ClinVar Miner

Submissions for variant NM_001134407.3(GRIN2A):c.4205G>C (p.Arg1402Pro)

dbSNP: rs74935155
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
CeGaT Center for Human Genetics Tuebingen RCV000762188 SCV000892457 uncertain significance not provided 2018-06-01 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001359825 SCV001555711 likely benign Landau-Kleffner syndrome 2024-10-30 criteria provided, single submitter clinical testing
Ambry Genetics RCV002332542 SCV002629995 uncertain significance Inborn genetic diseases 2018-01-04 criteria provided, single submitter clinical testing The p.R1402P variant (also known as c.4205G>C), located in coding exon 12 of the GRIN2A gene, results from a G to C substitution at nucleotide position 4205. The arginine at codon 1402 is replaced by proline, an amino acid with dissimilar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Pittsburgh Clinical Genomics Laboratory, University of Pittsburgh Medical Center RCV001359825 SCV005397660 uncertain significance Landau-Kleffner syndrome 2024-06-20 criteria provided, single submitter clinical testing This sequence variant is a single nucleotide substitution (G>C) at position 4205 of the coding sequence of the GRIN2A gene that results in an arginine to proline amino acid change at residue 1402 of the glutamate ionotropic receptor NMDA type subunit 2A protein. This is a previously reported variant (ClinVar 624081) that has not been observed in individuals affected by a GRIN2A-related disorder in the published literature, to our knowledge. This variant is present in 10 of 1613950 alleles (0.00062%) in the gnomAD v4.1.0 population dataset. Multiple bioinformatic tools predict that this amino acid change would be damaging, and the Arg1402 residue at this position is highly conserved across the vertebrate species examined. Studies examining the functional consequence of this variant have not been published, to our knowledge. At this time, there is insufficient evidence to determine if this variant is pathogenic or benign. Therefore, we consider this a variant of uncertain significance. ACMG Criteria: PM2, PP3

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