ClinVar Miner

Submissions for variant NM_001134407.3(GRIN2A):c.547T>A (p.Phe183Ile) (rs587780353)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory, University of Chicago RCV000117178 SCV000151342 likely benign not specified 2013-05-14 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000711852 SCV000842258 uncertain significance not provided 2017-09-18 criteria provided, single submitter clinical testing
Ambry Genetics RCV000716783 SCV000847626 uncertain significance History of neurodevelopmental disorder 2017-10-27 criteria provided, single submitter clinical testing The p.F183I variant (also known as c.547T>A), located in coding exon 2 of the GRIN2A gene, results from a T to A substitution at nucleotide position 547. The phenylalanine at codon 183 is replaced by isoleucine, an amino acid with highly similar properties. In one study, this variant was detected in an individual with benign epilepsy with centrotemporal spikes (rolandic epilepsy). The variant was not present in the patient's asymptomatic father (mother's variant status unknown) (Lemke JR et al. Nat. Genet., 2013 Sep;45:1067-72). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this variant remains unclear.
Invitae RCV000989528 SCV001011206 likely benign Epilepsy, focal, with speech disorder and with or without mental retardation 2020-05-22 criteria provided, single submitter clinical testing
Mendelics RCV000989528 SCV001139948 benign Epilepsy, focal, with speech disorder and with or without mental retardation 2019-05-28 criteria provided, single submitter clinical testing
GeneDx RCV000711852 SCV001815411 uncertain significance not provided 2020-06-17 criteria provided, single submitter clinical testing Reported previously in an individual with benign epilepsy with centrotemporal spikes (rolandic epilepsy) and mild developmental delay; however, the F183I variant was inherited from an unaffected parent and this individual also had a de novo variant in another gene that may have been responsible for the phenotype (Lemke et al., 2013; Reinthaler et al., 2015); Functional studies indicate that F183I minimally impacts basal receptor activation properties (Serraz et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 25921602, 29358611, 25904555, 26601054, 25726841, 23933819, 29124671, 27288002)
Bioinformatics Core,Luxembourg Center for Systems Biomedicine RCV000656052 SCV000588328 pathogenic Rolandic epilepsy 2017-01-01 no assertion criteria provided case-control CAADphred>15

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