ClinVar Miner

Submissions for variant NM_030777.4(SLC2A10):c.1616C>T (p.Ala539Val)

gnomAD frequency: 0.00002  dbSNP: rs140312420
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000200650 SCV000250732 uncertain significance not provided 2021-02-04 criteria provided, single submitter clinical testing Has not been previously published as pathogenic or benign to our knowledge; In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Not observed at a significant frequency in large population cohorts (Lek et al., 2016); Reported in ClinVar as a variant of uncertain significance (ClinVar Variant ID# 213743; Landrum et al., 2016)
Ambry Genetics RCV002310793 SCV000319570 uncertain significance Familial thoracic aortic aneurysm and aortic dissection 2017-02-23 criteria provided, single submitter clinical testing The p.A539V variant (also known as c.1616C>T), located in coding exon 5 of the SLC2A10 gene, results from a C to T substitution at nucleotide position 1616. The alanine at codon 539 is replaced by valine, an amino acid with 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 variant remains unclear.
Invitae RCV001857725 SCV002178108 uncertain significance Arterial tortuosity syndrome 2022-06-29 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 539 of the SLC2A10 protein (p.Ala539Val). This variant is present in population databases (rs140312420, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with SLC2A10-related conditions. ClinVar contains an entry for this variant (Variation ID: 213743). 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 SLC2A10 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.
Mayo Clinic Laboratories, Mayo Clinic RCV000200650 SCV004225502 uncertain significance not provided 2023-05-25 criteria provided, single submitter clinical testing BP4_strong

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