ClinVar Miner

Submissions for variant NM_001134407.3(GRIN2A):c.2346_2356+8del (rs1064795143)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000487147 SCV000570653 likely pathogenic not provided 2016-10-11 criteria provided, single submitter clinical testing A novel c.2346_2356+8del19 variant that is likely pathogenic has been identified in the GRIN2A gene. The c.2346_2356+8del19 variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. It was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. This variant results in the deletion of 19 nucleotides at the exon 12/intron 12 boundary including the splice acceptor site and is predicted to cause abnormal gene splicing. However, in the absence of RNA/functional studies, the actual effect of this sequence change in this individual is unknown. Therefore, this variant is likely pathogenic; however, the possibility that it is benign cannot be excluded.
Invitae RCV000688647 SCV000816269 pathogenic Epilepsy, focal, with speech disorder and with or without mental retardation 2018-02-22 criteria provided, single submitter clinical testing This variant is a gross deletion of the genomic region encompassing part of exon 12 of the GRIN2A gene, including the exon 12-intron 12 boundary (c.2346_2356+8del). This is expected to create a premature translational stop signal and result in an absent or disrupted protein product. This variant has not been reported in the literature in individuals with GRIN2A-related disease. Loss-of-function variants in GRIN2A are known to be pathogenic (PMID: 23933819, 23933820). For these reasons, this variant has been classified as Pathogenic.

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