Protein elongation variant of PUF60: Milder phenotypic end of the Verheij syndrome

Abstract

The PUF60 gene encodes a ubiquitously expressed essential splicing factor that is recruited to the U2snRNA complex. The complex binds to the 3 0 splice site of exons in specific target genes and regulates the inclusion or exclusion of such exons. Recently, pathogenic variants of PUF60 have been shown to cause a relatively specific and potentially recognizable pattern of malformation referred to as Verheij syndrome. Here, we report a 12-year-old female patient with a de novo mutation in PUF60 whose phenotype was representative of the milder end of the phenotypic spectrum of Verheij syndrome; the de novo mutation was a frameshift mutation p. (Ser558Cysfs*21) that resulted in the addition of 21 extra amino acids at the carboxy end of the protein. Among the frequent features of Verheij syndrome, the patient exhibited coloboma, cervical spinal segmentation defects, and borderline intellectual functioning, but lacked cardiac abnormalities, deafness, and urogenital abnormalities. The results of RNA analysis using peripheral blood showed the escape of the mutant allele from nonsense-mediated mRNA decay, possibly accounting for the mild phenotype in the presently reported patient. Based on our clinical observations, we inferred that two embryologic processes, closure of the ocular plate and cervical spinal segmentation, are particularly susceptible to deficient PUF60-mediated splicing regulation, compared with other embryogenetic processes leading to the central nervous system, heart, ear, and kidney.

The diverse pleiotropic effects of spliceosomal protein PUF60: A case series of Verheij syndrome

“…A limitation of this, and previous reports regarding VRJS Nevertheless, it is evident that there is significant variability in the degree of neurodevelopmental delay and/or intellectual disability across the published patients, the interpretation of which is limited by the often-young age of the patients at the time of reporting such that psychometric evaluations have not yet been completed and which could also represent selection bias. The recent report of a patient with early neurodevelopmental delay but borderline intellectual functioning at 12 years-of-age reaffirms this limitation (Yamada et al, 2020).…”

“… PUF60 gene schematic diagram indicating exonic locations of disease‐causing mutations in this cohort and those previously published. Orange arrows indicate missense variants, red arrows indicate predicted LoF variants, green arrows indicate splice‐site variants, and the purple arrow indicates a frameshift variant in exon 12 reported by Yamada et al (2020) which causes protein extension, escape from NMD, and is predicted to cause disease by an unknown mechanism.…”

“…These include neurodevelopmental delay/intellectual disability (98%), axial skeletal anomalies (74%), appendicular skeletal anomalies (73%), oral anomalies (68%), short stature (66%), cardiac anomalies (63%), brain malformations (48%), hearing loss (46%), microcephaly (41%), colobomata (38%), and other ocular anomalies (65%) (Alkhunaizi & Braverman, 2019;Dauber et al, 2013;Deciphering Developmental Disorders, 2017;El Chehadeh et al, 2017;Fromer et al, 2014;Graziano et al, 2017;Haug et al, 2021;Isidor & David, 2015;Jourdain et al, 2020;Kernohan et al, 2018;Latypova et al, 2021;Low et al, 2017;Moccia et al, 2018;Santos-Simarro et al, 2017;Q. Xu et al, 2018;Yamada et al, 2020;Zanolli et al, 2020;Zhao et al, 2018). A limitation of this, and previous reports regarding VRJS Nevertheless, it is evident that there is significant variability in the degree of neurodevelopmental delay and/or intellectual disability across the published patients, the interpretation of which is limited by the often-young age of the patients at the time of reporting such that psychometric evaluations have not yet been completed and which could also represent selection bias.…”

“…However, she has never undergone formal psychometric evaluation. Yamada et al (2020) recently reported a patient who, having had early developmental delays, was confirmed to have borderline intellectual functioning. Her mild phenotype, relative to previously reported patients who all had intellectual disability, was attributed to the expression of normal levels of a mutant PUF60 transcript, as opposed to the haploinsufficiency identified in other patients with VRJS.…”

“…To date, 30 substantively phenotyped patients (Table S1) with VRJS due to PUF60 SNVs have been reported in peer-reviewed publications (Alkhunaizi & Braverman, 2019;Charzewska et al, 2018;Dauber et al, 2013;El Chehadeh et al, 2017;Graziano et al, 2017;Isidor & David, 2015;Latypova et al, 2021;Low et al, 2017;Moccia et al, 2018;Santos-Simarro et al, 2017;Q. Xu et al, 2018;Yamada et al, 2020;Zhao et al, 2018). Seven additional patients (Table S1) with de novo PUF60 SNVs have been identified through several cohort studies and reported, although the phenotypic data presented are extremely limited (Deciphering Developmental Disorders, 2017;Fromer et al, 2014;Haug et al, 2021;Jourdain et al, 2020;Kernohan et al, 2018;Zanolli et al, 2020).…”