ClinVar Miner

Submissions for variant NM_000481.4(AMT):c.230C>T (p.Ser77Leu) (rs386833680)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000049641 SCV000789963 likely pathogenic Non-ketotic hyperglycinemia 2017-03-01 criteria provided, single submitter clinical testing
Invitae RCV000049641 SCV000949256 pathogenic Non-ketotic hyperglycinemia 2019-11-01 criteria provided, single submitter clinical testing This sequence change replaces serine with leucine at codon 77 of the AMT protein (p.Ser77Leu). The serine residue is moderately conserved and there is a large physicochemical difference between serine and leucine. This variant is present in population databases (rs386833680, ExAC 0.003%). This variant has been observed in individuals with glycine encephalopathy (PMID: 16450403, 26179960, 27362913, Invitae). In at least one individual the data is consistent with the variant being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 56229). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or 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.
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) RCV000049641 SCV000082048 probable-pathogenic Non-ketotic hyperglycinemia no assertion criteria provided not provided Converted during submission to Likely pathogenic.

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