ClinVar Miner

Submissions for variant NM_182961.4(SYNE1):c.16390-2A>C

dbSNP: rs759460806
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000727362 SCV000707864 pathogenic not provided 2017-04-25 criteria provided, single submitter clinical testing
Athena Diagnostics RCV000727362 SCV001476985 uncertain significance not provided 2019-12-27 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001380011 SCV001577935 pathogenic Autosomal recessive ataxia, Beauce type; Emery-Dreifuss muscular dystrophy 4, autosomal dominant 2024-12-24 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 84 of the SYNE1 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 SYNE1 are known to be pathogenic (PMID: 19542096, 24319099, 27086870). This variant is present in population databases (rs759460806, gnomAD 0.007%). Disruption of this splice site has been observed in individual(s) with cerebellar ataxia (PMID: 17159980). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 465779). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
Revvity Omics, Revvity RCV000727362 SCV002016824 likely pathogenic not provided 2019-08-07 criteria provided, single submitter clinical testing

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