Background Alport syndrome is a genetic disorder mostly caused by mutations in the COL4A3, COL4A4, and COL4A5 genes. The variability in symptoms and progression of renal disease may lead to a delayed diagnosis. We present a case of Alport syndrome in a patient whose mutation remained undetected despite numerous genetic tests but was promptly identified through genetic counseling, including three generations. Case A 20-year-old female patient exhibited microscopic hematuria detected during a health evaluation. Her medical history revealed that hematuria was first noted at around 3 to 4 years of age, leading to a preliminary diagnosis of Alport syndrome during primary education. Sequential genetic testing performed at university hospitals in Daejeon and Seoul did not identify any abnormalities. The patient's grandmother and the patient's father received a clinical diagnosis of Alport syndrome and were undergoing hemodialysis for end-stage renal disease, according to the family history. The patient exhibited no extra-renal symptoms. Her urinalysis revealed microscopic hematuria and proteinuria. The preliminary genetic counseling, which involved building a pedigree, concluded with a referral to a specialized genetic counseling clinic for the patient. We found a pathogenic mutation, c.2244+1G>A, in the COL4A5 locus (NM_033380.3) in the patient, her father, and her grandmother. After conducting extensive genetic testing on family members, we confirmed the diagnosis of X-linked Alport syndrome. Furthermore, we discovered that her younger brother carries a deleterious mutation, c.148C>T, in the CACNA1F gene (NM_001256789.3). Conclusions Genetic counseling facilitates a methodical assessment of clinical diagnoses and assists in the identification of appropriate genetic tests, significantly shortening the diagnostic duration. In rare genetic disorders, which exhibit complex inheritance patterns or atypical symptoms, early genetic counseling and management can significantly improve patient care. Genetic counseling prior to marriage, especially among young adults, helps prevent the transmission of inherited disorders to future generations.