ClinVar Miner

Submissions for variant NM_000262.3(NAGA):c.1009G>A (p.Ala337Thr)

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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV002988773 SCV003293385 uncertain significance Alpha-N-acetylgalactosaminidase deficiency type 1 2022-10-13 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 337 of the NAGA protein (p.Ala337Thr). This variant is present in population databases (rs144560510, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with NAGA-related conditions. 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 NAGA 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.

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