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Long-QT syndrome type 2 (LQT2) is a life-threatening Mendelian disease caused by genetic variants in KCNH2. Herein, we generated a human embryonic stem cell line (WAe009-A-88) carrying a LQT2 related mutation in KCNH2, c.1720 A>G. The WAe009-A-88 line maintained stem cell-like morphology, expressed high levels of pluripotent markers, had a normal karyotype, and could differentiate into all three germ layers in vivo. The cell line can serve as valuable tools for modeling LQT2 in vitro and investigating the pathological mechanisms related to KCNH2 mutations.