ClinVar Miner

Submissions for variant NM_014141.6(CNTNAP2):c.3382-2A>C

dbSNP: rs1085307838
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000489863 SCV000577442 likely pathogenic not provided 2022-07-27 criteria provided, single submitter clinical testing Canonical splice site variant predicted to result in a null allele in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge
Invitae RCV001856908 SCV002301338 likely pathogenic Cortical dysplasia-focal epilepsy syndrome 2022-08-31 criteria provided, single submitter clinical testing This variant has not been reported in the literature in individuals affected with CNTNAP2-related conditions. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 426876). This variant is not present in population databases (gnomAD no frequency). This sequence change affects an acceptor splice site in intron 20 of the CNTNAP2 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in CNTNAP2 are known to be pathogenic (PMID: 19896112, 21827697, 25045150, 26843181, 27439707).

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