Disease-causing Enhancer Variants: A Question of Penetrance


Studies of enhancer chromatin signatures and of chromatin conformation have reported hundreds of thousands of potential regulatory sequences interspersed with genes, yet few disease-causing regulatory mutations have been identified. Lecerf et al. (Hum Mutat 35:303-307, 2014) searched for mutations in enhancers previously identified by transgenic experiments as controlling SOX10. Variants in this neural crest transcription factor cause Waardenburg Syndrome (WS4), comprising pigmentation defects, deafness and intestinal aganglionosis (Hirschprung disease, HSCR), together or in isolation. The authors studied 144 patients with isolated HSCR in which SOX10 and 16 HSCR-susceptibility genes were intact. They identified a de novo deletion involving five SOX10-flanking enhancers in one patient and two point mutations in the U3 enhancer in two unrelated patients. These mutations interfere with SOX10 autoregulation. These cases, together with a previously identified de novo enhancer deletion in a WS4 patient, indicate that SOX10 enhancer mutations may cause HSCR.

It is noteworthy that the two point mutations identified involve only one of several functionally redundant enhancers and only moderately reduce SOX10 enhancer activity. Indeed, both mutations are detected in the non-affected mothers of the patients, indicating that the point mutations per se are insufficient to cause HSCR. A common RET hypomorphic allele (rs2435357:C>T) acts as a low-penetrance HSCR allele through loss of a SOX10 binding site in an enhancer. The HSCR phenotype is dependent on rs2435357:T in various syndromic cases in which the primary disease-causing gene has low penetrance, but not when the disease-causing gene has high penetrance (as in WS4 with SOX10 disruption). Intriguingly, both patients with SOX10-enhancer point mutations inherited a paternal RET hypomorphic allele, suggesting that it might increase the penetrance of the mild SOX10 mutation. This work highlights the potential for regulatory element analysis to dissect subtle predisposition to complex genetic defects.