ClinVar Miner

Submissions for variant NM_001128225.3(SLC39A13):c.31A>G (p.Met11Val)

gnomAD frequency: 0.00001  dbSNP: rs768592866
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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 RCV002023303 SCV002304213 uncertain significance Ehlers-Danlos syndrome, spondylocheirodysplastic type 2021-09-21 criteria provided, single submitter clinical testing This sequence change replaces methionine with valine at codon 11 of the SLC39A13 protein (p.Met11Val). The methionine residue is moderately conserved and there is a small physicochemical difference between methionine and valine. This variant is present in population databases (rs768592866, ExAC 0.002%). This variant has not been reported in the literature in individuals affected with SLC39A13-related conditions. 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: "Probably Damaging"; Align-GVGD: "Class C0"). 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 RCV002548767 SCV003572390 uncertain significance Inborn genetic diseases 2021-07-20 criteria provided, single submitter clinical testing The c.31A>G (p.M11V) alteration is located in exon 2 (coding exon 1) of the SLC39A13 gene. This alteration results from a A to G substitution at nucleotide position 31, causing the methionine (M) at amino acid position 11 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
GeneDx RCV003324844 SCV004030860 uncertain significance not provided 2023-02-23 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); 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

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