De Novo Heterozygous POLR2A Variants Cause a Neurodevelopmental Syndrome with Profound Infantile-Onset Hypotonia

Abstract

The RNA polymerase II complex (pol II) is responsible for transcription of all $21,000 human protein-encoding genes. Here, we describe sixteen individuals harboring de novo heterozygous variants in POLR2A, encoding RPB1, the largest subunit of pol II. An iterative approach combining structural evaluation and mass spectrometry analyses, the use of S. cerevisiae as a model system, and the assessment of cell viability in HeLa cells allowed us to classify eleven variants as probably disease-causing and four variants as possibly diseasecausing. The significance of one variant remains unresolved. By quantification of phenotypic severity, we could distinguish mild and severe phenotypic consequences of the disease-causing variants. Missense variants expected to exert only mild structural effects led to a malfunctioning pol II enzyme, thereby inducing a dominant-negative effect on gene transcription. Intriguingly, individuals carrying these variants presented with a severe phenotype dominated by profound infantile-onset hypotonia and developmental delay. Conversely, individuals carrying variants expected to result in complete loss of function, thus reduced levels of functional pol II from the normal allele, exhibited the mildest phenotypes. We conclude that subtle variants that are central in functionally important domains of POLR2A cause a neurodevelopmental syndrome characterized by profound infantile-onset hypotonia and developmental delay through a dominant-negative effect on pol-II-mediated transcription of DNA.

Germline mutation in POLR2A: a heterogeneous, multi-systemic developmental disorder characterized by transcriptional dysregulation

“…Very recently the first report of pathogenic germline mutations in POLR2A was published, describing a phenotypically heterogeneous neurodevelopmental syndrome with hypotonia (MIM: 618603). 6 Here, we report additional clinical and molecular evidence strengthening the case for POLR2A dysfunction as a multi-systemic, phenotypically heterogeneous Mendelian disorder.…”

“…Attempts were made to contact all individuals and recruit to a research protocol (see Material and methods ). After the initial report of de novo variation in POLR2A causing a Mendelian disorder, 6 five additional individuals were subsequently identified through the genetics clinic at Texas Children’s Hospital and a social media-based support group for families of individuals diagnosed with pathogenic variants in POLR2A ( Table 1 ), including one previously published individual for whom amended and additional phenotypic information is provided (individual 7; Haijes et al, 6 individual 15). The family of individual 7 reports that she is positive for a few phenotypes previously reported as negative: feeding difficulty/failure to thrive, decreased endurance, and decreased fetal movement.…”

“…Individuals 2–5 and 7 were ascertained for this study after the initial published discovery of a POLR2A -related developmental disorder, with analysis conducted by the Broad CMG or other commercial clinical laboratories. 6 …”

Exome sequencing in patients with microphthalmia, anophthalmia, and coloboma (MAC) from a consanguineous population

“…We also identified a variant with a classification of likely pathogenic in POLR2A (Table 3), but this gene is not known to be associated with MAC. 11 We found several variants of unknown significance (VUSs) in these patients. In EG38_1, with unilateral iris and chorioretinal colo- tary stalk interruption syndrome, but only congenital convergent strabismus was reported in these patients.…”

“…The presence of cataracts potentially expands the ocular phenotype associated with loss of function variants in TENM3 , as cataracts have not previously been described. We also identified a variant with a classification of likely pathogenic in POLR2A (Table 3), but this gene is not known to be associated with MAC 11 …”