Pediatric primary ciliary dyskinesia with rare genetic variants: Synonymous RSPH4A and potential NFE2L2 modifier of DNAH9 phenotype - 2-case report

<h4>Rationale</h4>Primary ciliary dyskinesia (PCD) is easily underdiagnosed in children without laterality defects. We report 2 pediatric cases of PCD, highlighting a candidate pathogenic synonymous RSPH4A variant and a possible modifier effect of NFE2L2 on DNAH9-related disease.<h4>Patient concerns</h4>Case 1: a 5-year-old girl presented with chronic wet cough and recurrent pulmonary consolidations. Case 2: a 5-year-old boy presented with chronic wet cough, recurrent wheeze, and rhinosinusitis.<h4>Diagnoses</h4>Case 1 had a normal immune work-up and underwent trio whole-exome sequencing (WES), which identified compound heterozygous RSPH4A variants (c.1391G>A and the synonymous c.1764G>T variant with a high predicted splicing impact), supporting a diagnosis of PCD. Case 2 had markedly elevated immunoglobulin E and an obstructive ventilatory defect; WES identified compound heterozygous DNAH9 variants together with an NFE2L2 exon 2-5 deletion, consistent with PCD with enhanced type 2 inflammation.<h4>Interventions</h4>Case 1 received antibiotic therapy. Case 2 was treated with antibiotics, bronchodilators, and inhaled corticosteroids.<h4>Outcomes</h4>Case 1 improved after antibiotic therapy, and no bronchiectasis was detected during follow-up. Case 2 also improved clinically, although moderate airflow obstruction persisted.<h4>Lessons</h4>These cases suggest that synonymous variants with strong splicing predictions in PCD genes may be pathogenic and that NFE2L2-related pathways may modify DNAH9-associated PCD severity. Early WES may facilitate diagnosis in children with chronic wet cough and recurrent infections, even without laterality defects.