Whole exome sequencing in family trios reveals de novo mutations in PURA as a cause of severe neurodevelopmental delay and learning disability

Abstract

Background: De novo mutations are emerging as an important cause of neurocognitive impairment, and whole exome sequencing of case-parent trios is a powerful way of detecting them. Here, we report the findings in four such trios.

Methods: The Deciphering Developmental Disorders study is using whole exome sequencing in family trios to investigate children with severe, sporadic, undiagnosed developmental delay. Three of our patients were ascertained from the first 1133 children to have been investigated through this large-scale study. Case 4 was a phenotypically isolated case recruited into an undiagnosed rare disorders sequencing study.

Results: Protein-altering de novo mutations in PURA were identified in four subjects. They include two different frameshifts, one inframe deletion and one missense mutation. PURA encodes Pur-α, a highly conserved multifunctional protein that has an important role in normal postnatal brain development in animal models. The associated human phenotype of de novo heterozygous mutations in this gene is variable, but moderate to severe neurodevelopmental delay and learning disability are common to all. Neonatal hypotonia, early feeding difficulties and seizures, or 'seizure-like' movements, were also common. Additionally, it is suspected that anterior pituitary dysregulation may be within the spectrum of this disorder. Psychomotor developmental outcomes appear variable between patients, and we propose a possible genotype-phenotype correlation, with disruption of Pur repeat III resulting in a more severe phenotype.

Conclusions: These findings provide definitive evidence for the role of PURA in causing a variable syndrome of neurodevelopmental delay, learning disability, neonatal hypotonia, feeding difficulties, abnormal movements and epilepsy in humans, and help clarify the role of PURA in the previously described 5q31.3 microdeletion phenotype.

Keywords: Clinical genetics; Developmental; Epilepsy and seizures; Neurology.

Figure 1

Depictions of the four mutations identified within PURA. (A) Schematic of Purα, depicting sites of the different mutations identified in our patients with respect to the Pur repeat regions (I–III). (B) Sequence alignment illustrating the high level of conservation of amino acids affected by the p.Ile206Phe and p.Phe233del mutations. Asterisk denotes complete conservation, colon denotes high conservation and single dot denotes moderate conservation. (C) and (D) illustrate the respective locations of the p.Ile206Phe and p.Phe233del mutations within the tertiary structure of the protein.

Figure 2

Clinical photographs. Patient 1 is shown at age 1 year 7 months (A and B) and 4 years 7 months (C). Patient 2 is shown at 7 years 3 months (D and E) and 14 years 3 months (F). Patient 3 is shown at 9 years 7 months (G and H) and 12 years 10 months (I). Patient 4 is shown at 6 years 9 months (J and K). While there is no obvious gestalt, all four patients were noted to have quite prominent foreheads with high anterior hairlines. Patients 1, 2 and 4 have mildly hypotonic facies.

Figure 3

Serial MRI brain scans from Patient 4. (A) At 1 week, there is patchy high attenuation within white matter and a right frontal horn cyst, which is not evident on subsequent scans. (B) At 14 months, the white matter appears normal but thickening of tissue at the ependymal margin of the right frontal horn is apparent. (C) At 2 years 2 months, subtle hypomyelination is apparent in that there is poor definition of the grey-white matter boundary in the frontal lobes. (D) At 3 years 10 months, subtle hypomyelination persists. (E) At 5 years, myelination is complete. However, there are excessive extra-axial fluid spaces and there is possible cerebral atrophy.