AMT
Chr 3aminomethyltransferase
Also known as: GCE, GCE2, GCST, GCVT, NKH
The protein is one of four essential components of the glycine cleavage system that catalyzes the degradation of glycine. Mutations cause glycine encephalopathy, a severe neurometabolic disorder that typically presents in the neonatal period with hypotonia, seizures, and developmental delay. Inheritance is autosomal recessive.
Definitive — sufficient evidence for diagnostic panels
Some data sources returned errors (1)
omim: Error: OMIM fetch failed: 429
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Typical tolerance to LoF variation
Tolerant to missense variation
Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.
The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.
ClinVar Variant Classifications
200 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 11 | 1 | 4 | 0 | 16 |
Likely Pathogenic | 17 | 3 | 2 | 0 | 22 |
VUS | 0 | 35 | 5 | 1 | 41 |
Likely Benign | 0 | 1 | 69 | 40 | 110 |
Benign | 0 | 0 | 1 | 0 | 1 |
Conflicting | — | 3 | |||
| Total | 28 | 40 | 81 | 41 | 193 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
AMT · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
3D Protein StructureAlphaFold
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
External Resources
Links to major genomics databases and tools