ATP6AP2-Related Disease Caused by Splicing Defects: Abnormal Glycosylation and the First Affected Female

ATP6AP2 splicing variants cause syndromic X-linked intellectual disability Hedera type (XPDS; OMIM#300423) and X-linked parkinsonism with spasticity (MRXSH; OMIM#300911). Alternatively, ATP6AP2 missense variants lead to hepatopathy, immunological abnormalities, cutis laxa and only mild intellectual disability with N-/O-glycosylation defects (ATP6AP2-CDG; OMIM#301045). The disparity between neurological and hepatic ATP6AP2-related disease entities is an ongoing puzzle. We aimed to investigate whether patients with an isolated neurological presentation of ATP6AP2-related disease, consistent with XPDS/MRXSH, also have abnormal glycosylation biomarkers, potentially implicating this as part of the pathological mechanism. We identified three males and one female from three families with ATP6AP2 splicing variants and ID/DD, epilepsy, axial hypotonia, axonal neuropathy and microcephaly; the heterozygous female has a milder phenotype. RNA-Seq in patient-derived fibroblasts validated defective splicing, correlated with lowered ATP6AP2 protein levels in fibroblasts alongside glycosylation abnormalities. We describe defective glycosylation alongside ATP6AP2 splicing variants in four patients, including the first female with ATP6AP2-related disease. This connects more closely the phenotypes of XPDS/MRXSH and ATP6AP2-CDG and indicates that abnormal glycosylation markers may be a consistent feature of splicing variants, and potentially part of the pathological mechanism underlying ATP6AP2-related disease caused by abnormal splicing. We also provide additional evidence that neurodevelopment is uniquely sensitive to the gene dosage of ATP6AP2, linked to the isolated neurological phenotype found in patients with splice variants and the attenuated, but still severe, phenotype of the female in our study. Glycosylation defects can be found in "splicing" forms of ATP6AP2-related diseases, bridging the gap between XPDS, MRXSH and ATP6AP2-CDG.