ClinVar Miner

Submissions for variant NM_018249.6(CDK5RAP2):c.2482A>G (p.Lys828Glu)

gnomAD frequency: 0.00009  dbSNP: rs549081765
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000766830 SCV000590695 uncertain significance not provided 2022-11-11 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant does not alter protein structure/function; Observed in a patient with sporadic Hirschsprung disease in published literature (Villalba-Benito et al., 2017); This variant is associated with the following publications: (PMID: 28740121)
Genetic Services Laboratory, University of Chicago RCV000498152 SCV000593955 likely benign not specified 2015-11-04 criteria provided, single submitter clinical testing
Invitae RCV000766830 SCV003269506 uncertain significance not provided 2023-05-22 criteria provided, single submitter clinical testing 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. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The glutamic acid amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. ClinVar contains an entry for this variant (Variation ID: 432919). This variant has not been reported in the literature in individuals affected with CDK5RAP2-related conditions. This variant is present in population databases (rs549081765, gnomAD 0.06%). This sequence change replaces lysine, which is basic and polar, with glutamic acid, which is acidic and polar, at codon 828 of the CDK5RAP2 protein (p.Lys828Glu).

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