ClinVar Miner

Submissions for variant NM_000262.3(NAGA):c.925C>T (p.Pro309Ser)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV003070483 SCV003476754 uncertain significance Alpha-N-acetylgalactosaminidase deficiency type 1 2022-07-20 criteria provided, single submitter clinical testing This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 309 of the NAGA protein (p.Pro309Ser). This variant is present in population databases (rs760857039, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with NAGA-related conditions. 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.
Ambry Genetics RCV003269440 SCV003947165 uncertain significance Inborn genetic diseases 2023-03-22 criteria provided, single submitter clinical testing The c.925C>T (p.P309S) alteration is located in exon 7 (coding exon 7) of the NAGA gene. This alteration results from a C to T substitution at nucleotide position 925, causing the proline (P) at amino acid position 309 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
PreventionGenetics, part of Exact Sciences RCV004736267 SCV005347681 uncertain significance NAGA-related disorder 2024-03-28 no assertion criteria provided clinical testing The NAGA c.925C>T variant is predicted to result in the amino acid substitution p.Pro309Ser. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.020% of alleles in individuals of South Asian descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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