ClinVar Miner

Submissions for variant NM_000836.4(GRIN2D):c.3127C>T (p.Pro1043Ser)

gnomAD frequency: 0.00001  dbSNP: rs1326711404
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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
New York Genome Center RCV004799563 SCV001468759 uncertain significance Developmental and epileptic encephalopathy, 46 2019-09-13 criteria provided, single submitter clinical testing The c.3127C>T(p.Pro1043Ser) variant identified in the GRIN2D gene substitutes a well conserved Proline for Serine at amino acid 1043/1337 (coding exon 13/13). This variant is absent from gnomAD and ExAC, suggesting it is not a common benign variant in the populations represented in these databases. In silico algorithms do not agree on the effect of this variant, as it is predicted both Neutral (Provean; score: 0.15) and Damaging (SIFT; score: 0.044) to the function of the canonical transcript. This variant is absent from ClinVar and to our current knowledge has not been reported in any affected individuals in the literature. The Pro1043 residue is located within the carboxyl-terminal domain of the protein, where other pathogenic variants have been described [PMID: 31504254]. Given the lack of compelling evidence for the pathogenicity of the c.3127C>T (p.Pro1043Ser) variant identified in the GRIN2D gene, it is reported here as a Variant of Uncertain Significance.

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