Hypomorphic mutations in POLR3A are a frequent cause of sporadic and recessive spastic ataxia

Abstract

Despite extensive efforts, half of patients with rare movement disorders such as hereditary spastic paraplegias and cerebellar ataxias remain genetically unexplained, implicating novel genes and unrecognized mutations in known genes. Non-coding DNA variants are suspected to account for a substantial part of undiscovered causes of rare diseases. Here we identified mutations located deep in introns of POLR3A to be a frequent cause of hereditary spastic paraplegia and cerebellar ataxia. First, whole-exome sequencing findings in a recessive spastic ataxia family turned our attention to intronic variants in POLR3A, a gene previously associated with hypomyelinating leukodystrophy type 7. Next, we screened a cohort of hereditary spastic paraplegia and cerebellar ataxia cases (n = 618) for mutations in POLR3A and identified compound heterozygous POLR3A mutations in ∼3.1% of index cases. Interestingly, >80% of POLR3A mutation carriers presented the same deep-intronic mutation (c.1909+22G>A), which activates a cryptic splice site in a tissue and stage of development-specific manner and leads to a novel distinct and uniform phenotype. The phenotype is characterized by adolescent-onset progressive spastic ataxia with frequent occurrence of tremor, involvement of the central sensory tracts and dental problems (hypodontia, early onset of severe and aggressive periodontal disease). Instead of the typical hypomyelination magnetic resonance imaging pattern associated with classical POLR3A mutations, cases carrying c.1909+22G>A demonstrated hyperintensities along the superior cerebellar peduncles. These hyperintensities may represent the structural correlate to the cerebellar symptoms observed in these patients. The associated c.1909+22G>A variant was significantly enriched in 1139 cases with spastic ataxia-related phenotypes as compared to unrelated neurological and non-neurological phenotypes and healthy controls (P = 1.3 × 10-4). In this study we demonstrate that (i) autosomal-recessive mutations in POLR3A are a frequent cause of hereditary spastic ataxias, accounting for about 3% of hitherto genetically unclassified autosomal recessive and sporadic cases; and (ii) hypomyelination is frequently absent in POLR3A-related syndromes, especially when intronic mutations are present, and thus can no longer be considered as the unifying feature of POLR3A disease. Furthermore, our results demonstrate that substantial progress in revealing the causes of Mendelian diseases can be made by exploring the non-coding sequences of the human genome.

Clinical spectrum of POLR3-related leukodystrophy caused by biallelic POLR1C pathogenic variants

“…6 It is also well established that hypomyelination on brain MRI is not obligate in POLR3-related disorder. [27][28][29][30] Therefore, we cannot exclude that the 5 patients with TCS attributed to variants in POLR1C could have a mild form of POLR3-HLD, with only subtle neurologic manifestations, if any. We suspect that there is a spectrum of disease severity for both the hypomyelination and the non-neurologic manifestations in POLR3-HLD caused by biallelic POLR1C variants, as it is the case in patients carrying pathogenic variants in POLR3A or POLR3B.…”

Autosomal Recessive Cerebellar Ataxias: Paving the Way toward Targeted Molecular Therapies

“…Despite all progress with NGS, z50% of patients with the clinical suspicion of ARCA remain without a molecular diagnosis. This may reflect not only new ARCA genes but also mutations in established genes that escape current diagnostic strategies such as deep intronic mutations, mutations in regulatory regions, epigenetic changes, gene dosage effects, or digenic modes of inheritance (for examples, see Bonifert et al, 2014;Minnerop et al, 2017).…”

Molecular genetic testing for hereditary ataxia

“…However, deep intronic pathogenic variants that have been described in some individuals with hereditary ataxia are not reliably detected by clinical exome sequencing. 8 How to compare molecular genetic testing options? If the clinical features or family history suggest a specific hereditary ataxia, single gene testing can be considered.…”