochondrial Complex V Deficiency Panel (Nuclear Genes)


  • 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
  • Jonckheere A.I. et al. 2013. Brain. 136:1544-54. PubMed ID: 23599390
  • Lieber D.S. et al. 2013. Neurology. 80:1762-70. PubMed ID: 23596069
  • Rodenburg R.J. 2011. Journal of Inherited Metabolic Disease. 34:283-92. PubMed ID: 20440652


Ordering Options

We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.

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.
  • PGnome sequencing panels can be ordered via the myPrevent portal only at this time.

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.

For Requisition Forms, visit our Forms page

If ordering a Duo or Trio test, the proband and all comparator samples are required to initiate testing. If we do not receive all required samples for the test ordered within 21 days, we will convert the order to the most effective testing strategy with the samples available. Prior authorization and/or billing in place may be impacted by a change in test code.

Specimen Types

Specimen Requirements and Shipping Details

PGxome (Exome) Sequencing Panel

PGnome (Genome) Sequencing Panel

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Note: acceptable specimen types are whole blood and DNA from whole blood only.
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