ClinVar Miner

Submissions for variant NM_203446.3(SYNJ1):c.3478+1G>A

dbSNP: rs1085307987
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000489521 SCV000577783 likely pathogenic not provided 2024-05-14 criteria provided, single submitter clinical testing Canonical splice site variant predicted to result in an in-frame loss of the adjacent exon 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
Labcorp Genetics (formerly Invitae), Labcorp RCV002527036 SCV002982543 likely pathogenic Early-onset Parkinson disease 20; Developmental and epileptic encephalopathy, 53 2023-07-25 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: 427149). This variant has not been reported in the literature in individuals affected with SYNJ1-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.0009%). This sequence change affects a donor splice site in intron 27 of the SYNJ1 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 SYNJ1 are known to be pathogenic (PMID: 25316601, 27435091).

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