ClinVar Miner

Submissions for variant NM_000038.6(APC):c.6186A>C (p.Lys2062Asn) (rs1064796527)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000481933 SCV000573328 uncertain significance not provided 2017-02-14 criteria provided, single submitter clinical testing The K2062N variant has not, to our knowledge, been published in the literature as pathogenic or benign. This variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The K2062N variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This variant occurs at a position that is conserved in mammals and is not located in a known functional domain. In silico analyses are inconsistent regarding the effect this variant may have on protein structure and function. Based on currently available evidence, we consider K2062N to be a variant of uncertain significance.
Invitae RCV000807054 SCV000947082 uncertain significance Familial adenomatous polyposis 1 2018-12-22 criteria provided, single submitter clinical testing This sequence change replaces lysine with asparagine at codon 2062 of the APC protein (p.Lys2062Asn). The lysine residue is highly conserved and there is a moderate physicochemical difference between lysine and asparagine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with APC-related conditions. ClinVar contains an entry for this variant (Variation ID: 423610). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. 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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