ClinVar Miner

Submissions for variant NM_033409.4(SLC52A3):c.706G>A (p.Val236Met)

gnomAD frequency: 0.00003  dbSNP: rs927297761
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000810466 SCV000950667 uncertain significance Brown-Vialetto-van Laere syndrome 1 2023-07-07 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 236 of the SLC52A3 protein (p.Val236Met). This variant is present in population databases (no rsID available, gnomAD 0.0009%). 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: 654493). 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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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 RCV002363092 SCV002663018 uncertain significance Inborn genetic diseases 2022-03-25 criteria provided, single submitter clinical testing The p.V236M variant (also known as c.706G>A), located in coding exon 2 of the SLC52A3 gene, results from a G to A substitution at nucleotide position 706. The valine at codon 236 is replaced by methionine, an amino acid with highly similar properties. This amino acid position is poorly 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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