Case Study Reveals Novel Intragenic Deletion of the FXN Gene in Friedreich Ataxia


In a recent case study of a 32-year-old man diagnosed with Friedreich ataxia, parental sample testing identified a novel intragenic deletion involving the 5'UTR upstream region and exons 1 and 2 of the FXN gene.

Ariadna Padró-Miquel, PhD, the associate medical professor of clinical and molecular genetics at Bellvitge University Hospital

Ariadna Padró-Miquel, PhD

In a recently published case report study of a 32-year-old man with typical clinical features of Friedreich ataxia (FA), parental sample testing led to the identification of a novel intragenic deletion. Overall, the report raises awareness about the potentially higher prevalence of intragenic deletions and highlights the important role of parental sample testing in providing more accurate genetic counseling.1

In the genetic analysis, polymerase chain reaction (PCR) fragment showed the paternal sample carried an allele of 7 GAA repeats as well as an expansion observed by Triplet Repeat Primed PCR (TP-PCR) which corresponded to a healthy carrier of the disease. Notably, the maternal sample only showed a peak corresponding to 9 GAA repeats, but investigators observed no expansion. The proband’s sibling had 2 normal alleles of 7 and 9 GAA repeats. The mother’s result did not correlate with a biallelic expansion in the proband. In a subsequent new DNA sample from the proband, results showed no peaks in the PCR fragment analysis although a band at the same level as the positive control (NA16216) was observed in the agarose gel.

Clinical Takeaways

  • Study suggests intragenic deletions in Friedreich ataxia (FA) may be more prevalent than assumed, urging thorough genetic analysis.
  • Conflicting results in diagnosing FA reveal complexity; a presumed common expansion led to the discovery of a novel intragenic deletion.
  • Essential parental sample testing uncovers a new FA deletion, emphasizing the need for accurate genetic counseling and hinting at a higher prevalence of deletions.

Senior author Ariadna Padró-Miquel, PhD, the associate medical professor of clinical and molecular genetics at Bellvitge University Hospital, and colleagues wrote, “Proband’s TP-PCR showed an expansion, suggesting that the patient may carry a biallelic expansion, which was in agreement with the first genetic test performed in the patient. The lack of an expansion in the mother and the fact that no normal allele was observed in the proband’s PCR fragment analysis led us to hypothesize the presence of a deletion.”1

READ MORE: Multicompartment Models of Free-Water Imaging Shows Distinctive Brain Pathology in Friedreich Ataxia

The patient was diagnosed with FA at the age of 23 after 5 years of progressive evolution of gait and limb ataxia, and mild dysarthria. Examinations of the patient showed hypotonia, dysmetria, dyschronometry, dysdiadochokinesia, Stewart Holmes sign in all 4 extremities, hypopalesthesia and arthro-kinetic hypoesthesia, positive Romberg sign, flexor plantar reflexes and universal areflexia. The patient also presented scoliosis, pes cavus, and muscle weakness. Despite the observations shown in the examinations, cranial and spinal MRI were normal, along with no hearing, vision or endocrine manifestations. In addition, he had an “unremarkable” cardiovascular assessment.

In the current case study, investigators performed a genetic analysis of FXN gene intron 1 in which the parental and sibling’s DNA samples were extracted from peripheral blood using an automatable extraction method. Duplication/deletion analysis of FXN gene was also conducted using the Multiplex Ligation-dependent Probe Amplification Probemix P316-B4 Recessive Ataxias kit (MRC Holland, Amsterdam, The Netherlands). In the breakpoints of the deletion whole genome sequencing, using xGen DNA Library Prep Kit EZ (Integrated DNA Technologies, Iowa, USA), researchers observed that the deletion spanned 151,09 kb (chr9:71,510,734–71,661,828) and included exons 9–16 of the PIP5K1B gene (NM_003558.4), the entire PRKACG gene (NM_002732.4) and exons 1–2 of the FXN gene (NM_000144.5).

“We report a novel intragenic deletion that includes the 5’UTR upstream region and exons 1 and 2 of the FXN gene. This unreported deletion is predicted to eliminate the start codon, and consequently no protein will be produced. Loss of function is a known disease-causing mechanism for this condition, so the deletion was classified as pathogenic,” Padró-Miquel et al noted.1

Investigators observed a 50% reduction in the relative peak height of the probes corresponding to FXN exons 1 and 2. In addition, the authors observed a normal diploid dosage in the probes corresponding to FXN exons 3, 4 and 5. Overall, the authors concluded that the mother carried an allele of 9 GAA repeats and a deletion spanning the 5’UTR as well as exons 1–2 of FXN gene. Additionally, authors noted that the proband had an expansion inherited from the father and a deletion encompassing 5’UTR and exons 1–2 of FXN gene of maternal origin. As a noted limitation with the methods used in this study, the size of the expanded allele could not be determined. The study authors also recommended to either conduct a paternity test or verify the size of the shared allele through alternative means to confirm the shared allele between the father and the son.

“Parental sample testing was essential in the case presented, as we were able to detect that the mother and the proband were carriers of an intragenic deletion not reported before. This finding also has implications for other family members who could be possible carriers of the deletion and taking into account the elevated carrier frequency of FA, they could be at high risk of having children with FA,” Padró-Miquel et al noted.1 “This is the reason why we suggest that, if available, parental sample testing should be performed and not assume that parents are obligate carriers of an expansion since it is possible that deletions may be more prevalent than it was initially thought.”

1. Aguilera C, Esteve-Garcia A, Casasnovas C, et al. Novel intragenic deletion within the FXN gene in a patient with typical phenotype of Friedreich ataxia: may be more prevalent than we think?. BMC Med Genomics. 2023;16(1):312. Published 2023 Dec 1. doi:10.1186/s12920-023-01743-0
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