ClinVar Miner

Submissions for variant NM_000262.3(NAGA):c.103C>T (p.Arg35Cys)

gnomAD frequency: 0.00006  dbSNP: rs376933189
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000493540 SCV000582080 uncertain significance not provided 2023-01-13 criteria provided, single submitter clinical testing Observed in apparent homozygous state in a patient with Schindler disease in the literature (Ortiz et al., 2018); patient was also reported to have an apparently homozygous pathogenic NAGA variant; In silico analysis supports that this missense variant has a deleterious effect on protein structure/function
Labcorp Genetics (formerly Invitae), Labcorp RCV002524028 SCV003258669 uncertain significance Alpha-N-acetylgalactosaminidase deficiency type 1 2022-10-17 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 35 of the NAGA protein (p.Arg35Cys). This variant is present in population databases (rs376933189, gnomAD 0.04%). 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: 429497). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on NAGA 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.
Revvity Omics, Revvity RCV000493540 SCV003813414 uncertain significance not provided 2020-03-30 criteria provided, single submitter clinical testing

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