ClinVar Miner

Submissions for variant NM_014141.6(CNTNAP2):c.1679C>G (p.Pro560Arg)

dbSNP: rs1064795313
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000485461 SCV000571002 uncertain significance not provided 2019-01-08 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the CNTNAP2 gene. The P560R varianthas not been published as a pathogenic variant, nor has it been reported as a benign variant to ourknowledge. It was not observed in approximately 6,500 individuals of European and AfricanAmerican ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benignvariant in these populations. The P560R 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. This substitution occurs at a position that is conserved acrossspecies, and in silico analysis predicts this variant is probably damaging to the proteinstructure/function. Based on the currently available information, it is unclear whether this variantis a pathogenic variant or a rare benign variant.
Labcorp Genetics (formerly Invitae), Labcorp RCV000644712 SCV000766415 uncertain significance Cortical dysplasia-focal epilepsy syndrome 2018-04-04 criteria provided, single submitter clinical testing This sequence change replaces proline with arginine at codon 560 of the CNTNAP2 protein (p.Pro560Arg). The proline residue is moderately conserved and there is a moderate physicochemical difference between proline and arginine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with CNTNAP2-related disease. ClinVar contains an entry for this variant (Variation ID: 421713). Algorithms developed to predict the effect of missense changes on protein structure and function 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.

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