ClinVar Miner

Submissions for variant NM_005670.4(EPM2A):c.143G>A (p.Gly48Asp)

gnomAD frequency: 0.00023  dbSNP: rs946076987
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000434593 SCV000512937 uncertain significance not provided 2023-08-03 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Labcorp Genetics (formerly Invitae), Labcorp RCV000536343 SCV000636472 uncertain significance Progressive myoclonic epilepsy 2022-11-01 criteria provided, single submitter clinical testing This sequence change replaces glycine, which is neutral and non-polar, with aspartic acid, which is acidic and polar, at codon 48 of the EPM2A protein (p.Gly48Asp). This variant is present in population databases (no rsID available, gnomAD 0.04%). This variant has not been reported in the literature in individuals affected with EPM2A-related conditions. ClinVar contains an entry for this variant (Variation ID: 377829). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). 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.
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago RCV000768208 SCV000898672 uncertain significance Lafora disease 2021-03-30 criteria provided, single submitter clinical testing EPM2A NM_005670.3 exon 1 p.Gly48Asp (c.143G>A):This variant has not been reported in the literature but is present in 8/29388 European alleles in the Genome Aggregation Database (http://gnomad.broadinstitute.org/). This variant is present in ClinVar (Variation ID:377829). Evolutionary conservation and computational predictive tools for this variant are limited or unavailable. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.
Athena Diagnostics RCV000434593 SCV001143864 uncertain significance not provided 2018-09-18 criteria provided, single submitter clinical testing
Ambry Genetics RCV002392951 SCV002702894 uncertain significance Inborn genetic diseases 2022-11-18 criteria provided, single submitter clinical testing The c.143G>A (p.G48D) alteration is located in exon 1 (coding exon 1) of the EPM2A gene. This alteration results from a G to A substitution at nucleotide position 143, causing the glycine (G) at amino acid position 48 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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