ClinVar Miner

Submissions for variant NM_172107.4(KCNQ2):c.1270C>T (p.Pro424Ser)

gnomAD frequency: 0.00001  dbSNP: rs748120886
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000456695 SCV000543198 likely benign Early infantile epileptic encephalopathy with suppression bursts 2024-01-14 criteria provided, single submitter clinical testing
GeneDx RCV000524020 SCV000616938 uncertain significance not provided 2017-07-28 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the KCNQ2 gene. The P424S variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The P424S variant is observed in 6/7862 (0.1%) alleles from individuals of Latino background (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). This substitution occurs at a position that is not conserved. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. However, the P424S variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. Additionally, the majority of missense variants in this gene are considered pathogenic (Stenson et al., 2014). Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Ambry Genetics RCV002318515 SCV000851726 benign Inborn genetic diseases 2017-05-25 criteria provided, single submitter clinical testing This alteration is classified as 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.

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