ClinVar Miner

Submissions for variant NM_000834.5(GRIN2B):c.4015_4016del (p.Met1339fs)

dbSNP: rs1565453023
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV002312761 SCV000847180 likely pathogenic Inborn genetic diseases 2016-07-14 criteria provided, single submitter clinical testing The c.4015_4016delAT variant (also known as p.M1339VFS*2), located in coding exon 12 of the GRIN2B gene, results from a deletion of two nucleotides at nucleotide positions 4015 to 4016, causing a translational frameshift with a predicted alternate stop codon. This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. In the ESP, this variant was not observed in 6503 samples (13006 alleles) with coverage at this position. This amino acid position is well conserved in available vertebrate species. This alteration is expected to result in loss of function by premature protein truncation. Based on the majority of available evidence to date, this variant is likely to be pathogenic.
Invitae RCV001212292 SCV001383872 uncertain significance Intellectual disability, autosomal dominant 6; Developmental and epileptic encephalopathy, 27 2019-06-05 criteria provided, single submitter clinical testing This sequence change results in a premature translational stop signal in the GRIN2B gene (p.Met1339Valfs*2). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 146 amino acids of the GRIN2B protein. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with GRIN2B-related conditions. ClinVar contains an entry for this variant (Variation ID: 588039). 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.
GeneDx RCV003318633 SCV004022854 likely pathogenic not provided 2023-07-27 criteria provided, single submitter clinical testing Frameshift variant predicted to result in protein truncation, as the last 146 amino acids are replaced with 1 incorrect amino acid, and other loss-of-function variants have been reported downstream at GeneDx.; Not observed in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge

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