ClinVar Miner

Submissions for variant NM_000262.3(NAGA):c.983T>C (p.Met328Thr)

gnomAD frequency: 0.00006  dbSNP: rs140356002
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000732043 SCV000859919 uncertain significance not provided 2018-02-21 criteria provided, single submitter clinical testing
Invitae RCV001305248 SCV001494577 uncertain significance Alpha-N-acetylgalactosaminidase deficiency type 1 2021-08-30 criteria provided, single submitter clinical testing This sequence change replaces methionine with threonine at codon 328 of the NAGA protein (p.Met328Thr). The methionine residue is weakly conserved and there is a moderate physicochemical difference between methionine and threonine. This variant is present in population databases (rs140356002, ExAC 0.008%). 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: 596276). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. 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.
Mayo Clinic Laboratories, Mayo Clinic RCV000732043 SCV001713911 uncertain significance not provided 2020-03-17 criteria provided, single submitter clinical testing
Ambry Genetics RCV003243282 SCV003941485 uncertain significance Inborn genetic diseases 2023-05-05 criteria provided, single submitter clinical testing The c.983T>C (p.M328T) alteration is located in exon 8 (coding exon 8) of the NAGA gene. This alteration results from a T to C substitution at nucleotide position 983, causing the methionine (M) at amino acid position 328 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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