The present invention relates to methods of diagnosing spondylocostal dysostosis (SCD) disorders, such as Jarcho-Levin syndrome, in humans for use in genetic counseling and linkage analyses. Methods and compositions for measuring the presence or absence of a specific mutation to Mesp2 associated with Jarcho-Levin syndrome, alone or in combination with other mutations associated with spondylocostal dysostosis, are provided.