Nonsense pathogenic variants in exon 1 of PHOX2B lead to translational reinitiation in congenital central hypoventilation syndrome

Abstract

Pathogenic variants in PHOX2B lead to congenital central hypoventilation syndrome (CCHS), a rare disorder of the nervous system characterized by autonomic dysregulation and hypoventilation typically presenting in the neonatal period, although a milder late-onset (LO) presentation has been reported. More than 90% of cases are caused by polyalanine repeat mutations (PARMs) in the C-terminus of the protein; however non-polyalanine repeat mutations (NPARMs) have been reported. Most NPARMs are located in exon 3 of PHOX2B and result in a more severe clinical presentation including Hirschsprung disease (HSCR) and/or peripheral neuroblastic tumors (PNTs). A previously reported nonsense pathogenic variant in exon 1 of a patient with LO-CCHS and no HSCR or PNTs leads to translational reinitiation at a downstream AUG codon producing an N-terminally truncated protein. Here we report additional individuals with nonsense pathogenic variants in exon 1 of PHOX2B. In vitro analyses were used to determine if these and other reported nonsense variants in PHOX2B exon 1 produced N-terminally truncated proteins. We found that all tested nonsense variants in PHOX2B exon 1 produced a truncated protein of the same size. This truncated protein localized to the nucleus and transactivated a target promoter. These data suggest that nonsense pathogenic variants in the first exon of PHOX2B likely escape nonsense mediated decay (NMD) and produce N-terminally truncated proteins functionally distinct from those produced by the more common PARMs.

Causative and common PHOX2B variants define a broad phenotypic spectrum

“…Proximal N‐terminal truncated proteins seem to be less damaging than C‐terminal truncated proteins, as supported by functional studies showing that exon 1 nonsense mutations produce proteins able to translocate into the nucleus where they can still transactivate target genes, while exon 3 nonsense mutations produce proteins with impaired localization and function . Moreover, nonsense mutations are mainly found in exon 1, upstream the translational reinitiation codon, where they are much more tolerated and can segregate in families (Figure ) .…”

“…Among NPARMs, nonsense mutations lying in the proximal portion of exon 1 are associated with very mild phenotypes though a very short truncated protein is expected . Indeed, despite their proximity to the start codon, the nonsense‐mediated decay (NMD) control system fails to degrade the corresponding transcript because an alternative start codon is used for translation (Met18 or Met21), thus leading to the production of N‐terminal truncated proteins shorter than the wild type but still retaining some functionality able to avoid the expected PHOX2B haploinsufficiency . The mild effect of exon 1 truncated mutations have been reproduced by the Dilp1 mouse model, carrying a stop codon close to the start of the phox2b coding sequence and showing only an ocular phenotype, a clinical feature sometimes associate with CCHS …”

“…Among NPARMs, nonsense mutations lying in the proximal portion of exon 1 are associated with very mild phenotypes though a very short truncated protein is expected. 47,48 Indeed, despite their proximity to the start codon, the nonsense-mediated decay (NMD)…”

What is new about the genetic background of Hirschsprung disease?

“…The interaction among this transcription factor and RET HSCR‐associated SNPs increases the susceptibility to this pathology . Different mutations in this gene have been associated with HSCR and/or CCHS …”

“…95,117,118 Different mutations in this gene have been associated with HSCR and/or CCHS. 26,[119][120][121][122]…”