ClinVar Miner

Submissions for variant NM_000170.3(GLDC):c.1183T>C (p.Phe395Leu)

dbSNP: rs767200188
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000670162 SCV000794987 uncertain significance Non-ketotic hyperglycinemia 2017-10-24 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000670162 SCV004295999 pathogenic Non-ketotic hyperglycinemia 2023-11-10 criteria provided, single submitter clinical testing This sequence change replaces phenylalanine, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 395 of the GLDC protein (p.Phe395Leu). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with non-ketotic hyperglycinemia (PMID: 27362913). 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: 554514). 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 not expected to disrupt GLDC protein function with a negative predictive value of 80%. For these reasons, this variant has been classified as Pathogenic.

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