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Point mutations in  TBX1  can recapitulate many of the structural defects of 22q11 deletion syndromes (22q11DS), usually associated with a chromosomal deletion at 22q1.2. 22q11DS often includes specific cardiac and pharyngeal organ anomalies, but the presence of characteristic craniofacial defects is highly variable. Even among family members with a single  TBX1  point mutation but no cytological deletion, cleft palate and low-set ears may or may not be present. In theory, such differences could depend on an unidentified, second-site lesion that modifies the craniofacial consequences of  TBX1  deficiency. We present evidence for such a locus in a mouse model. Null mutations of  chordin  have been reported to cause severe defects recapitulating 22q11DS, which we show are highly dependent on genetic background. In an inbred strain in which  chordin −/−   is fully penetrant, we found a closely linked, strong modifier—a mutation in a  Tbx1  intron causing severe splicing defects. Without it, lack of  chordin  results in a low penetrance of mandibular hypoplasia but no cardiac or thoracic organ malformations. This hypomorphic  Tbx1  allele per se results in defects resembling 22q11DS but with a low penetrance of hallmark craniofacial malformations, unless  chordin  is mutant. Thus,  chordin  is a modifier for the craniofacial anomalies of  Tbx1  mutations, demonstrating the existence of a second-site modifier for a specific subset of the phenotypes associated with 22q11DS.

Chordin Is a Modifier of Tbx1 for the Craniofacial Malformations of 22q11 Deletion Syndrome Phenotypes in Mouse