Secret series by Pseudonymous Bosch - Cass (Cassandra) is the main character in the series. I highly recommend it. It's somewhat similar to MBS, though I think it's a bit snappier and got more twists and plots. There's also considerably more humor. Lots of magic, time travel, and mystery involved. Though the author doesn't claim Cass is gifted outright, there's no doubt that she is but not a more traditional way.
Terry Pratchett's Wee Free Men is a good suggestion. It's about a girl who becomes a witch and plays with magic.
Dahl's Matilda might be an option, though I think that's got a lower lexile score than the secret series or MBS but I'm not positive. Most of Dahl's books are aimed at 4th grade and books with a lexile score of 850L are aimed at 5th/6th graders. Matilda is a gifted girl.
Of course, there's the classics like Little Women, Alice in Wonderland, Dr. Doolittle.
