Previously identified cleft lip and palate susceptibility genes clf1 and clf2 were fine mapped in this study and candidate genes were identified. clf1 maps to mouse chromosome 11 and clf2 maps to mouse chromosome 13. A population of A/WySnJ x (AXB4/PgnJ x A/WySnJ)F1 backcross embryos at E14 were used for phenotype analysis and fine mapping. The recombinant inbred strain AXB4/PgnJ is derived from progenitor strains A/J and C57BL/6J, and is homozygous for C57BL/6J-derived alleles at clf1 and homozygous forA/J-derived alleles at clf2. Inbred A strains, such as A/J, A/WySnJ, and A/HeJ exhibit increased incidence of cleft lip and palate (5%-30%) compared to other inbred strains such as C57BL/6J. A parent of origin effect also appears to be present with increasing penetrance of cleft lip and palate when the mother is an A strain. Animals homozygous for A/WySnJ-derived alleles at both clf1 and clf2 exhibit the highest incidence of cleft lip and palate.
clf1 mapped to an interval spanning approximately 58 cM -65 cM on mouse Chromosome 11 between flanking markers D11Mit132 and D11Mit258. No recombinants were identified for this interval so the candidate region could not be narrowed further. However, Dlx3, a previously identified candidate gene for clf1 was excluded. Candidate genes found within the clf1 interval are Gosr2, Wnt9b, Wnt3, Nsf, Arf2, Crhr1, Mapt, Cdc27, Myl4, and Itgb3. The clf1 interval is syntenic to human Chromosome 17q21. A/WySnJ-derived alleles confer recessive susceptibility to cleft lip andpalate at clf1.
clf2 mapped to an interval spanning approximately 36 cM - 43 cM on mouse Chromosome 13 between flanking markers Ntrk2 and Irx2. Several candidate genes are found in the clf2 interval, the strongest of which are Mtrr, Zfp72, Adcy2, Pols, Srd5a1, and Adamts16. These candidate genes are found in a region syntenic to human Chromosome 5p15. Ptch1 (36 cM) is also a candidate gene for clf2 as mutations in the human ortholog PTCH shows some association to human cleft lip and palate. Sequence analysis of Ptch1 revealed a single nucleotide polymorphism between C57BL/6J and A/WySnJ but it does not segregate with the cleft lip and palate phenotype. The A/WySnJ-derived allele at clf2 confers semidominant susceptibility to cleft lip and palate.
A potential third locus named clf3 was mapped to either mouse Chromosome 7 or mouse Chromosome 18 in a previous study. Further examination in the current backcross population disputed the existence of a third cleft lip and palate locus.