ClinVar Miner

Submissions for variant NM_001040142.2(SCN2A):c.5412G>T (p.Lys1804Asn)

gnomAD frequency: 0.00001  dbSNP: rs759697991
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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 RCV000810283 SCV000950476 uncertain significance Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 11 2022-06-08 criteria provided, single submitter clinical testing 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. 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 disruptive. ClinVar contains an entry for this variant (Variation ID: 654341). This variant has not been reported in the literature in individuals affected with SCN2A-related conditions. This variant is present in population databases (rs759697991, gnomAD 0.0009%). This sequence change replaces lysine, which is basic and polar, with asparagine, which is neutral and polar, at codon 1804 of the SCN2A protein (p.Lys1804Asn).
Revvity Omics, Revvity RCV003141820 SCV003820762 uncertain significance not provided 2021-03-26 criteria provided, single submitter clinical testing
Ambry Genetics RCV004962832 SCV005500045 uncertain significance Inborn genetic diseases 2024-09-09 criteria provided, single submitter clinical testing The c.5412G>T (p.K1804N) alteration is located in exon 27 (coding exon 26) of the SCN2A gene. This alteration results from a G to T substitution at nucleotide position 5412, causing the lysine (K) at amino acid position 1804 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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