...when it specifies a different fold! At least that's the latest word from Kimchi-Sarfaty et. al., who reported in the Jan 26 issue of Science that a supposedly "silent" mutation in the multidrug resistance gene MDR1 changes the function of the encoded protein.

http://www.gnxp.com/blog/2007/02/when-is-synonymous-sequence-not.php

A "silent" polymorphism in the MDR1 gene changes substrate specificity. Kimchi-Sarfaty C (2007) Science.
February 8, 2007