ClinVar Miner

Submissions for variant NM_001199107.2(TBC1D24):c.1490T>C (p.Met497Thr)

gnomAD frequency: 0.00004  dbSNP: rs367710709
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000766894 SCV000243348 uncertain significance not provided 2021-10-11 criteria provided, single submitter clinical testing Not observed in large population cohorts (Lek et al., 2016); Has not been previously published as pathogenic or benign to our knowledge; 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: 24291220)
Genetic Services Laboratory, University of Chicago RCV000189701 SCV000249120 uncertain significance not specified 2015-02-06 criteria provided, single submitter clinical testing
Invitae RCV001069416 SCV001234580 uncertain significance Developmental and epileptic encephalopathy, 1; Autosomal dominant nonsyndromic hearing loss 65; Caused by mutation in the TBC1 domain family, member 24 2023-11-10 criteria provided, single submitter clinical testing This sequence change replaces methionine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 497 of the TBC1D24 protein (p.Met497Thr). This variant is present in population databases (rs367710709, gnomAD 0.005%). This variant has not been reported in the literature in individuals affected with TBC1D24-related conditions. ClinVar contains an entry for this variant (Variation ID: 207514). 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 TBC1D24 protein function with a positive predictive value of 80%. 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.

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