ClinVar Miner

Submissions for variant NM_024884.3(L2HGDH):c.829C>T (p.Arg277Ter)

gnomAD frequency: 0.00001  dbSNP: rs752025180
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001070930 SCV001236210 pathogenic L-2-hydroxyglutaric aciduria 2022-01-14 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 863865). This premature translational stop signal has been observed in individual(s) with L-2-hydroxyglutaric aciduria (PMID: 20052767). This variant is present in population databases (rs752025180, gnomAD 0.002%). This sequence change creates a premature translational stop signal (p.Arg277*) in the L2HGDH gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in L2HGDH are known to be pathogenic (PMID: 16134148, 20052767).
GeneDx RCV002269335 SCV002552717 pathogenic not provided 2022-07-21 criteria provided, single submitter clinical testing Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 25525159, 20052767)
Neuberg Supratech Reference Laboratories Pvt Ltd, Neuberg Centre for Genomic Medicine RCV001070930 SCV004047655 pathogenic L-2-hydroxyglutaric aciduria criteria provided, single submitter clinical testing The stop gained variant c.829C>T (p.Arg277Ter) in L2HGDH gene has been observed in an individual affected with L-2-hydroxyglutaric aciduria (Steenweg ME et.al.,2010).This variant has been reported to the ClinVar database as Pathogenic. The c.829C>T variant is novel (not in any individuals) in 1000 Genomes and allele frequency of 0.0007955% is reported in gnomAD. The nucleotide change c.829C>T in L2HGDH is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. This variant is predicted to cause loss of normal protein function. Loss of function variants have been previously reported to be disease causing. For these reasons, this variant has been classified as Pathogenic.

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