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Introduction Congenital nephrotic syndrome (CNS) is a severe disease complicated by hemodynamic instability, infections, thrombosis, growth disorder and progressive renal failure leading to end-stage kidney disease within a few years. The mutations of NPHS1 encoding nephrin is the most common cause of the CNS. The aim of this paper was to present a patient with NPHS1 homozygous Ser350Pro missense mutation that unexpectedly caused a mild clinical course of CNS. Case outline We present a female patient who was diagnosed with severe nephrotic syndrome at 2.5 months of age. While waiting for the result of the genetic analysis, she was treated unsuccessfully with corticosteroids and angiotensin converting inhibitor (ACEI) four weeks, and then under Cyclosporine A (CsA) and ACEI she achieved partial remission within three months. Initially, the milder clinical course was explained by the positive effect of CsA, but as partial remission persisted even after the discontinuation of this drug, it remains unclear what influenced the improvement of the clinical course of the disease. At the time of writing this paper, the patient was 10.9 years old with normal serum creatinine, normal blood pressure and non-nephrotic proteinuria. Conclusion NPHS1 homozygous Ser350Pro missense mutation may be presented by a mild clinical course of CNS. Further studies are needed to clarify a more predictive CNS genotype/phenotype relationship. © 2024, Serbia Medical Society. All rights reserved.