COL4A5 gene mutations are known as the cause of Alport syndrome (AS), which typically manifests with hematuria, progressive renal failure, sensorineural hearing loss, and ocular abnormalities. Here we report a case of a 20-year-old male patient presenting with nephrotic syndrome who was diagnosed as having AS with focal segmental glomerulosclerosis (FSGS) lesion after the renal biopsy was performed. In this patient, the link between AS and FSGS lesion is complicated. Whole-exome sequencing was performed to identify its causal genetic variants, and the results revealed that AS with FSGS lesion is caused by mutation of the COL4A5 gene. COL4A5 gene mutations have phenotypic heterogeneity and thus, we suggest that genetic testing should be considered in such patients for accurate diagnosis and appropriate treatment.