One of the 27 True Runes, the Sovereign Rune allows its bearer protection against any form of magic, including the Gate Rune. The rune was formerly a relic of the Holy Kingdom of Harmonia before it's caretakers, Rugner Family, took it for their own when they initiated their bloodless revolt and formed the Scarlet Moon Empire. It is believed to be the symbol of the royal family.
Barbarossa used it to negate the effects of Windy's Black Rune which she tried to use to control him with. He had the True Rune embedded not in his body, but in a family heirloom weapon called the Dragon King Sword. During his final battle with the Liberation Army, he used the power of the True Rune to transform himself into a giant three-headed Golden Hydra.
Beyond that, the full powers of the rune as well as its current whereabouts are unknown.