ClinVar Miner

Submissions for variant NM_012330.4(KAT6B):c.4510G>A (p.Glu1504Lys)

gnomAD frequency: 0.00011  dbSNP: rs200393557
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV002016302 SCV002297682 uncertain significance Genitopatellar syndrome 2024-02-01 criteria provided, single submitter clinical testing This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 1504 of the KAT6B protein (p.Glu1504Lys). This variant is present in population databases (rs200393557, gnomAD 0.03%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with KAT6B-related conditions. ClinVar contains an entry for this variant (Variation ID: 1508713). 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 not expected to disrupt KAT6B protein function with a negative predictive value of 80%. 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.
PreventionGenetics, part of Exact Sciences RCV004538733 SCV004121251 uncertain significance KAT6B-related disorder 2023-07-18 criteria provided, single submitter clinical testing The KAT6B c.4510G>A variant is predicted to result in the amino acid substitution p.Glu1504Lys. To our knowledge, this variant has not been reported in the literature in affected individuals. This variant is reported in 0.031% of alleles in individuals of Latino descent in gnomAD (http://gnomad.broadinstitute.org/variant/10-76789092-G-A). Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.
CeGaT Center for Human Genetics Tuebingen RCV003883739 SCV004701928 likely benign not provided 2024-03-01 criteria provided, single submitter clinical testing KAT6B: BP4, BS1

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