Self-DNA must be efficiently cleared from extracellular spaces, lysosomes, and the cytosol to prevent activation of innate immune sensors such as TLR9 and cGAS–STING. Genetic polymorphisms in nucleases including dnase1, dnase1l3, dnase2 and trex1 impair DNA degradation by reducing catalytic activity, secretion, stability, or expression. These defects allow accumulation of immunostimulatory DNA in vivo, promoting type I interferon production, autoantibody formation, and inflammatory diseases. This mini review summarizes key nuclease variants across cellular compartments and their impact on DNA metabolism and immunity.