If
VSX1 is not playing a major role in PPCD and keratoconus, why has it been implicated with these diseases in so many studies? The simplest possibility is that these are nonpathogenic naturally occurring variants. When assessing a variant for a causative role in a dominant Mendelian disease, like PPCD, the general, albeit oversimplified rule is that the frequency of a variant in a reference sample should not exceed disease prevalence.
59 Mining of the gnomAD database (r2.0.2) revealed that the allele frequency of the six
VSX1 mutations examined in our study (
Table 1) ranges between 2.63 × 10
−3 and 4.06 × 10
−6. Although the disease prevalence of PPCD has not been well described, one study estimated what was considered by the authors to be a high prevalence of PPCD of 1:100,000 in the Czech Republic.
60 Assuming that PPCD is just as or less prevalent in other populations, the allele frequency of
VSX1 variant p.H244R (2.63 × 10
−3) makes it about 100 times more prevalent than PPCD1, and therefore more likely to be nonpathogenic. p.247R and p.A256S, on the other hand have an allele frequency about an order of magnitude greater than the disease prevalence, while p.R166W, p.Q175H and p.G239R have an allele frequency that is in a similar range or less than the disease prevalence, thus any definitive conclusions on pathogenicity based of this criterion alone are not possible. It is also difficult to compare
VSX1 allele frequency with keratoconus as this disease does not appear to have strong evidence supporting a simple Mendelian mode of inheritance and instead appears to be complex. Finally, it is important to note that there are several amino acid residues in the homeodomain and CVC domain, including some of the mutated residues examined in our current study, that are conserved across all vertebrate and invertebrate
VSX orthologues. This indicates that these amino acids are critical to some function of
VSX1. We suggest that in humans, as in mouse,
VSX1 is primarily required for fine-tuning optimal retinal function. While it is clear that
VSX1 does not play a causative role in PPCD1, we cannot not rule out, at this time, a role for
VSX1 in keratoconus, although it likely does not play a major causative role.