De Novo Variants Disturbing the Transactivation Capacity of POU3F3 Cause a Characteristic Neurodevelopmental Disorder

Abstract

POU3F3, also referred to as Brain-1, is a well-known transcription factor involved in the development of the central nervous system, but it has not previously been associated with a neurodevelopmental disorder. Here, we report the identification of 19 individuals with heterozygous POU3F3 disruptions, most of which are de novo variants. All individuals had developmental delays and/or intellectual disability and impairments in speech and language skills. Thirteen individuals had characteristic low-set, prominent, and/or cupped ears. Brain abnormalities were observed in seven of eleven MRI reports. POU3F3 is an intronless gene, insensitive to nonsense-mediated decay, and 13 individuals carried protein-truncating variants. All truncating variants that we tested in cellular models led to aberrant subcellular localization of the encoded protein. Luciferase assays demonstrated negative effects of these alleles on transcriptional activation of a reporter with a FOXP2-derived binding motif. In addition to the loss-of-function variants, five individuals had missense variants that clustered at specific positions within the functional domains, and one small in-frame deletion was identified. Two missense variants showed reduced transactivation capacity in our assays, whereas one variant displayed gain-of-function effects, suggesting a distinct pathophysiological mechanism. In bioluminescence resonance energy transfer (BRET) interaction assays, all the truncated POU3F3 versions that we tested had significantly impaired dimerization capacities, whereas all missense variants showed unaffected dimerization with wild-type POU3F3. Taken together, our identification and functional cell-based analyses of pathogenic variants in POU3F3, coupled with a clinical characterization, implicate disruptions of this gene in a characteristic neurodevelopmental disorder.

Coexistence of severe developmental delay, epilepsy, and hemangioma in Snijders Blok‐Fisher syndrome suggests the presence of a POU3F3‐related SNIBFIS endophenotype: A case report

“…Conservation alignment indicating that the POU‐S domain is highly conserved across different species. To date, three variants affecting the POU‐S have been reported, including the current study (red) and the previous study (blue) (* Snijders Blok et al, 2019). POU‐S (yellow): POU‐specific domain; POU‐H (turquoise): POU homeodomain [Color figure can be viewed at wileyonlinelibrary.com]…”

“…POU3F3 has two known functional domain, POU‐Specific (POU‐S) and POU‐Homeodomain (POU‐H), and both required for the site‐specific binding to the different target genes (He et al, 1989; Li et al, 1993; Phillips et al, 2000). Recently, pathogenic POU3F3 variants have been associated with a neurodevelopmental disorder called Snijders Blok‐Fisher syndrome (SNIBFIS) (OMIM: #618604), which is characterized by intellectual disability (ID) and developmental delay (DD), speech problems, hypotonia, autism spectrum disorders, and overlapping dysmorphic features (Snijders Blok et al, 2019). In their report, 19 individuals with heterozygous POU3F3 variants have been reported: frameshift (9 of 19), missense (5 of 19), nonsense (4 of 19), and inframe deletion (1 of 19) type of variants constituted the spectrum.…”

Loss-of-function tolerance of enhancers in the human genome

“…The two TF families with strongest enrichment and lowest p-values are POU domain genes (POU3F1/2/3, POU1F1, POU2F2) and GSX1/2 (S8B Fig). Both of them are involved in neurogenesis [54][55][56]. Motifs of SOX10, which is critical during embryonic development, are also enriched in low-LoF-tolerance enhancers [57][58][59].…”

De novo variants in population constrained fetal brain enhancers and intellectual disability

“…We identified recurrent variants within three fetal brain enhancer clusters associated with genes involved in nervous system development (CSMD1, OLFM1, POU3F3), and found that this enrichment was significant relative to expectations. All three genes show high pLI score (1, 1, 0.88 respectively), indicating that they are intolerant to loss of function variants and dosage sensitive, and one of them (POU3F3) was recently shown to harbor disease-causing heterozygous variants in patients with ID 52 . Our results suggest that enhancer variants could lead to dysregulation of these genes during nervous system development and thereby contribute to the etiology of ID.…”

“…All three genes (CSMD1, OLFM1 and POU3F3) play a role in nervous system development [48][49][50] . Heterozygous variants in POU3F3 protein coding regions have been recently implicated in ID 51,52 . A known role of these genes in nervous system development and the presence of recurrent variant in enhancer clusters associated with these genes in ID cohort suggest that these enhancer DNVs may contribute to ID.…”