ClinVar Miner

Submissions for variant NM_000262.3(NAGA):c.487G>A (p.Glu163Lys)

gnomAD frequency: 0.00004  dbSNP: rs372458856
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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 RCV000817487 SCV000958051 uncertain significance Alpha-N-acetylgalactosaminidase deficiency type 1 2022-07-18 criteria provided, single submitter clinical testing This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 163 of the NAGA protein (p.Glu163Lys). This variant is present in population databases (rs372458856, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with NAGA-related conditions. ClinVar contains an entry for this variant (Variation ID: 660319). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The lysine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect 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.
GenomeConnect - Invitae Patient Insights Network RCV001535647 SCV001749688 not provided Alpha-N-acetylgalactosaminidase deficiency type 2; Alpha-N-acetylgalactosaminidase deficiency type 1; Alpha-N-acetylgalactosaminidase deficiency type 3 no assertion provided phenotyping only Variant interpreted as Uncertain significance and reported on 08-28-2020 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information.

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