ClinVar Miner

Submissions for variant NM_000244.3(MEN1):c.1682_1684AGA[1] (p.Lys562del) (rs794728661)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000182464 SCV000234809 likely pathogenic not provided 2018-08-28 criteria provided, single submitter clinical testing This in-frame deletion of three nucleotides in MEN1 is denoted c.1670_1672delAGA at the cDNA level and p.Lys557del (K557del) at the protein level. The normal sequence, with the bases that are deleted in brackets, is GAGA[delAGA]TGAA. This variant, also published as 1780delAGA using alternate nomenclature, was observed in several individuals with clinical histories consistent with multiple endocrine neoplasia type 1 (MEN1) (Giraud 1998, Cebri?n 2002, Wautot 2002, Cebri?n 2003). This variant was not observed in large population cohorts (Lek 2016). This deletion of a single Lysine amino acid is not located in a known functional domain. In-silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect. Based on currently available evidence, we consider this deletion to be likely pathogenic.
Invitae RCV001223385 SCV001395532 uncertain significance Multiple endocrine neoplasia, type 1 2019-06-13 criteria provided, single submitter clinical testing This variant, c.1670_1672del, results in the deletion of 1 amino acid(s) of the MEN1 protein (p.Lys557del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individuals affected with multiple endocrine neoplasia type 1 (PMID: 9683585, 22026581). This variant is also known as 1780delAGA in the literature. ClinVar contains an entry for this variant (Variation ID: 201023). Experimental studies and prediction algorithms are not available or were not evaluated for this variant, and the functional significance of the affected amino acid(s) is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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