ClinVar Miner

Submissions for variant NM_001363118.2(SLC52A2):c.1258G>A (p.Ala420Thr)

gnomAD frequency: 0.00001  dbSNP: rs368924997
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000237019 SCV000292900 likely pathogenic not provided 2022-08-25 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 24253200, 22864630, 32709422)
Eurofins Ntd Llc (ga) RCV000237019 SCV000344749 likely pathogenic not provided 2016-08-16 criteria provided, single submitter clinical testing
Invitae RCV000191988 SCV001229688 pathogenic Brown-Vialetto-van Laere syndrome 2 2024-01-17 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 420 of the SLC52A2 protein (p.Ala420Thr). This variant is present in population databases (rs368924997, gnomAD 0.006%). This missense change has been observed in individuals with Brown-Vialetto-Van Laere syndrome (PMID: 24253200; Invitae). ClinVar contains an entry for this variant (Variation ID: 210043). 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 SLC52A2 protein function with a negative predictive value of 80%. For these reasons, this variant has been classified as Pathogenic.
Laboratory of Medical Genetics, National & Kapodistrian University of Athens RCV000191988 SCV001976825 pathogenic Brown-Vialetto-van Laere syndrome 2 2021-10-05 criteria provided, single submitter clinical testing PM1, PM2, PP3, PP5
GeneReviews RCV000191988 SCV000246251 not provided Brown-Vialetto-van Laere syndrome 2 no assertion provided literature only

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