ClinVar Miner

Submissions for variant NM_000834.5(GRIN2B):c.4017G>A (p.Met1339Ile)

gnomAD frequency: 0.00002  dbSNP: rs752473485
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001060891 SCV001225608 uncertain significance Intellectual disability, autosomal dominant 6; Developmental and epileptic encephalopathy, 27 2022-09-27 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 not expected to disrupt GRIN2B protein function. ClinVar contains an entry for this variant (Variation ID: 855592). This variant has not been reported in the literature in individuals affected with GRIN2B-related conditions. This variant is present in population databases (rs752473485, gnomAD 0.007%). This sequence change replaces methionine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 1339 of the GRIN2B protein (p.Met1339Ile).
Illumina Laboratory Services, Illumina RCV001095761 SCV001251604 uncertain significance Intellectual disability, autosomal dominant 6 2020-01-16 criteria provided, single submitter clinical testing The GRIN2B c.4017G>A (p.Met1339Ile) variant is a missense variant. A literature search was performed for the gene, cDNA change, and amino acid change. No publications were found based on this search. This variant is found at a frequency of 0.000062 in East Asian population in the Genome Aggregation Database in a region of good sequence coverage, however this frequency is based on one allele. Based on the limited evidence, the p.Met1339Ile variant is classified as a variant of unknown significance for GRIN2B-related neurodevelopmental disorder.

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