Mutation spectrum of the OPA1 gene in a large cohort of patients with suspected dominant optic atrophy: Identification and classification of 48 novel variants

Abstract

Autosomal dominant optic atrophy is one of the most common inherited optic neuropathies. This disease is genetically heterogeneous, but most cases are due to pathogenic variants in the OPA1 gene: depending on the population studied, 32–90% of cases harbor pathogenic variants in this gene. The aim of this study was to provide a comprehensive overview of the entire spectrum of likely pathogenic variants in the OPA1 gene in a large cohort of patients. Over a period of 20 years, 755 unrelated probands with a diagnosis of bilateral optic atrophy were referred to our laboratory for molecular genetic investigation. Genetic testing of the OPA1 gene was initially performed by a combined analysis using either single-strand conformation polymorphism or denaturing high performance liquid chromatography followed by Sanger sequencing to validate aberrant bands or melting profiles. The presence of copy number variations was assessed using multiplex ligation-dependent probe amplification. Since 2012, genetic testing was based on next-generation sequencing platforms. Genetic screening of the OPA1 gene revealed putatively pathogenic variants in 278 unrelated probands which represent 36.8% of the entire cohort. A total of 156 unique variants were identified, 78% of which can be considered null alleles. Variant c.2708_2711del/p.(V903Gfs*3) was found to constitute 14% of all disease-causing alleles. Special emphasis was placed on the validation of splice variants either by analyzing cDNA derived from patients´ blood samples or by heterologous splice assays using minigenes. Splicing analysis revealed different aberrant splicing events, including exon skipping, activation of exonic or intronic cryptic splice sites, and the inclusion of pseudoexons. Forty-eight variants that we identified were novel. Nine of them were classified as pathogenic, 34 as likely pathogenic and five as variant of uncertain significance. Our study adds a significant number of novel variants to the mutation spectrum of the OPA1 gene and will thereby facilitate genetic diagnostics of patients with suspected dominant optic atrophy.

Mutations at a split codon in the GTPase-encoding domain of OPA1 cause dominant optic atrophy through different molecular mechanisms

“…Of note, we have recently published a mutation overview of our cohort of 755 unrelated DOA patients, 278 of which harbor putatively pathogenic variants in OPA1 ( 31 ). Adding the recently identified patient with the c.1312G > C, p.(D438H) variant, nine cases of our cohort harbor variants at codon 438 ( Table 1 ).…”

“…The diagnosis of DOA was based on a history of gradual, bilateral loss of vision associated with the presence of central or caeco-central scotoma on visual field evaluation and symmetric temporal or diffuse optic disc pallor ( 31 ). Considering the known reduced penetrance of OPA1 -associated DOA, a pedigree demonstrating autosomal dominant inheritance was not a prerequisite for diagnosis.…”

The Role of Mitochondria in Optic Atrophy With Autosomal Inheritance

“…Autosomal OA is a genetically heterogeneous, monogenic disorder, primarily caused by mutations in nuclear genes encoding mitochondrial proteins. Mutations in OPA1 are the most common cause of autosomal OA ( Almind et al, 2012 ; Weisschuh et al, 2021 ). However, as discussed in detail below, mutations in at least 10 other genes are also associated with autosomal OA.…”

“…However, as discussed in detail below, mutations in at least 10 other genes are also associated with autosomal OA. Identified disease-causing mutations run the spectrum from nonsense, missense frameshift and splice mutations, but chromosomal rearrangements including copy number variants and inversions were also identified ( Fuhrmann et al, 2009 ; Weisschuh et al, 2021 ). The majority of disease-causing mutations are predicted to impair the function of the encoded protein, pointing to haploinsuffiency as the primary mechanism of pathogenicity in dominant forms of autosomal OA ( Neumann et al, 2020 ; Sun et al, 2021 ).…”

“…The majority of disease-causing mutations are predicted to impair the function of the encoded protein, pointing to haploinsuffiency as the primary mechanism of pathogenicity in dominant forms of autosomal OA ( Neumann et al, 2020 ; Sun et al, 2021 ). However, several cases report semi-dominant inheritance, where individuals carrying more than one OA-causing mutation present with much more severe disease than heterozygotic parents or siblings ( Pesch et al, 2001 ; Weisschuh et al, 2021 ). Several forms of recessively inherited OA have also been identified (associated with mutations in TMEM126A/OPA7 , SCL25A46 , MCAT and RTN4IP1/OPA10 ) and mutations in WFS1 , ACO2/OPA9 and OPA3 are associated with both recessive and dominant forms of OA ( Reynier et al, 2004 ; Meyer et al, 2010 ; Kloth et al, 2019 ; Charif et al, 2021b ).…”