ClinVar Miner

Submissions for variant NM_005751.5(AKAP9):c.1204G>A (p.Glu402Lys)

gnomAD frequency: 0.00019  dbSNP: rs146022334
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000617314 SCV000737724 likely benign Cardiovascular phenotype 2022-10-03 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Labcorp Genetics (formerly Invitae), Labcorp RCV001238149 SCV001410948 uncertain significance Long QT syndrome 2023-05-01 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. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. ClinVar contains an entry for this variant (Variation ID: 519331). This variant has not been reported in the literature in individuals affected with AKAP9-related conditions. This variant is present in population databases (rs146022334, gnomAD 0.07%), and has an allele count higher than expected for a pathogenic variant. This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 402 of the AKAP9 protein (p.Glu402Lys).
Baylor Genetics RCV001332665 SCV001525048 uncertain significance Long QT syndrome 11 2020-02-10 criteria provided, single submitter clinical testing This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].
Fulgent Genetics, Fulgent Genetics RCV001332665 SCV002775620 uncertain significance Long QT syndrome 11 2021-09-14 criteria provided, single submitter clinical testing
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago RCV001332665 SCV003919882 uncertain significance Long QT syndrome 11 2021-03-30 criteria provided, single submitter clinical testing AKAP9 NM_005751.4 exon 8 p.Glu402Lys (c.1204G>A): This variant has not been reported in the literature but is present in 0.06% (17/24482) of African alleles in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/7-91630435-G-A). This variant is present in ClinVar (Variation ID:519331). Evolutionary conservation and computational predictive tools suggest that this variant may impact the protein. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.

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