Is there a certain protein that is affected by velocardiofacial syndrome?

I believe the disorder affects certain protein, since it is a deletion disorder caused by the deletion of a small piece of chromosomes. Velocardiofacial syndrome is a genetic conditioned characterized by abnormal pharyngeal arch development that results in defective development of the parathyroid glands, thymus, and conotruncal region of the heart. 

the answer to that question is d