A Colombian Boy with a Novel de novo PURA Variant: A Case Report

Abstract

Introduction

PURA syndrome is a neurodevelopmental disease caused by de novo pathogenic variants in PURA encoding the purine-binding element alpha protein. It is characterized by autosomal dominant inheritance and a heterogeneous phenotype.

Case Presentation

We describe a 7-year-old patient with history of congenital pneumonia, accompanied by hypotonia, convulsive episodes, poor sucking ability, neurodevelopmental delay. Physical examination revealed some dysmorphic features. Molecular analysis identified a de novo, heterozygous variant in PURA (NM_005859.5): c.692T>C; p.Phe231Ser, which was classified as pathogenic.

Conclusion

In this report, we present a Colombian case of PURA syndrome. This case highlights the challenges associated with the early diagnosis of a newly described syndrome, in a limited-resources health system.

Established Facts

• PURA syndrome is an autosomal dominant condition caused by de novo pathogenic variants in Purine-rich element-binding protein A (PURA) gene, located on the chromosome region 5q31.2-q31.3.

• Nonspecific white hyperintensities and a dilated ventricular system are the most frequently encountered anomalies on MRI.

Novel Insights

• Patient presents with a missense variant c.692T>C p.(Phe231Ser) in exon 1 of the PURA gene classified as pathogenic according to the ACMG guidelines, not previously described in the literature but enlisted as pathogenic in the ClinVar variant database with one entry, confirming the diagnosis of PURA syndrome.

• Mild parenchymal atrophy, dysgenesis of the corpus callosum, and cerebellar vermis hypoplasia have been described but are not present in this case.

Introduction

PURA syndrome is a neurodevelopmental disease caused by de novo pathogenic variants in PURA. Its phenotype is heterogeneous and can include moderate to severe intellectual disability, hypotonia, movement disorders, epilepsy, dysmorphic facial features, and brain abnormalities; associated with respiratory insufficiency, feeding difficulties, and cardiovascular, urogenital, skeletal, and endocrine abnormalities [1, 2].

Purine-rich element-binding protein A (PURA) gene, located on chromosome 5q31, has a single exon and encodes the Pur-α protein, which is 322 amino acids long [2, 3]. The protein is highly conserved and is essential for normal postnatal brain development, namely the formation and proliferation of neuronal synapses [4]. PURA syndrome was first described in 2014, and subsequently, more than 70 patients with de novo variants in PURA have been described [5, 6]. This report presents a Colombian case of PURA syndrome with a matching phenotype and molecular diagnosis, highlighting the challenges associated with early diagnosis of a recently described syndrome, and emphasizes the importance of whole-exome sequencing (WES) in identifying new pathogenic variants.

Case Report

The patient is a 7-year-old Colombian boy, who was born from a non-consanguineous union after a full-term pregnancy. At birth, the child had normal weight and length but required neonatal intensive care due to jaundice and congenital pneumonia. This was accompanied by hypotonia, convulsive episodes, and poor sucking ability associated with oropharyngeal dysphagia and micro aspirations revealed in cine video-deglutition, for which he received symptomatic supportive management. Metabolic disorders were ruled out. The patient demonstrated neurodevelopmental delays, achieving cephalic support at 6 months, sitting at 12 months, walking at 6 years, and language delay. Additionally, from birth, the patient had recurrent pneumonia caused by aspiration and swallowing dysfunction. Furthermore, a severe hypopnea apnea syndrome developed, requiring continuous positive airway pressure in the night, and dystonic movements became evident.

The patient underwent a medical genetic consultation at the age of 5-years. Short stature (p < 1, 3.0 SD), and normal weight and a head circumference (p 7, −1.48 SD and p 41, −0.22 SD, respectively) were noted. He had some dysmorphic features, including a high hairline, right strabismus, almond shape eyes, high arched palate, and a flattened philtrum. He demonstrated excessive salivation, his chest had increased anteroposterior diameter; in extremities he had a single right palmar crease, flat feet, acropachy of the hands and feet, and hirsutism of the extremities (Fig. 1). Additionally, neurologic evaluation showed axial hypotonia, spasticity with occasional dystonic movements affecting motor function and gait. He had severe psychomotor development delay, lack of interaction with others, and a lack of expressive language.

Fig. 1.

High hairline, right strabismus, almond shape eye, high arched palate, flattened philtrum, excessive salivation, chest with increased anteroposterior diameter.

Routine hematologic test and routine blood biochemestries were normal, including creatine kinase. Brain magnetic resonance imaging revealed basal ganglia hyperintensities on T1-weighted slices (Fig. 2) and a dilated ventricular system. A electroencephalogram indicated baseline cortical dysfunction and acute epileptiform paroxysms predominantly on the right bitemporal region. The chromosome microarray analysis was normal, so a trio WES analysis was performed and revealed a pathogenic de novo heterozygous variant PURA: (NM_005859.5) c.692T>C; p.Phe231Ser, which was absent in parental samples.

Fig. 2.

Magnetic resonance imaging head findings in the patient: T1-weighted image reveal T1 hyperintensities in the ganglio basal region on axial images.

Material and Methods

Chromosome Microarray Analysis

The Affymetrix CytoScan 750K gene chip (Applied Biosystems) was used for microarray analysis and ChAS software was used to analyze the data. The established size threshold for reporting copy number variants was ≥100 Kb for gains and losses, and ≥5 Mb for reduction of heterozygosity.

Whole-Exome Sequencing

Genomic DNA of the proband and his parents was sequenced using next-generation sequencing. Whole-exome trio sequencing was performed. Capture was performed using the SureSelectXT Human All Exon V6 (Agilent Technologies) and sequencing was performed on an Illumina NovaSeq, with a read length of 2 × 150 bp.

