The proteasome is a large, multiple subunit complex that is capable of degrading most intracellular proteins. Polymorphisms in proteasome subunits are associated with cardiovascular diseases, diabetes, neurological diseases, and cancer. One polymorphism in the proteasome gene PSMA6 (？8C/G) is associated with three different diseases: type 2 diabetes, myocardial infarction, and coronary artery disease. One type of proteasome, the immunoproteasome, which contains inducible catalytic subunits, is adapted to generate peptides for antigen presentation. It has recently been shown that mutations and polymorphisms in the immunoproteasome catalytic subunit PSMB8 are associated with several inflammatory and autoinflammatory diseases including Nakajo-Nishimura syndrome, CANDLE syndrome, and intestinal M. tuberculosis infection. This comprehensive review describes the disease-related polymorphisms in proteasome genes associated with human diseases and the physiological modulation of proteasome function by these polymorphisms. Given the large number of subunits and the central importance of the proteasome in human physiology as well as the fast pace of detection of proteasome polymorphisms associated with human diseases, it is likely that other polymorphisms in proteasome genes associated with diseases will be detected in the near future. While disease-associated polymorphisms are now readily discovered, the challenge will be to use this genetic information for clinical benefit. 1. Introduction Over the last decade, significant improvements have been made in genotyping efficiency, sequencing technology, and statistical methodology, providing researchers with better opportunities to define the role of sequence variation in the development of human diseases [1–3]. Many human diseases are now known to have a genetic component. All humans start their lives with germ-line mutations inherited from their parents. However, the human genetic code is constantly subjected to mutations which can happen during cell division or after exposure to environmental factors such as UV radiation, chemicals, or viruses. These mutations can result in proteins with altered functions, malformed proteins, or even missing proteins. Some of these changes that occur due to a particular mutation have no effect on biological function (silent mutations), some may be beneficial, and some may lead to disease. These genetic variations are important for genetic diversity within the population. Genome-wide association (GWA) studies have identified alleles related to complex disorders; however some of
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