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Introduction This study evaluated the phenotypic and pathology characteristics of patients undergoing kidney biopsy at a single center, while also determining the frequency and factors associated with clinical outcomes. Methods The incidence and distribution of biopsy-proven kidney diseases in 2000-2019 were surveyed. Consecutive individuals diagnosed with membranous nephropathy (MN), immunoglobulin A nephropathy (IgAN), and minimal change disease (MCD) between August 2015 and December 2019 were enrolled in the prospective two-year follow-up study. Outcomes included remission of proteinuria and kidney disease progression events. Multivariable adjusted Cox proportional hazards model was applied. Results 4,550 kidney biopsies were performed in 2000–2019, showing a noticeable increase in the proportion of MN. 426 patients were enrolled in follow-up cohort. 346 (81.2%) achieved remission of proteinuria, 39 (9.2%) suffered kidney disease progression and 51.3% of them were diagnosed with IgAN. Kidney pathological diagnosis (MN vs. MCD: hazard ratio [HR], 0.42; 95% confidence interval [95% CI], 0.31–0.57; IgAN vs. MCD: 0.58; 0.39–0.85), levels of 24-h urine protein at biopsy (1.04; 1.00–1.08) and presence of nodular mesangial sclerosis (0.70; 0.49–0.99) were significantly correlated with remission of proteinuria after adjusting for baseline variables. 24-h urine protein levels at biopsy (1.14; 1.04–1.25) and the presence of crescents (2.30; 1.06–4.95) were the independent risk factors for kidney disease progression events after adjusting for baseline variables. Conclusion The increasing frequency of MN was affirmed over the past two decades. The therapeutic status, clinical outcomes, and factors influencing these outcomes were presented in this single-center study for the three primary glomerular diseases. Number of China Clinical Trial Registry: ChiCTR2100043001.

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