The sequencing reads were aligned to the human reference genome (GRCh37/hg19). Variants were filtered using analysis software according to their predicted effects, allele frequencies, with a read count, ≥10× and variant reads/total reads ratio ≥0.2. The analyzed regions include the coding exons and adjacent intronic regions (±8 bp) of the captured genes. The Integrative Genomics Viewer was used for visual exploration of the clinically relevant variants. The American College of Medical Genetics and Genomics (ACMG) criteria was used for variant classification [7].

Results

Genetic Testing

The chromosome microarray analysis showed no chromosome numerical abnormalities or pathogenic copy number variants. Trio whole-exome analysis yielded an average read depth of 133.25x. Coverage (≥20×) of the coding regions of the genes was 97.44%. A pathogenic, de novo, heterozygous variant PURA: (NM_005859.5) c.692T>C; p.Phe231Ser, was identified in the patient and was absent in the parental sequence datasets.

Discussion

PURA syndrome is an autosomal dominant condition caused by de novo pathogenic variants in Purine-rich element-binding protein A (PURA) gene, located on the chromosome region 5q31.2-q31.3; that encodes a highly conserved protein that regulates DNA replication, gene transcription, and mRNA translation. It is expressed in the brain, and influences the proliferation of neurons, oligodendrocytes and astrocytes, and synapse formation [5, 7, 8].

The disease is a neurodevelopmental disorder with significant delays in neurodevelopment, particularly in language and ambulation, associated with neonatal respiratory insufficiency with recurrent central and obstructive apneas from early in infancy, hypotonia, feeding difficulties, seizures, abnormal nonepileptic movements, and visual impairment [6]. Less frequently, there are cardiovascular, urogenital, skeletal, and endocrine abnormalities associated with this condition.

Our patient presented with hypotonia and poor feeding from the neonatal period, associated with progressive oropharyngeal dysphagia and micro aspirations, global neurodevelopmental delay, nonverbal (achieving only babbling), epilepsy, and nonepileptic movements and difficulties for independent ambulation [9, 10]. All of this is consistent with the previously reported PURA syndrome. Also, nonspecific white hyperintensities are the most frequently reported brain abnormalities. Mild parenchymal atrophy, dysgenesis of the corpus callosum, and cerebellar vermis hypoplasia have been described but are absent in our case [3, 4]. The facial phenotype was characterized as having a hypotonic face, almond shape eyes, high arched palate, high anterior hairline, flat nasal bridge, and a well-defined philtrum [1], which coincides with our patient.

According to the patient’s phenotype and early presentation, it is important to note that this type of clinical presentation often poses challenges for clinicians in terms of diagnosis and management due to a lot of conditions that should be considered as differential diagnoses. In this instance WES is recommended due to the numerous entities that can present with a similar clinical picture [11]. It should be noted that PURA syndrome is a rare entity that has been recently described.

However, in the Colombian context, although the evaluation by specialists, including geneticists, alongside advanced studies such as exome sequencing, are covered under the country's health benefits plan guaranteed to all persons affiliated with the Social Security Health System, it is often not feasible to carry out these specialized investigations. Furthermore, the limited number of hospitals with genetics clinics significantly restricts patient access to these evaluation, particularly for those that live in isolated areas with limited access to specialized medicine.

Our patient presents with a missense variant c.692T>C p.(Phe231Ser) in exon 1 of the PURA gene, which involve a substitution from thymine to cytosine at the highly conserved nucleotide position 692, leading to a change from phenylalanine to serine at the evolutionarily conserved amino acid position, classified as pathogenic according to ACMG College of Medical Genetics and Genomics (criteria PM1, PM2, PM5, PM1, PP2, PP3, PP5) [12], not previously described in the literature but enlisted as pathogenic in the ClinVar variant database with one entry, confirming the diagnosis of PURA syndrome.

Currently, the patient is receiving comprehensive management, including physical, occupational, and speech therapy, as well as follow-up by various pediatric specialties including neuropediatric, pediatric palliative care (due a program in our hospital for pediatric patients with chronic diseases and rare diseases that support and improve the quality of life of patients and their families), and psychiatry. The patient’s progress is being monitored in the medical genetics clinic, and Genetic counseling was provided to the parents, explaining that this is a de novo disorder with a low recurrence risk.

PURA syndrome is not a degenerative disorder, so survival into adulthood is expected, barring illness or complications. As of now, no specific therapy has been discovered for the disease and management is essentially symptomatic.

In conclusion, PURA syndrome is a rare disease with an autosomal dominant inheritance pattern, with a broad phenotypic spectrum, characterized by hypotonia, feeding difficulties, respiratory disorders, epileptic events, abnormal nonepileptic movements, and visual impairment. These patients require multidisciplinary management given the multisystemic clinical involvement.

Acknowledgments

The authors would like to thank the patient's family for agreeing to the publication of this report. We also thank the people who have contributed to the development and execution of this study.

Statement of Ethics

This study was approved by the Ethics Committee of Fundación Valle del Lili, Colombia (human study protocol #617) and performed in accordance with the Declaration of Helsinki. Written informed consent was obtained from the patient. Information revealing the subject’s identity was not included in the manuscript. The proband’s parents were consented for sample collection, subsequent analysis, and written informed consent for the publication and accompanying images.

Conflict of Interest Statement

The authors have no conflicts of interest to declare.

Funding Sources

There is no funding to declare.

Author Contributions

All authors listed have made a substantial, direct, and intellectual contribution to the work and approved it for publication.

Funding Statement

There is no funding to declare.

Data Availability Statement

The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.