ClinVar Miner

Submissions for variant NM_001323289.2(CDKL5):c.89G>A (p.Cys30Tyr)

dbSNP: rs1555940536
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Rett and Angelman-like Disorders Variant Curation Expert Panel RCV002281116 SCV002569940 uncertain significance CDKL5 disorder 2022-08-25 reviewed by expert panel curation The p.Cys30Tyr variant occurs in the well-characterized ATP binding region of the CDKL5 (PM1). The p.Cys30Tyr variant in CDKL5 is absent from gnomAD (PM2_Supporting). In summary, the p.Cys30Tyr variant in CDKL5 is classified as variant of unknown significance based on the ACMG/AMP criteria (PM1, PM2_Supporting).
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology RCV000518084 SCV000616331 likely pathogenic Developmental and epileptic encephalopathy, 2 2017-10-24 criteria provided, single submitter research
Laboratory of Inherited Metabolic Diseases, Research centre for medical genetics RCV000518084 SCV001245196 uncertain significance Developmental and epileptic encephalopathy, 2 2020-02-14 criteria provided, single submitter clinical testing
Invitae RCV001859996 SCV002285743 uncertain significance Developmental and epileptic encephalopathy, 2; Angelman syndrome-like 2022-07-06 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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt CDKL5 protein function. ClinVar contains an entry for this variant (Variation ID: 487576). This variant has not been reported in the literature in individuals affected with CDKL5-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces cysteine, which is neutral and slightly polar, with tyrosine, which is neutral and polar, at codon 30 of the CDKL5 protein (p.Cys30Tyr).

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