ClinVar Miner

Submissions for variant NM_001378609.3(OTOGL):c.5449C>T (p.Arg1817Ter)

gnomAD frequency: 0.00003  dbSNP: rs768620276
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000497321 SCV000589683 likely pathogenic not provided 2023-01-18 criteria provided, single submitter clinical testing Identified in a patient with sensorineural hearing loss who also harbored a second variant in the OTOGL gene (phase unknown) in published literature (Reiss et al., 2022); Identified in an individual with autism who harbored a second OTOGL variant (phase unknown) in published literature (Lim et al., 2013); detailed clinical information was not provided; Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 23352160, 35580552)
CeGaT Center for Human Genetics Tuebingen RCV000497321 SCV001747658 likely pathogenic not provided 2021-12-01 criteria provided, single submitter clinical testing
MGZ Medical Genetics Center RCV002289684 SCV002580419 pathogenic Autosomal recessive nonsyndromic hearing loss 84B 2021-12-22 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV002289684 SCV002805687 pathogenic Autosomal recessive nonsyndromic hearing loss 84B 2021-08-25 criteria provided, single submitter clinical testing
Invitae RCV000497321 SCV003290828 pathogenic not provided 2023-12-20 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg1808*) in the OTOGL gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in OTOGL are known to be pathogenic (PMID: 23122586). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with OTOGL-related conditions. ClinVar contains an entry for this variant (Variation ID: 432017). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ RCV000497321 SCV001952780 pathogenic not provided no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000497321 SCV001974850 pathogenic not provided no assertion criteria provided clinical testing

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