Strong founder effect of p.P240L in CDH23 in Koreans and its significant contribution to severe-to-profound nonsyndromic hearing loss in a Korean pediatric population

The prevalence of recessive CDH23 mutations in our pediatric cohort with severe-to-profound nonsyndromic arSNHL was
3.1 %. This was in agreement with findings for CDH23 variants in other studies on East Asian populations, the prevalences of which ranged
from 1.6 to 15.4 %, using cohorts with nonsyndromic arSNHL not necessarily limited
to prelingual pediatric deaf subjects (Table 2) 18], 19], 24], 25]. The wide range in the frequency from 1.6 to 15.4 % may be attributed to ethnicity
differences among East Asians. Alternatively, an intrinsic difference in the study
cohort, such as cohort size or onset age of SNHL, could also account for these differences.
In this study, the cohort consisted exclusively of prelingual nonsyndromic arSNHL
pediatric subjects. Therefore, significantly higher frequency of CDH23 mutations (15.4 vs 3.1 %) obtained from a different Korean cohort with nonsyndromic
arSNHL not limited to prelingual SNHL cases 18] (Table 2) may suggest CDH23 mutations also significantly contribute to adult-onset postlingual arSNHL in Koreans.
Indeed, in contrast to the p.P240L mutation, which presented mostly as prelingual
severe-to-profound hearing loss, certain CDH23 mutations, such as p.R2029W and p.T1368M, were reported to be associated with postlingual
onset of moderate hearing loss, and most CDH23-affected subjects showed progressive hearing loss 13]. These results warrant further investigation in a separate study.

CDH23 mutations were the third-most prevalent molecular etiology in the pediatric prelingual
arSNHL cohort, after SLC26A4 and GJB2, which accounted for 18.0 and 17.2 %, respectively. A mutation of p.P240L in CDH23 was detected in all four DFNB12 subjects, as either a compound heterozygote or a
homozygote, in the Korean cohort. Screening of p.P240L alone significantly facilitated
detection of DFNB12 or DFNB12 candidates in Korean subjects, despite the large size
of this gene. Given the prevalence of p.P240L, incorporation of a test for p.P240L
in CDH23 as a next step in GJB2 sequencing in non-EVA subjects would be cost-effective (Fig. 1).

Indeed, several studies have reported the predominance of the p.P240L mutation in
Japanese and Korean populations affected by the prelingual or postlingual arSNHL 18], 19], 24]. In line with these studies, our results showed that 85.7 % (6/8) of the alleles
of the CDH23 mutation carriers in the Korean pediatric population had p.P240L (Table 2). Based on the frequency of this variant, we hypothesized that p.P240L of CDH23 had a founder effect in East Asians. Based on our haplotype analyses, p.P240L was
mainly carried on a single common haplotype and the common haplotype linked to p.P240L
was not detected at all in normal controls, indicating that the p.P240L mutation arose
from a common founder in Koreans.

This is the first documented evidence for the founder mutation hypothesis of p.P240L
of CDH23. Previous studies on CDH23 mutations in Caucasian populations did not show clear founder mutations due to the
heterogeneous ethnicities of these populations 5], 6], 11], 14]. Instead, most of the CDH23 variants from different ethnic backgrounds were assumed to be private 26], 27]. Several reports identified founder effects of frequently encountered mutations in
specific ethnic populations. Regarding mutations in GJB2, several studies reported the frequency of 235delC among East Asians 22], 35delG in the Caucasians 28], and 167delT in Ashkenazi Jews 29], suggesting that these were the result of a founder effect, rather than a mutational
hot spot. The most common deafness gene in our cohort, SLC26A4, contained the H723R and IVS7-2AG founder mutations, which are unique to East Asians
30]. The p.A306 mutation of TMPRSS3 was also recently reported to possess a founder role in Koreans 23].

Most CDH23 missense mutations localized in the calcium-binding sequences were associated with
nonsyndromic hearing loss, which was presumed to be attributable to the increased
sensitivity of the cochlear function to calcium-dependent cell adhesion, compared
to that of the retinal function 15]. p.P240L is a missense mutation that affects a residue localized in the EC3 domain,
with the highly conserved calcium-binding motifs, and therefore does not interfere
with calcium binding. Instead, the change from the rigid cyclic side chain of proline
to a longer and more flexible leucine residue, results in instability in the structure
and function of the protein 18]. To date, the functional defects caused by the p.P240L mutation have not been determined
in vitro or in vivo. However, this mutation has been identified only in subjects with
nonsyndromic hearing loss (DFNB12) 13], 18], 19]. Furthermore, based solely on a previous audiologic phenotypic study, p.P240L carriers
usually show congenital and more severe SNHL than do carriers of other missense mutations
in CDH2313]. In accordance with this finding, the four pediatric subjects in this study with
p.P240L showed prelingual and severe-to-profound nonsyndromic SNHL with minimal residual
hearing at all frequencies.

The p.P240L allele can be classified as a DFNB12 allele, rather than an USH1D allele,
based on a previous hypothesis 11] and the phenotype of p.P240L carriers in East Asian populations 13], 18], 19]. The higher prevalence of this DFNB12 allele of p.P240L compared to other CDH23 mutant alleles implies that in Koreans the nonsyndromic hearing loss (DFNB12) phenotype
is more commonly associated with CDH23 mutations than is the syndromic hearing loss phenotype (USH1D).

The geographic or ethnic spectra of founder mutations vary, and whether the most frequent
mutation allele represents a founder mutation and/or a mutational hot spot is often
unclear. Some founder mutations have a narrow distribution; for example, due to the
practice of consanguineous marriage, the high prevalence of GJB2 mutations in some Western cultures can be attributed to a single ancestor mutation
31]. On the other hand, the p.A306T mutation of TMPRSS3 affects a wide ethnic spectrum, encompassing East Asians and Europeans, and hence
is predicted to be a mutational hot spot 23], 32], 33]. However, the distribution of several founder alleles, such as the 235delC mutation
of GJB2 and the H723R and IVS7-2AG mutations of SLC26A4, is restricted to East Asians 22], 30]. Only a single cohort of Koreans was investigated in this study, a high prevalence
of the p.P240L mutation in East Asians has been reported by others 13], 18], 19], 34], whereas this mutation was rarely reported in other ethnic groups 5], 6], 14]. Therefore, p.P240L is likely a founder mutation exclusive to East Asians. Information
on the distinct distribution pattern of the deafness mutations may facilitate determination
of the phylogenetic evolution of the deafness genes. Although its value would be limited
due to a lack of data on Mongolian or other Asian populations, the different frequency
of the p.P240L mutation between East Asian populations and other ethnicities suggests
that the p.P240L mutation occurred sometime after the divergence of several ethnic
groups from Central or East Asia ~40,000 years ago 35], 36]. Further studies using other genetic polymorphisms, such as single-nucleotide polymorphisms
(SNPs) and STR markers adjacent to the p.P240L mutation, would enable a more accurate
estimate of the age of this mutation. Further data on the prevalence of CDH23 mutations and the haplotypes in other ethnic groups would enable tracing of the common
ancestor or route of divergence of the CDH23 mutation. This information would have phylogenetic applications.