ClinVar Miner

Submissions for variant NM_152783.5(D2HGDH):c.515G>A (p.Cys172Tyr)

gnomAD frequency: 0.00001  dbSNP: rs773735172
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001063278 SCV001228116 uncertain significance D-2-hydroxyglutaric aciduria 1 2024-06-04 criteria provided, single submitter clinical testing This sequence change replaces cysteine, which is neutral and slightly polar, with tyrosine, which is neutral and polar, at codon 172 of the D2HGDH protein (p.Cys172Tyr). This variant is present in population databases (rs773735172, gnomAD 0.005%). This missense change has been observed in individual(s) with D-2-hydroxyglutaric aciduria (PMID: 20020533). ClinVar contains an entry for this variant (Variation ID: 857572). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt D2HGDH protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects D2HGDH function (PMID: 30908763, 33431826). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
GeneDx RCV005253702 SCV005906389 likely pathogenic not provided 2024-10-06 criteria provided, single submitter clinical testing Published functional studies demonstrate a damaging effect on D-2-hydroxyglutarate dehydrogenase enzyme activity (PMID: 30908763); 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: 20020533, 30908763)

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