Omeprazole is a proton pump inhibitor (PPI) that may cause kidney injury and result in low blood magnesium levels. This does not occur in all patients but can occur in some individuals. You have Autosomal Dominant Polycystic Kidney Disease (ADPCKD) and should be monitored for blood magnesium levels. If you are benefiting from the medication and not suffering any ill effects, it should be safe for you to continue. Ranitidine (Zantac) is a histamine blocker and may be an alternative to the PPI. I suggest that you discuss this issue with your physician and have further monitoring both of kidney function, urine testing and blood magnesium levels.