ClinVar Miner

Submissions for variant NM_000487.6(ARSA):c.826A>T (p.Thr276Ser)

gnomAD frequency: 0.00004  dbSNP: rs140966324
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV002029692 SCV002300266 likely pathogenic Metachromatic leukodystrophy 2024-01-04 criteria provided, single submitter clinical testing This sequence change replaces threonine, which is neutral and polar, with serine, which is neutral and polar, at codon 276 of the ARSA protein (p.Thr276Ser). This variant is present in population databases (rs140966324, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with ARSA-related conditions. ClinVar contains an entry for this variant (Variation ID: 1514967). 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 expected to disrupt ARSA protein function with a positive predictive value of 95%. This variant disrupts the p.Thr276 amino acid residue in ARSA. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 7825603, 8104633, 19815439, 26462614). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
Gelb Laboratory, University of Washington RCV002029692 SCV005046538 not provided Metachromatic leukodystrophy no assertion provided in vitro

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