ClinVar Miner

Submissions for variant NM_014141.6(CNTNAP2):c.806G>A (p.Ser269Asn)

gnomAD frequency: 0.00001  dbSNP: rs1057518565
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000412993 SCV000492333 uncertain significance not specified 2016-12-09 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the CNTNAP2 gene. The S269N variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The S269N variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The S269N variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. This substitution occurs at a position where amino acids with similar properties to Serine are tolerated across species. However, in silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Labcorp Genetics (formerly Invitae), Labcorp RCV002521437 SCV003000476 uncertain significance Cortical dysplasia-focal epilepsy syndrome 2022-03-04 criteria provided, single submitter clinical testing This variant has not been reported in the literature in individuals affected with CNTNAP2-related conditions. ClinVar contains an entry for this variant (Variation ID: 373714). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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. This variant is present in population databases (no rsID available, gnomAD 0.007%). This sequence change replaces serine, which is neutral and polar, with asparagine, which is neutral and polar, at codon 269 of the CNTNAP2 protein (p.Ser269Asn).

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