ClinVar Miner

Submissions for variant NM_001165963.4(SCN1A):c.1706A>G (p.Asn569Ser)

gnomAD frequency: 0.00001  dbSNP: rs796052978
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000188877 SCV000242507 uncertain significance not provided 2021-06-18 criteria provided, single submitter clinical testing Missense variants in this gene are often considered pathogenic (Stenson et al., 2014); In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 27535533, 24077912)
Labcorp Genetics (formerly Invitae), Labcorp RCV005089950 SCV005828859 uncertain significance Early infantile epileptic encephalopathy with suppression bursts 2024-07-02 criteria provided, single submitter clinical testing This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 569 of the SCN1A protein (p.Asn569Ser). This variant is present in population databases (rs796052978, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with SCN1A-related conditions. ClinVar contains an entry for this variant (Variation ID: 206772). 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) performed at Invitae indicates that this missense variant is not expected to disrupt SCN1A protein function with a negative predictive value of 95%. 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.

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