Linkage analysis and chromosomal rearrangement revealed the cause of SCS to be mutations in the TWIST gene (twist transcription factor gene) located on chromosome 7p21. The TWIST gene encodes a basic helix-loop-helix (b-HLH) transcription factor that controls head mesenchyme development as the cranial tube forms. More than 35 varying TWIST mutations involving the b-HLH domain of the protein have been identified in people with SCS. The mutations include missense, nonsense, and frameshift deletion/insertion mutations that either shorten or disrupt the b-HLH domain. Most individuals with SCS have a single large deletion in the region 7p21, which contains the region that codes for the TWIST gene.