By integrating multiomics evidence, we found that the mitochondrial SPATA20 (spermatogenesis-associated protein 20) gene was negatively correlated with the risk of SLE and that the mitochondrial CASP9 (caspase-9) and MSRA (methionine sulfoxide reductase A) genes might be associated with SLE. The gene discussed is CASP9; the disease is systemic lupus erythematosus.