ClinVar Miner

Submissions for variant NM_014141.6(CNTNAP2):c.3154C>T (p.Arg1052Cys)

gnomAD frequency: 0.00016  dbSNP: rs139930720
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000187224 SCV000240806 uncertain significance not provided 2021-11-16 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Labcorp Genetics (formerly Invitae), Labcorp RCV000824329 SCV000965223 uncertain significance Cortical dysplasia-focal epilepsy syndrome 2022-09-01 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 1052 of the CNTNAP2 protein (p.Arg1052Cys). This variant is present in population databases (rs139930720, gnomAD 0.03%). 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: 205279). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The cysteine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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.
New York Genome Center RCV000824329 SCV001431184 uncertain significance Cortical dysplasia-focal epilepsy syndrome 2019-12-13 criteria provided, single submitter clinical testing
Ambry Genetics RCV002321752 SCV002610141 uncertain significance Inborn genetic diseases 2018-01-18 criteria provided, single submitter clinical testing The p.R1052C variant (also known as c.3154C>T), located in coding exon 19 of the CNTNAP2 gene, results from a C to T substitution at nucleotide position 3154. The arginine at codon 1052 is replaced by cysteine, an amino acid with highly dissimilar properties. This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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