ClinVar Miner

Submissions for variant NM_014141.6(CNTNAP2):c.2368C>T (p.Arg790Cys)

gnomAD frequency: 0.00006  dbSNP: rs200089329
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000187209 SCV000240791 uncertain significance not provided 2022-07-18 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; In-silico analysis is inconclusive as to whether the variant alters gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown.; Has not been previously published as pathogenic or benign to our knowledge
Labcorp Genetics (formerly Invitae), Labcorp RCV000795983 SCV000935468 uncertain significance Cortical dysplasia-focal epilepsy syndrome 2022-07-26 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 790 of the CNTNAP2 protein (p.Arg790Cys). This variant is present in population databases (rs200089329, gnomAD 0.06%). 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: 205265). 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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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.
Ambry Genetics RCV002453687 SCV002736933 uncertain significance Inborn genetic diseases 2017-12-27 criteria provided, single submitter clinical testing The p.R790C variant (also known as c.2368C>T), located in coding exon 15 of the CNTNAP2 gene, results from a C to T substitution at nucleotide position 2368. The arginine at codon 790 is replaced by cysteine, an amino acid with highly dissimilar 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.

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