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Researchers have identified variations in several genes that may influence the risk of developing systemic scleroderma. The most commonly associated genes belong to a family of genes called the human leukocyte antigen (HLA) complex. The HLA complex helps the immune system distinguish the body's own proteins from proteins made by foreign invaders (such as viruses and bacteria). Each HLA gene has many different normal variations, allowing each person's immune system to react to a wide range of foreign proteins. Specific normal variations of several HLA genes seem to affect the risk of developing systemic scleroderma.

Normal variations in other genes related to the body's immune function, such as IRF5 and STAT4, are also associated with an increased risk of developing systemic scleroderma. Variations in the IRF5 gene are specifically associated with diffuse cutaneous systemic scleroderma, and a variation in the STAT4 gene is associated with limited cutaneous systemic scleroderma. The IRF5 and STAT4 genes both play a role in initiating an immune response when the body detects a foreign invader (pathogen) such as a virus.

It is not known how variations in the associated genes contribute to the increased risk of systemic scleroderma. Variations in multiple genes may work together to increase the risk of developing the condition, and researchers are working to identify and confirm other genes associated with increased risk. In addition, a combination of genetic and environmental factors seems to play a role in developing systemic scleroderma.

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