Pierce will perform during a service dedicating the instrument on Sunday. He was an assistant to the church organist as a teen.
The rebuilt organ will be named the George and Laura Pierce Gallery Organ in memory of Pierce's parents.
Pierce was a four-time Emmy winner during his 11-year role as Dr. Niles Crane on TV's "Frasier," and he won a Tony in 2007 for his role as a musical-theater-loving detective in the Broadway musical, "Curtains."
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