Total submissions: 8
| Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
|---|---|---|---|---|---|---|---|---|
| Women's Health and Genetics/Laboratory Corporation of America, |
RCV005237462 | SCV005886368 | pathogenic | Nonsyndromic genetic hearing loss | 2025-02-05 | criteria provided, single submitter | clinical testing | Variant summary: OTOF c.5375G>A (p.Arg1792His) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 8e-06 in 251482 control chromosomes. c.5375G>A has been reported in the literature in multiple homozygous or compound heterozygous individuals affected with Nonsyndromic Hearing Loss And Deafness, Type 9 (e.g. Almontashiri_2018, Iwasa_2019). These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 29048421, 31095577). ClinVar contains an entry for this variant (Variation ID: 48259). Based on the evidence outlined above, the variant was classified as pathogenic. |
| Genomic Medicine Center of Excellence, |
RCV000656336 | SCV004804932 | pathogenic | Autosomal recessive nonsyndromic hearing loss 9 | 2024-03-17 | criteria provided, single submitter | research | |
| Labcorp Genetics |
RCV000171287 | SCV004292075 | pathogenic | not provided | 2023-12-30 | criteria provided, single submitter | clinical testing | This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 1792 of the OTOF protein (p.Arg1792His). This variant is present in population databases (rs111033349, gnomAD 0.0009%). This missense change has been observed in individual(s) with autosomal recessive OTOF-related conditions (PMID: 29048421, 31095577, 34424407). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 48259). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on OTOF protein function. This variant disrupts the p.Arg1792 amino acid residue in OTOF. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 31095577, 34416374, 34536124; Invitae). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. |
| Gene |
RCV000171287 | SCV002526636 | pathogenic | not provided | 2024-09-09 | criteria provided, single submitter | clinical testing | Not observed at significant frequency in large population cohorts (gnomAD); 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: 27124789, 29048421, 34424407, 38378725, 31095577) |
| Laboratory for Molecular Medicine, |
RCV000041571 | SCV000065266 | likely pathogenic | Rare genetic deafness | 2016-12-08 | criteria provided, single submitter | clinical testing | The p.Arg1792His variant in OTOF has been previously reported by our laboratory in 3 individuals with hearing loss, including two homozygotes and one with audit ory neuropathy spectrum disorder (ANSD) who was compound heterozygous for a seco nd pathogenic variant in OTOF. This variant has been reported in 1/11258 Europea n chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadins titute.org; dbSNP rs111033349); however, its frequency is low enough to be consi stent with a recessive carrier frequency. Computational prediction tools and con servation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In summary, al though additional studies are required to fully establish its clinical significa nce, this variant is likely pathogenic for autosomal recessive hearing loss. |
| OMIM | RCV000656336 | SCV000804276 | pathogenic | Autosomal recessive nonsyndromic hearing loss 9 | 2018-08-31 | no assertion criteria provided | literature only | |
| Biochemical Molecular Genetic Laboratory, |
RCV000656336 | SCV000778299 | likely pathogenic | Autosomal recessive nonsyndromic hearing loss 9 | 2018-02-13 | no assertion criteria provided | clinical testing | |
| Genomic Medicine Center of Excellence, |
RCV000171287 | SCV000221484 | likely pathogenic | not provided | flagged submission | research |