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The defender, who was part of the Germany team which won the World Cup this summer, signed the five-year deal on Wednesday and will undergo a medical on Thursday morning before being presented to the media.
A statement on the Spanish club's website read: "Valencia CF has reached an agreement with Sampdoria for the transfer of German international center back Shkodran Mustafi.
"The player signed a contract on Wednesday to become a Valencia player until June 30, 2019.
"Mustafi, 22 and a champion with Germany in the World Cup in Brazil, will complete a medical review on Thursday at 9:45 a.m. then at 10:00, the player will be presented to the media."