ClinVar Miner

Submissions for variant NM_000836.4(GRIN2D):c.3697C>G (p.Pro1233Ala)

gnomAD frequency: 0.00026  dbSNP: rs891894351
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV002144337 SCV002468354 likely benign not provided 2024-12-22 criteria provided, single submitter clinical testing
Ambry Genetics RCV003081047 SCV003722045 uncertain significance Inborn genetic diseases 2022-12-15 criteria provided, single submitter clinical testing The c.3697C>G (p.P1233A) alteration is located in exon 13 (coding exon 12) of the GRIN2D gene. This alteration results from a C to G substitution at nucleotide position 3697, causing the proline (P) at amino acid position 1233 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV005406383 SCV006071086 likely benign not specified 2025-03-17 criteria provided, single submitter clinical testing Variant summary: GRIN2D c.3697C>G (p.Pro1233Ala) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 3.8e-05 in 1076760 control chromosomes, predominantly at a frequency of 0.0022 within the Latino subpopulation in the gnomAD database. The observed variant frequency within Latino control individuals in the gnomAD database exceeds the estimated maximal expected allele frequency for a pathogenic variant in GRIN2D causing Epileptic Encephalopathy, Early Infantile, 46 phenotype. To our knowledge, no occurrence of c.3697C>G in individuals affected with Epileptic Encephalopathy, Early Infantile, 46 and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 1649814). Based on the evidence outlined above, the variant was classified as likely benign.

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