ClinVar Miner

Submissions for variant NM_000834.5(GRIN2B):c.1658C>T (p.Pro553Leu)

dbSNP: rs397514556
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Institute of Human Genetics, University of Leipzig Medical Center RCV000032865 SCV001335404 likely pathogenic Intellectual disability, autosomal dominant 6 2017-04-04 criteria provided, single submitter clinical testing This variant was identified as de novo (maternity and paternity confirmed).
Genetics and Molecular Pathology, SA Pathology RCV002466416 SCV002761953 likely pathogenic Developmental and epileptic encephalopathy, 27 2020-08-03 criteria provided, single submitter clinical testing The GRIN2B c.1658C>T missense variant is classified as LIKELY PATHOGENIC (PM2, PP3, PP5, PS2) The GRIN2B c.1658C>T missense variant is a single nucleotide change in exon 8 of the GRIN2B gene, which is predicted to change the amino acid proline at position 553 in the protein to leucine. This variant has been reported in a patient with severe intellectual disability and hypotonia, with early post-natal onset (PMID:23033978). In that patient, this variant was found to be de novo and was reported as likely pathogenic (PS2). This variant is in dbSNP (rs397514556) but is absent from population databases (PM2). This variant has been reported in ClinVar as Likely pathogenic by another diagnostic laboratory (Variation ID: VCV000039661.2), and has also been reported as damaging in HGMD (CM1211463) and pathogenic in LOVD (GRIN2B_000083) (PP5). Computational predictions support a deleterious effect on the gene or gene product (PP3).
OMIM RCV000032865 SCV000056634 pathogenic Intellectual disability, autosomal dominant 6 2022-04-07 no assertion criteria provided literature only

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