ClinVar Miner

Submissions for variant NM_000262.3(NAGA):c.487G>A (p.Glu163Lys) (rs372458856)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000817487 SCV000958051 uncertain significance Alpha-N-acetylgalactosaminidase deficiency type 1 2018-08-28 criteria provided, single submitter clinical testing This sequence change replaces glutamic acid with lysine at codon 163 of the NAGA protein (p.Glu163Lys). The glutamic acid residue is weakly conserved and there is a small physicochemical difference between glutamic acid and lysine. This variant is present in population databases (rs372458856, ExAC 0.02%). This variant has not been reported in the literature in individuals with NAGA-related disease. 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, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. 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; Schindler disease, 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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