ClinVar Miner

Submissions for variant NM_001378609.3(OTOGL):c.3213+1G>A

gnomAD frequency: 0.00004  dbSNP: rs370730786
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000373203 SCV000345840 likely pathogenic not provided 2016-09-06 criteria provided, single submitter clinical testing
Ambry Genetics RCV000622886 SCV000741180 likely pathogenic Inborn genetic diseases 2016-02-22 criteria provided, single submitter clinical testing
GeneDx RCV000373203 SCV001789997 likely pathogenic not provided 2022-08-01 criteria provided, single submitter clinical testing Canonical splice site variant expected to result in aberrant splicing, although in the absence of functional evidence the actual effect of this sequence change is unknown.; Not observed at significant frequency in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge
Revvity Omics, Revvity RCV001782780 SCV002020204 likely pathogenic Autosomal recessive nonsyndromic hearing loss 84B 2019-07-05 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV001782780 SCV002788721 likely pathogenic Autosomal recessive nonsyndromic hearing loss 84B 2021-08-11 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000373203 SCV003503241 likely pathogenic not provided 2023-04-06 criteria provided, single submitter clinical testing This variant has not been reported in the literature in individuals affected with OTOGL-related conditions. This variant is present in population databases (rs370730786, gnomAD 0.007%). This sequence change affects a donor splice site in intron 27 of the OTOGL gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in OTOGL are known to be pathogenic (PMID: 23122586). ClinVar contains an entry for this variant (Variation ID: 291138). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site.
PreventionGenetics, part of Exact Sciences RCV003401277 SCV004105226 likely pathogenic OTOGL-related disorder 2023-10-10 criteria provided, single submitter clinical testing The OTOGL c.3186+1G>A variant is predicted to disrupt the GT donor site and interfere with normal splicing. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0070% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/12-80696564-G-A). Variants that disrupt the consensus splice donor site in OTOGL are expected to be pathogenic. This variant is interpreted as likely pathogenic.

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