ClinVar Miner

Submissions for variant NM_014141.6(CNTNAP2):c.3919G>A (p.Ala1307Thr)

gnomAD frequency: 0.00001  dbSNP: rs139234992
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000483325 SCV000566613 uncertain significance not provided 2016-11-14 criteria provided, single submitter clinical testing The A1307T variant in the CNTNAP2 gene has not been published as a pathogenic variant, nor has it been reported as a benign polymorphism to our knowledge. The A1307T variant was not observed at any significant frequency in approximately 6,500 individuals of European and African American ancestry by the NHLBI Exome Sequencing Project. The A1307T 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 across species. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. We interpret A1307T as a variant of unknown significance.
Labcorp Genetics (formerly Invitae), Labcorp RCV001321445 SCV001512274 uncertain significance Cortical dysplasia-focal epilepsy syndrome 2022-10-24 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 1307 of the CNTNAP2 protein (p.Ala1307Thr). This variant is present in population databases (rs139234992, gnomAD 0.01%). 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: 419062). 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: "Tolerated"; PolyPhen-2: "Possibly 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.
Ambry Genetics RCV002525786 SCV003643562 uncertain significance Inborn genetic diseases 2022-09-05 criteria provided, single submitter clinical testing The c.3919G>A (p.A1307T) alteration is located in exon 24 (coding exon 24) of the CNTNAP2 gene. This alteration results from a G to A substitution at nucleotide position 3919, causing the alanine (A) at amino acid position 1307 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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