ClinVar Genomic variation as it relates to human health

The c.5098G>C (p.Glu1700Gln) variant in OTOF is a missense variant predicted to cause a substitution of glutamic acid by glutamine at amino acid 1700. The filtering allele frequency (the lower threshold of the 95% CI of 152/44874) of the c.5098G>C (p.Glu1700Gln) is 0.2948% for East Asian chromosomes by gnomAD v4.1.0, which meets the ClinGen Hearing Loss VCEP threshold (≥0.003) for BS1. However, based on the evidence outlined below, the ClinGen Hearing Loss Expert Panel believes that the evidence for the pathogenicity of this variant for nonsyndromic hearing loss outweighs its high allele frequency the East Asian population, given it is reported as a founder mutation in the Taiwanese population (PMID: 20224275). Therefore, the BS1 code will not contribute to the overall classification. The computational predictor REVEL gives a score of 0.85 which is above the threshold of ≥ 0.7 (PP3). This variant has been detected in at least 18 individuals with autosomal recessive nonsyndromic hearing loss. Eight individuals were homozygous for the variant (PMIDs: 20224275, 35106950). Six individuals were compound heterozygous for the variant and a pathogenic or likely pathogenic variant with phase unknown (p.Glu841Lys, c.4961-1G>A, p.Arg1344*, p.Arg500*; PMID: 28766844). Four individuals were compound heterozygous for the variant and a pathogenic or likely pathogenic variant and confirmed in trans by parental testing (p.Pro1628Thr; PMID: 34692690) (PM3_VeryStrong). At least one patient with this variant displayed features of auditory neuropathy spectrum disorder, which is highly specific for OTOF (PP4; PMID: 28766844). The variant has been reported to segregate with hearing loss in multiple affected family members from two families (PP1_Strong; PMIDs: 20224275, 34692690). In summary, this variant meets the criteria to be classified as pathogenic for nonsyndromic genetic hearing loss, based on the ACMG/AMP criteria applied, as specified by the ClinGen Hearing Loss VCEP (PP3, PM3_VeryStrong, PP4, PP1_Strong; Version 2; 5/15/24).

Variant summary: OTOF c.5098G>C (p.Glu1700Gln) results in a conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00051 in 249992 control chromosomes, predominantly at a frequency of 0.0069 within the East Asian subpopulation in the gnomAD database, including 1 homozygotes. The observed variant frequency within East Asian control individuals in the gnomAD database is approximately 6 fold of the estimated maximal expected allele frequency for a pathogenic variant in OTOF causing Nonsyndromic Hearing Loss And Deafness, Type 9 phenotype (0.0011), strongly suggesting that the variant is a benign polymorphism found primarily in populations of East Asian origin. c.5098G>C has been reported in the literature as a frequent founder variant in the Taiwanese population (example, Chiu_2010), and as homozygous and compound heterozygous genotypes in individuals of East Asian ethnicity (EAS) from many simplex families affected with auditory neuropathy spectrum disorder (ANSD) (example, Chiu_2010, Lee_2014, Chen_2018, Qiu_2019). These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Six clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Multiple laboratories reported the variant with conflicting assessments (VUS, n=3; Pathogenic, n=3). Some submitters cite overlapping evidence utilized in the context of this evaluation. Based on the evidence outlined above, the variant was classified as uncertain significance.

In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 34416374, 31827501, 20224275, 24746455, 20301429, 31180159, 25326637, 28766844, 32508568, 30368385, 31980526, 32555439, 33256196, 34325055, 35114279, 34943631, 34335733, 35106950, 36837553, 34536124, 34424407, 34692690, 30311386, 35884828)

This sequence change replaces glutamic acid, which is acidic and polar, with glutamine, which is neutral and polar, at codon 1700 of the OTOF protein (p.Glu1700Gln). This variant is present in population databases (rs199766465, gnomAD 0.7%), including at least one homozygous and/or hemizygous individual. This missense change has been observed in individuals with OTOF-related conditions (PMID: 20224275, 25326637, 31827501). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 48253). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt OTOF protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

The p.Glu1700Gln variant in OTOF has been reported in >15 compound heterozygous or homozygous individuals with auditory neuropathy and/or hearing loss and segregated with disease in at least 3 affected individuals from 2 families. However some of these individuals had pathogenic variants in other genes which explained their phenotype (Chiu 2010 PMID: 20224275, Lee 2014 PMID: 25326637, Chen 2018 PMID: 30368385, Wu 2018 PMID: 28766844, Qiu 2019 PMID: 31827501, Guan 2021 PMID: 34416374, Zhu 2021 PMID: 34692690, Liu 2022 PMID: 35106950, LMM data). It has also been identified in 0.33% (152/44874) of East Asian chromosomes by gnomAD including 1 homozygote (http://gnomad.broadinstitute.org, v.4.0.0). This variant was classified as Uncertain Significance on Jun 23, 2021 by the ClinGen-approved Hearing Loss Variant Curation expert panel (Variation ID 48253). Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In summary, while there is some suspicion for a pathogenic role, the clinical significance of this variant is uncertain due to conflicting information. ACMG/AMP Criteria applied: BS1, PM3_Strong, PP1_Strong, PP3.

Across a selection of availabe literature, the OTOF c.5098G>C (p.Glu1700Gln) variant has been reported in at least three studies and is found in at least 21 probands including at least eight in a homozygous state, eight in a compound heterozygous state, and three in a heterozygous state (Chiu et al. 2010; Wu et al. 2011; Wu et al. 2018). The p.Glu1700Gln variant is described as founder variant that has been seen in up to 20% of Taiwanese auditory neuropathy/auditory dys-synchrony probands (Jin et al. 2014). The p.Glu1700Gln variant was absent from 100 ethnically-matched control individuals and is reported at a frequency of 0.007430 in the East Asian population of the Exome Aggregation Consortium. Based on the evidence, the p.Glu1700Gln variant is classified as pathogenic for autosomal recessive nonsyndromic hearing loss. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

The c.5098G>C (p.Glu1700Gln) variant was observed with the other variant, c.4882C>A (p.Pro1628Thr), in compound heterozygosity in a Chinese family with temperature-sensitive auditory neuropathy, segregated with the disease in 4 patients in the present study, and was absent in 200 normal-hearing controls matched for Chinese ethnicity. It has also been reported in several other patients (Chiu et al., 2010; Chen et al., 2018; Qiu et al., 2019; Wu et al., 2019). Additionally, in vitro bioinformatics analysis indicate that the c.5098G>C (p.Glu1700Gln) variant perturbs an amino acid side chain and has lost the hydrogen bonds between p.Glu1700 and p.Leu1704. In summary, the c.5098G>C (p.Glu1700Gln) variant meets our criteria to be classified as pathogenic based upon segregation studies, absence from controls, and functional prediction.