ClinVar Miner

Submissions for variant NM_004519.4(KCNQ3):c.2338C>T (p.Arg780Cys)

gnomAD frequency: 0.00007  dbSNP: rs138852641
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000467985 SCV000543208 uncertain significance Benign neonatal seizures 2024-01-28 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 780 of the KCNQ3 protein (p.Arg780Cys). This variant is present in population databases (rs138852641, gnomAD 0.02%). This missense change has been observed in individual(s) with benign familial neonatal-infantile seizures (PMID: 23360469). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 405218). 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 KCNQ3 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.
CeGaT Center for Human Genetics Tuebingen RCV000585180 SCV000693279 uncertain significance not provided 2019-08-01 criteria provided, single submitter clinical testing
GeneDx RCV000585180 SCV001784123 likely benign not provided 2019-09-26 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 28488083, 27064559, 24851285, 25982755, 23360469, 28717674)
Ambry Genetics RCV002446778 SCV002732534 likely benign Inborn genetic diseases 2020-03-18 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
GeneReviews RCV001814157 SCV002061346 not provided Seizures, benign familial neonatal, 2 no assertion provided literature only

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