ClinVar Miner

Submissions for variant NM_001199107.2(TBC1D24):c.28G>A (p.Val10Met)

gnomAD frequency: 0.00001  dbSNP: rs767293945
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000800917 SCV000940661 uncertain significance Developmental and epileptic encephalopathy, 1; Autosomal dominant nonsyndromic hearing loss 65; Caused by mutation in the TBC1 domain family, member 24 2022-02-05 criteria provided, single submitter clinical testing 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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 646598). This variant has not been reported in the literature in individuals affected with TBC1D24-related conditions. This variant is present in population databases (rs767293945, gnomAD 0.003%). This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 10 of the TBC1D24 protein (p.Val10Met).
3billion RCV001809818 SCV002058476 uncertain significance Developmental and epileptic encephalopathy, 16 2022-01-03 criteria provided, single submitter clinical testing This vairant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000008, PM2_M). In silico tool predictions suggest damaging effect of the variant on gene or gene product (3CNET: 0.941, PP3_P). A missense variant is a common mechanism associated with Epileptic encephalopathy (PP2_P). Therefore, this variant is classified as uncertain significance according to the recommendation of ACMG/AMP guideline.
Ambry Genetics RCV002534661 SCV003629834 uncertain significance Inborn genetic diseases 2022-06-10 criteria provided, single submitter clinical testing The c.28G>A (p.V10M) alteration is located in exon 2 (coding exon 1) of the TBC1D24 gene. This alteration results from a G to A substitution at nucleotide position 28, causing the valine (V) at amino acid position 10 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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