Indian hedgehog (IHH) is a secreted signaling molecule of the hedgehog family 
known to play important roles in the regulation of chondrocyte differentiation, 
cortical bone formation, and the development of joints. Here, we describe that 
copy-number variations of the IHH locus involving conserved noncoding elements 
(CNEs) are associated with syndactyly and craniosynostosis. These CNEs are able 
to drive reporter gene expression in a pattern highly similar to wild-type Ihh 
expression. We postulate that the observed duplications lead to a misexpression 
and/or overexpression of IHH and by this affect the complex regulatory signaling 
network during digit and skull development.