AMT

Chr 3

aminomethyltransferase

Also known as: GCE, GCE2, GCST, GCVT, NKH

NCBI Gene: 275ENSG00000145020UniProt: P48728

This gene encodes one of four critical components of the glycine cleavage system. Mutations in this gene have been associated with glycine encephalopathy. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]

GeneReviewsResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtGlycine encephalopathy 2

Clinical highlights

Gene-disease validity (ClinGen)
glycine encephalopathy · ARDefinitivesufficient evidence for diagnostic panels
Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype), though the gene is not strongly LoF-constrained in the population — weigh truncating variants against that tolerance.Curated gene-level mechanism — a prior for triage, not a per-variant call.
1
Active trials
344
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.79
LOEUF
LOF
Mechanism· G2P
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GeneReview available — AMT
Authoritative clinical overview · Recommended first read
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Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?
0.79LOEUF
pLI 0.003
Z-score 2.19
OE 0.42 (0.24–0.79)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?
-0.10Z-score
OE missense 1.02 (0.92–1.13)
244 obs / 239.6 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?
LoF OE?0.42 (0.24–0.79)
0≤0.351.4
Missense OE?1.02 (0.92–1.13)
0≤0.61.4
Synonymous OE?1.06
0≤1.21.6
LoF obs/exp: 7 / 16.7Missense obs/exp: 244 / 239.6Syn Z: -0.47

ClinVar Variant Classifications

0 submitted variants in ClinVar

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.

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients