ClinVar Miner

Submissions for variant NM_000702.4(ATP1A2):c.1496G>A (p.Ser499Asn)

gnomAD frequency: 0.00002  dbSNP: rs767230468
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001545188 SCV001764467 likely benign not provided 2020-04-06 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV002032553 SCV002289160 uncertain significance Familial hemiplegic migraine 2023-12-09 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with asparagine, which is neutral and polar, at codon 499 of the ATP1A2 protein (p.Ser499Asn). This variant is present in population databases (rs767230468, gnomAD 0.008%). This variant has not been reported in the literature in individuals affected with ATP1A2-related conditions. ClinVar contains an entry for this variant (Variation ID: 1186181). 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 ATP1A2 protein function with a negative predictive value of 80%. 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 RCV003346611 SCV004060525 uncertain significance Inborn genetic diseases 2023-08-31 criteria provided, single submitter clinical testing The c.1496G>A (p.S499N) alteration is located in exon 12 (coding exon 12) of the ATP1A2 gene. This alteration results from a G to A substitution at nucleotide position 1496, causing the serine (S) at amino acid position 499 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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