The maximum likelihood model specified 100% penetrance of craniosynostosis when risk alleles at both loci are present, 9% penetrance when only a damaging SMAD6 allele is present, 0.08% or 0.32% penetrance when only one or two BMP2 risk alleles are present, and a 0.02% phenocopy rate, with zero recombination between trait and both marker loci. Here, BMP2 is linked to craniosynostosis.