In Western countries, complement component 2 deficiency is estimated to affect 1 in 20,000 individuals; its prevalence in other areas of the world is unknown.

Complement component 2 deficiency is caused by mutations in the C2 gene. This gene provides instructions for making the complement component 2 protein, which helps regulate a part of the body's immune response known as the complement system. The complement system is a group of proteins that work together to destroy foreign invaders, trigger inflammation, and remove debris from cells and tissues. The complement component 2 protein is involved in the pathway that turns on (activates) the complement system when foreign invaders, such as bacteria, are detected.

The most common C2 gene mutation, which is found in more than 90 percent of people with complement component 2 deficiency, prevents the production of complement component 2 protein. A lack of this protein impairs activation of the complement pathway. As a result, the complement system's ability to fight infections is diminished. It is unclear how complement component 2 deficiency leads to an increase in autoimmune disorders. Researchers speculate that the dysfunctional complement system is unable to distinguish what it should attack, and it sometimes attacks normal tissues, leading to autoimmunity. Alternatively, the dysfunctional complement system may perform partial attacks on invading molecules, which leaves behind foreign fragments that are difficult to distinguish from the body's tissues, so the complement system sometimes attacks the body's own cells. It is likely that other factors, both genetic and environmental, play a role in the variability of the signs and symptoms of complement component 2 deficiency.