Severe hypertension can lead to irreversible kidney failure and end-stage renal disease (ESRD) and vice versa. Patients are often classified as hypertensive ESRD with no confirmative proof and the true cause of disease can therefore be missed, affecting outcomes. We present a case of chronic thrombotic microangiopathy (TMA) after kidney transplantation in a recipient who had been classified as hypertensive ESRD and found to have a genetic defect in CD46, a transmembrane protein that regulates complement activation, indicating atypical hemolytic uremic syndrome (HUS). The pathogenic variant in <i>CD46</i> was also found in the mother who donated the kidney, indicating that the TMA occurred on the background of atypical HUS instead of severe hypertension. The patient died from disseminated cancer originated in the mother’s kidney. Knowledge of the genetic background would have prevented recurrent disease and the cancer to occur. Patients classified as hypertensive ESRD suspect for TMA should therefore be screened for variants in complement genes to make informed decisions and save kidneys.