ClinVar Miner

Submissions for variant NM_001182.5(ALDH7A1):c.1547A>G (p.Tyr516Cys)

gnomAD frequency: 0.00001  dbSNP: rs200102503
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000802615 SCV000942454 pathogenic Pyridoxine-dependent epilepsy 2024-02-15 criteria provided, single submitter clinical testing This sequence change replaces tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 516 of the ALDH7A1 protein (p.Tyr516Cys). This variant is present in population databases (rs200102503, gnomAD 0.1%). This missense change has been observed in individual(s) with pyridoxine-dependent epilepsy (PMID: 29852413, 31737911, 31965297). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 647989). 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 ALDH7A1 protein function with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic.
Revvity Omics, Revvity RCV000802615 SCV002024329 pathogenic Pyridoxine-dependent epilepsy 2021-04-28 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000802615 SCV004050017 pathogenic Pyridoxine-dependent epilepsy 2023-04-11 criteria provided, single submitter clinical testing
Juno Genomics, Hangzhou Juno Genomics, Inc RCV000802615 SCV005415861 pathogenic Pyridoxine-dependent epilepsy criteria provided, single submitter clinical testing PM2_Supporting+PP3_Strong+PM3_VeryStrong+PP4
Center of Excellence for Medical Genomics, Chulalongkorn University RCV000802615 SCV002570075 likely pathogenic Pyridoxine-dependent epilepsy 2002-09-08 no assertion criteria provided research

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