ClinVar Miner

Submissions for variant NM_006950.3(SYN1):c.528-2A>T

dbSNP: rs1556860663
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000555972 SCV000639954 likely pathogenic Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders 2022-08-16 criteria provided, single submitter clinical testing 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: 465099). This variant has not been reported in the literature in individuals affected with SYN1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change affects an acceptor splice site in intron 3 of the SYN1 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 SYN1 are known to be pathogenic (PMID: 14985377, 21441247).
GeneDx RCV001770437 SCV002004062 pathogenic not provided 2021-10-25 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 (Lek et al., 2016); Has not been previously published as pathogenic or benign to our knowledge
Revvity Omics, Revvity RCV001770437 SCV002016823 likely pathogenic not provided 2020-05-01 criteria provided, single submitter clinical testing
Institute for Human Genetics, University Hospital Essen RCV000555972 SCV002558879 pathogenic Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders 2022-07-30 criteria provided, single submitter clinical testing

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