Understanding the genetic and mechanistic basis of craniofacial microsomia

A recent Genome-Wide Association Study identified SHROOM3 as a susceptibility locus for craniofacial microsomia (CFM). In a large cohort of CFM patients, we identified specific haplotype combinations containing likely pathogenic coding SHROOM3 variants and CFM-associated expression quantitative trait loci (eQTLs) of SHROOM3 expression. Further investigations implicated specific eQTL combinations, each located in regulatory enhancers, which we term Combined eQTL Phenotype Modifiers (CePmods). Our findings suggest that CePmods can serve as pathogenic determinants even in the absence of rare deleterious coding variants in SHROOM3. Our data highlight the critical role of allelic expression in determining the penetrance and severity of craniofacial abnormalities, including microtia and facial asymmetry. Additionally, we demonstrate by qualitative and quantitative phenotypic analyses that both Shroom3 null heterozygous and Shroom3 null homozygous mouse embryos exhibit both microtia and facial asymmetry, the severity of which is dependent on gene dosage. Our study establishes SHROOM3 as a likely pathogenic gene for CFM and demonstrates eQTLs as determinants of modified penetrance in the manifestation of the disease in individuals carrying likely pathogenic rare coding variants.