ClinVar Miner

Submissions for variant NM_177550.5(SLC13A5):c.1372G>A (p.Val458Met)

gnomAD frequency: 0.00017  dbSNP: rs372801738
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000417892 SCV000517986 uncertain significance not provided 2019-08-05 criteria provided, single submitter clinical testing In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Labcorp Genetics (formerly Invitae), Labcorp RCV000541177 SCV000655323 uncertain significance Developmental and epileptic encephalopathy, 25 2022-08-09 criteria provided, single submitter clinical testing This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 458 of the SLC13A5 protein (p.Val458Met). This variant is present in population databases (rs372801738, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with SLC13A5-related conditions. ClinVar contains an entry for this variant (Variation ID: 380207). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The methionine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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.
CeGaT Center for Human Genetics Tuebingen RCV000417892 SCV001961649 likely benign not provided 2022-09-01 criteria provided, single submitter clinical testing SLC13A5: BP4, BP5
Genome-Nilou Lab RCV000541177 SCV002055640 uncertain significance Developmental and epileptic encephalopathy, 25 2021-07-15 criteria provided, single submitter clinical testing
Ambry Genetics RCV002379316 SCV002697221 uncertain significance Inborn genetic diseases 2022-10-12 criteria provided, single submitter clinical testing The c.1372G>A (p.V458M) alteration is located in exon 10 (coding exon 10) of the SLC13A5 gene. This alteration results from a G to A substitution at nucleotide position 1372, causing the valine (V) at amino acid position 458 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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