We established a novel ENU-induced mutant mouse, named I-A12%, with ~8-fold reduced I-A expression on the surface of B cells, DCs, cTECs, and mTECs. I-A100% and I-A12% mice displayed highly similar levels of T cell development. Transfer of I-A12% CD25-CD4+ T cells into RAG-KO hosts revealed increased auto-aggression activity against the liver. Infection of I-A12% mice with Listeria monotcytogenes or influenza virus revealed significantly reduced generation of antigen-specific CD4+ T cells. Polyclonal activation of endogenous memory-like I-A12% CD44hiCD4+ T cells revealed elevated production of multiple cytokines. We conclude that there exist distinct thresholds for different MHC-II-dependent immunological processes. The I-A12% mutant mouse model is a valuable tool for investigations on quantitative causal-effect relationship in MHC-II-dependent normal and autoimmune responses.