The prevalence of congenital plasminogen deficiency has been estimated at 1.6 per one million people. This condition is believed to be underdiagnosed, because growths in one area are often not recognized as being a feature of a disorder that affects many body systems. Mild cases likely never come to medical attention.

Congenital plasminogen deficiency is caused by mutations in the PLG gene. This gene provides instructions for making a protein called plasminogen. Enzymes called plasminogen activators convert plasminogen into the protein plasmin, which breaks down another protein called fibrin. Fibrin is the main protein involved in blood clots and is important for wound healing, creating the framework for normal tissue to grow back. Excess fibrin is broken down when no longer needed, and the new, more flexible normal tissue takes its place.

PLG gene mutations can decrease the amount of plasminogen that is produced, its function, or both. When the mutations affect plasminogen levels as well as the activity of the protein, affected individuals may be said to have type I congenital plasminogen deficiency, characterized by the ligneous growths previously described. People with mutations that result in normal levels of plasminogen with reduced activity are said to have type II congenital plasminogen deficiency or dysplasminogenemia. This form of the condition often has no symptoms.

A reduction in functional plasminogen results in less plasmin to break down fibrin, leading to a buildup of fibrin. The excess fibrin and the resulting inflammation of the tissue result in the inflamed woody growths characteristic of congenital plasminogen deficiency.

It is unclear why the excess fibrin builds up in the mucous membranes but does not usually result in abnormal clots in the blood vessels (thromboses). Researchers suggest that other enzymes in the blood may also break down fibrin, helping to compensate for the reduced plasminogen levels.