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The absence of azoospermia factor c (AZFc) is a common molecular cause of sperm failure. In men with non-obstructive azoospermia or severe oligospermia, the incidence of AZFc is around 10%. The AZFc region is located at the far end of the Yqll chromosome which has three non-overlapping sub-regions with a high frequency of deletion. Now, we generated a human embryonic stem cell line (SKLRMe001-A) that carries a deleted AZFc gene on the Y chromosome. The ESC line maintains a stem cell-like morphology, pluripotency, and has a normal karyotype. The cells can also differentiate into all three germ layers in vivo.