ClinVar Miner

Submissions for variant NM_033409.4(SLC52A3):c.203G>C (p.Cys68Ser)

gnomAD frequency: 0.00015  dbSNP: rs149622425
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000521405 SCV000621401 uncertain significance not provided 2021-04-26 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Invitae RCV000653712 SCV000775599 uncertain significance Brown-Vialetto-van Laere syndrome 1 2024-01-15 criteria provided, single submitter clinical testing This sequence change replaces cysteine, which is neutral and slightly polar, with serine, which is neutral and polar, at codon 68 of the SLC52A3 protein (p.Cys68Ser). This variant is present in population databases (rs149622425, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with SLC52A3-related conditions. ClinVar contains an entry for this variant (Variation ID: 452583). 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 not expected to disrupt SLC52A3 protein function with a negative 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.
Ambry Genetics RCV002420322 SCV002723040 uncertain significance Inborn genetic diseases 2022-06-01 criteria provided, single submitter clinical testing The p.C68S variant (also known as c.203G>C), located in coding exon 1 of the SLC52A3 gene, results from a G to C substitution at nucleotide position 203. The cysteine at codon 68 is replaced by serine, an amino acid with dissimilar properties. This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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