ClinVar Miner

Submissions for variant NM_172107.4(KCNQ2):c.88G>A (p.Gly30Ser)

gnomAD frequency: 0.00001  dbSNP: rs915805727
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Institute of Human Genetics, University Hospital Muenster RCV002276255 SCV002562225 uncertain significance Seizure 2022-06-20 criteria provided, single submitter clinical testing ACMG categories: PM2,PP3,BP1
Ambry Genetics RCV002373067 SCV002687459 uncertain significance Inborn genetic diseases 2019-06-21 criteria provided, single submitter clinical testing The p.G30S variant (also known as c.88G>A), located in coding exon 1 of the KCNQ2 gene, results from a G to A substitution at nucleotide position 88. The glycine at codon 30 is replaced by serine, an amino acid with similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
CeGaT Center for Human Genetics Tuebingen RCV003434463 SCV004150936 likely benign not provided 2022-04-01 criteria provided, single submitter clinical testing KCNQ2: PP2, PP3, BS2
Invitae RCV003774879 SCV004678366 uncertain significance Early infantile epileptic encephalopathy with suppression bursts 2023-12-21 criteria provided, single submitter clinical testing This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 30 of the KCNQ2 protein (p.Gly30Ser). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with KCNQ2-related conditions. ClinVar contains an entry for this variant (Variation ID: 1700699). 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 expected to disrupt KCNQ2 protein function with a positive 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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