SLC20A2 Intragenic Structural Variants as a Cause of Primary Brain Calcification

BACKGROUND: Intragenic structural variants of SLC20A2 remain poorly characterized in primary brain calcification (PBC). OBJECTIVES: The aim was to identify and characterize intragenic SLC20A2 structural variants in PBC. METHODS: One familial PBC pedigree and two sporadic patients underwent whole-genome sequencing and copy-number analysis, followed by polymerase chain reaction (PCR) and Sanger validation. Long-read sequencing (LRS) resolved complex architecture. Transcript and protein effects were assessed by reverse transcription (RT)-PCR, RT-quantitative PCR, and western blotting. RESULTS: We identified three intragenic SLC20A2 structural variants: exon 2-3 and exon 5 tandem duplications in F1 and F3, respectively, and a complex exon 2-3 inverted insertion in F2. F1 and F3 showed aberrant, frameshift-generating transcripts, and F3 showed reduced SLC20A2 mRNA and protein. Accordingly, the F1 and F3 variants were classified as pathogenic, whereas the F2 variant remained of uncertain significance. CONCLUSIONS: Our study expands the spectrum of intragenic SLC20A2 structural variation in PBC and highlights the value of copy number variation analysis and LRS in genetically unresolved individuals.