SMO mutation findings in HPE patients
We recently reported the results of a Targeted Capture analysis of 153 developmental genes (and a similar number of conserved non-coding elements) among 333 HPE probands in an effort to identify both driver mutations and potential modifiers (Roessler et al., 2018a). TheSMO gene was identified as a potential candidate gene based on the identification of six families with gene variants of undetermined significance. As described in Table 1, two of these families had a detectable driver mutation with a co-morbid variant in SMO (see summary Suppl. TableS7, and annotations for each proband Tables S8-13). In order to better understand the potential roles of these variants we developed functional studies.
Proband #1 has a maternal FGF8 driver mutation yet also inherited a complex SMO variant with two variants of uncertain significant (VOUS, in cis ) from the father (Hong et al., 2018). We chose to investigate both SMO variants individually to better determine the potential for digenic inheritance in this case. Similarly, although proband #6 has a typical de novo driver mutation inSHH , we chose to directly examine the predicted “likely benign” predictions for the co-inherited SMO variant. Our working hypothesis continues to be that modifier genes need not meet the same guideline considerations as more conspicuous driver mutations with respect to allele frequency (Hong et al., 2017; Roessler et al., 2018a; Roessler et al., 2018b).
Probands #2 and #3 present with findings that appear to reflect common benign SMO variants inherited from otherwise healthy parents. In neither case are the potentially co-morbid alterations predicted to be functionally abnormal. In the case of proband #3, almost all of the co-variants were inherited from the healthy father suggesting that even if they had synergistic effects it would raise the question of why the father was not similarly affected. Nevertheless, we included theseSMO variants as likely negative controls.
Probands #4 represents a similar case of exclusive maternal inheritance of the potentially interacting loci. Although the SMO variant is common in the general population it is predicted to be deleterious. Thus, since we classified it as a rare VOUS we felt compelled to try to determine its biological activity.
Perhaps the most interesting SMO variant was identified in proband #5 as an initially novel alteration of p.V404M. Later it was identified as a single detection in the gnomad data base. Its rarity and location in the heptahelical domain suggested that of the seven variants identified in HPE probands this missense alteration deserved closer examination in functional studies.