Reclassification of Two COL4A4 Gene Variants of Uncertain Significance in a Korean Family with Alport Syndrome by Transcript Analysis and Trio Testing

Hereditary nephritis, also known as Alport syndrome, is a genetic disorder characterized by progressive loss of kidney function and frequent sensorineural hearing loss and/or eye abnormalities.Alport syndrome is frequently caused by mutations in the COL4A3, COL4A4, and COL4A5 genes.We identified two novel variants in the COL4A4 gene originally classified as variants of uncertain significance (VUS) in a Korean pediatric patient and her older sibling, both diagnosed with Alport syndrome.Their father also had chronic kidney disease of unknown origin.Next-generation sequencing (NGS) revealed a COL4A4 c.489+6A>G (p.?) intronic variant and a c.3317G>T (p.Gly1106Val) exonic variant in the proband.The intronic variant caused aberrant splicing, resulting in a frameshift mutation due to the addition of five base pairs between c.489+1 and c.489+5.Parental testing confirmed that the two variants in the proband existed in an in-trans configuration.The older sibling was also confirmed to carry both variants.This case emphasizes the importance of RNA sequencing and parental testing in reclassifying novel genetic variants.