So I remember this book where this girl has a brother who disappears or something and then he has this spell that makes him very slowly turn to stone. And there's a whole society with a queen of stone people and I remember that there have to go to this witch's house along the way and they also go underground to the stone people's lair. This is all happening where the girl steps through a portal from our world into some magical place.
Reckless, by Cornelia Funke. The boy actually has a brother, not a sister: the girl is the brother's girlfriend.
Soon after Will arrives, he is attacked and scratched by a Goyl, a humanoid race with stone skin. As a result of the attack, Will's skin begins turning to stone.
With time running out, Jacob, Will, Clara and Jacob's vixen friend, Fox, journey to the witch's house ...
... on their mission to rescue Will, they travel cross country to the mountains underneath which the Goyl have built their capital city.