Supplementary file 2_Retropseudogene insertion generated through retrotransposition in the ATP7A gene results in premature stop codons and a case of Menkes disease.docx

Pathogenic variants in the ATP7A gene, which encodes a transmembrane copper-transporting P-type ATPase, underlie Menkes disease, a rare X-linked recessive disorder of copper metabolism. We report a 3-year-old boy presenting with progressive neurodegeneration, refractory epilepsy, connective tissue abnormalities, and characteristic kinky hair. Whole-exome sequencing and confirmatory analysis identified a retropseudogene insertion (~500 bp) in exon 3 of ATP7A, displaying the hallmarks of target-primed reverse transcription. PCR and RNA-seq revealed a marked reduction in ATP7A transcript levels in the patient. This case underscores the diagnostic relevance of retropseudogene insertions in disease genes and highlights their role in human pathology.