Our study compares the AF and distribution of OTOG rare variants across different populations to assess if the reported FMD variants may have an OTOG-related founder effect that would explain the higher prevalence of FMD in NFE population.
Familial MD has a significant familial aggregation in the NFE population, and most reported families with MD have an European ancestry (7). Epidemiological studies estimate that the prevalence of FMD is 5 to 23.5% (29). In the European population, an overall percentage of 9–15% has been calculated, 9–13% in Spain (7, 30), 12% in Sweden (31) and 9.3% in Finland (32.7% for relatives with Meniere-like symptoms) (32), while in the Asian population, the estimated proportion is approximately 6% in Japan (5.8%) (33) and South Korea (6.3% for relatives with definite FMD and 9.8% FMD-like syndrome) (8). The familial aggregation data are likely to be overestimated due to the use of questionnaires and patient interviews and the difficulty of collecting a large cohort of FMD (34), combined with the challenge of MD diagnosis and the different diagnostic criteria in studies published before 1995.
The reported differences in the FMD prevalence may be due to differences in the genetic structure of each population. More frequent and founder variants in hearing impairment genes have already been described in European, African, Asian, and American populations (14, 35), therefore, finding founder variants in specific genes that cause FMD would not be surprising. Founder variants are those pathogenic variants found with a high frequency within a particular population caused by the presence of the variant in an ancestor or small group of ancestors (36).
Among the known FMD genes, OTOG seems one of the most relevant, with several Spanish families sharing the same variants with a compound heterozygous recessive inheritance pattern (10). For this reason, the OTOG gene was chosen as the best candidate to study the frequency of its variants across different populations to test whether OTOG could explain the higher prevalence of FMD in the European population and whether there are variants with a founder effect.
Our study shows 13 missense variants in FMD and 8 of them are located in constrained regions in NFE: NC_000011.10:g.17553211G > A (rs552304627), NC_000011.10:g.17599671C > T (rs117005078), NC_000011.10:g.17610645T > C (rs61744602), NC_000011.10:g.17611118C > T (rs748280789), NC_000011.10:g.17611374C > T (rs61736002), NC_000011.10:g.17612217G > A (rs188527711), NC_000011.10:g.17635125G > A (rs76461792) and NC_000011.10:g.17640936C > T (rs567966154) (Table 1).
Among all variants found, 3 rare variants are shared in different unrelated FMD patients. The variants NC_000011.10:g.17557227G > A and NC_000011.10:g.17611374C > T are in the same 4 FMD patients (3 heterozygous and 1 homozygous). Of note, these 2 variants are also overrepresented in the African and American populations, and this could be explained by the mixed ancestry of North African and American with the Spanish population. These variants, which are within the same haplotype and have been previously described in FMD patients, could impact the splicing processing and protein stability, increasing the susceptibility to develop a MD-like phenotype. The variant NC_000011.10:g.17557227G > A, although classified as VUS (variant of uncertain significance) by the ACMG criteria, is in the last position of exon 4. This could disrupt the consensus splicing site, generating possible non-functional alternative forms of the protein. Further functional studies would be required. In addition, both variants have been associated in ClinVar (37) with autosomal recessive non syndromic hearing loss 18B (DFNB18B), supporting their possible pathogenic effect in FMD.
On the other hand, the NC_000011.10:g.17642200G > A variant has been found in 2 FMD patients. This variant, classified as VUS and enriched in NFE population, is in the otogelin's tail, close to the CTCK domain, which is involved in the formation of antiparallel homodimers (12). Since this variant is predicted to be destabilizing, it could potentially interfere with the correct dimer formation. However, the CTCK-mediated dimer forms a highly resistant structure, with 11 pairs of cysteine residues forming disulphide bonds (38), so the effect of the NC_000011.10:g.17642200G > A variant on otogelin functionality is unclear.
The variants NC_000011.10:g.17638480C > A and NC_000011.10:g.17640936C > T, classified as benign and more frequent in the African population, were both found in the same FMD patient and in the same haplotype. Although these variants were found in the otogelin`s tail, they were predicted to have no effect on the protein's stability, so it was not possible to determine whether they will have a functional impact.
The rest of the variants described were each found in different single FMD patients. Since only the exonic variants have been explored, it cannot be excluded that these patients have a second variant in intronic or expression-regulating regions.
According to the population frequency of the 13 variants, 8 have a higher frequency in the NFE population than in the rest of the populations, which may indicate a founder effect of these variants in the European population. Three arguments supports this hypothesis: a) the pathogenicity CADD score > 20 (39), b) the predicted change in protein stability, and c) their occurrence in constrained regions or regions of low variant density, since constrained regions are enriched in pathogenic variants in ClinVar (40).
The finding of 8/13 enriched variants in the NFE population, could be because the FMD cohort mainly includes Spanish patients. For this reason, the high proportion of Spanish individuals in this cohort may explain the finding of 3 variants that were more frequent in the African than in the NFE population, since North African ancestry in the Spanish population may be up to 11% (41). Accordingly, it is possible that the prevalence of FMD could be similar in the North African and Spanish populations; thus, current epidemiological studies of MD and familial aggregation (FMD) are needed to support this hypothesis.
We also found that most of the variants found in OTOG in our FMD cohort are not found or have a very low frequency in the East Asian population (EAS). This may be due to the greater genetic divergence between both populations (42), but it could also anticipate a lower prevalence of OTOG-mediated FMD in East Asian population.
Some of these missense variants are in the protein's tail and may interfere with the interaction with other structural proteins or the dimers formation; however, the interactions of otogelin with other proteins in the tectorial or otolithic membrane are not know.
Limitations
This study is based on exome sequencing datasets that found a burden of missense variants in the CDS in the OTOG gene in FMD (9); however, most families remain undiagnosed and the discovery of variants in intronic or intergenic regulatory regions could change the current picture of the genetic architecture of FMD. Therefore, whole genome sequencing studies are needed. Besides, the lack of genetic studies of FMD in other populations (43), prevents estimating the genetic contribution of OTOG to FMD.