ClinVar Miner

Submissions for variant NM_000170.2(GLDC):c.2584G>A (p.Glu862Lys) (rs925908885)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000671933 SCV000796973 likely pathogenic Non-ketotic hyperglycinemia 2018-01-05 criteria provided, single submitter clinical testing
Invitae RCV000671933 SCV000829710 pathogenic Non-ketotic hyperglycinemia 2019-12-22 criteria provided, single submitter clinical testing This sequence change replaces glutamic acid with lysine at codon 862 of the GLDC protein (p.Glu862Lys). The glutamic acid residue is highly conserved and there is a small physicochemical difference between glutamic acid and lysine. This variant is not present in population databases (ExAC no frequency). This variant has been observed on the opposite chromosome (in trans) from a pathogenic variant in GLDC in an individual affected with glycine encephalopathy and in combination with another GLDC variant in several individuals affected with the same condition (PMID: 26179960, 27362913). ClinVar contains an entry for this variant (Variation ID: 555999). Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: Deleterious; PolyPhen-2: Probably Damaging; Align-GVGD: Class C0). For these reasons, this variant has been classified as Pathogenic.

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