ClinVar Miner

Submissions for variant NM_152783.5(D2HGDH):c.1183C>T (p.Arg395Trp)

gnomAD frequency: 0.00073  dbSNP: rs149628174
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services,Illumina RCV001082053 SCV000429408 benign D-2-hydroxyglutaric aciduria 1 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
GeneDx RCV000498804 SCV000590384 uncertain significance not provided 2017-06-06 criteria provided, single submitter clinical testing The R395W variant in the D2HGDH gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The R395W variant is observed in 108/8608 (1.25%) alleles from individuals of East Asian background, in the ExAC dataset (Lek et al., 2016). The R395W variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is not conserved. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. We interpret R395W as a variant of uncertain significance.
Invitae RCV001082053 SCV001030469 benign D-2-hydroxyglutaric aciduria 1 2021-12-01 criteria provided, single submitter clinical testing

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