PROTHROMBIN GENE MUTATION Prothrombin gene mutation is the second most common cause of inherited thrombophilia in the United States. It is present in about 2% of Caucasians. It is caused by a cha nge or mutation in the gene for the blood clotting protein called prothrombin (which is also called Factor II).People with the prothrombin gene mutation have higher than normal levels of prothrombin in their blood, making them prone to blood clots, most common in the veins.t is caused by a cha nge or mutation in the gene for the blood clotting protein called prothrombin (which is also called Factor II). People with the prothrombin gene mutation have higher than normal levels of prothrombin in their blood, making them prone to blood clots, most common in the veins.