ClinVar Miner

Submissions for variant NM_000244.3(MEN1):c.799-1G>C (rs1555165377)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000520872 SCV000617615 pathogenic not provided 2015-11-16 criteria provided, single submitter clinical testing The c.784-1 G>C splice site variant in the MEN1 gene has been previously reported as c.894-1 using alternate nomenclature in association with multiple endocrine neoplasia type 1 (Giraud et al., 1998), and is consistent with the diagnosis in this patient. This pathogenic variant destroys the canonical splice acceptor site in intron 4, and is expected to cause abnormal gene splicing. The pathogenic variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations.
Invitae RCV000794756 SCV000934183 likely pathogenic Multiple endocrine neoplasia, type 1 2018-08-17 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 4 of the MEN1 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been observed in an individual affected with clinical features of multiple endocrine neoplasia type 1 syndrome (PMID: 9683585). This variant is also known as c.894-1G>C in the literature. ClinVar contains an entry for this variant (Variation ID: 449445). Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in MEN1 are known to be pathogenic (PMID: 12112656, 17853334). 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.

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