AMT p.Ala53=
c.159G>C · rs201080782 · VCV1098135
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
glycine encephalopathy
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.022 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -6.8 | GERP -4.2 |
| Overall | ||
| CADD | 2.92 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- AMT
- Protein
- p.Ala53=
- Coding
- c.159G>C
- MANE Select
- NM_000481
- dbSNP
- rs201080782
- Type
- single nucleotide variant
- Location
- chr3:49422203 (GRCh38)
- Gene constraint
- LOEUF 0.805 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.66 · 2 PDB
Disease context
glycine encephalopathy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Glycine encephalopathy (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy, Neonatal
- Prevalence
- 1-9 / 1 000 000 (Europe)
Similar variants
- AMT p.Ala53Val Uncertain significance ★ ⚠ same residue
- AMT c.339+2T>C Likely pathogenic ★★ same condition
- AMT c.471+2T>C Pathogenic ★★ same condition
- AMT c.697-1G>A Likely pathogenic ★★ same condition
- AMT c.878-1G>A Pathogenic ★★ same condition
- AMT c.91-2A>G Likely pathogenic ★★ same condition
- AMT c.-58C>T Pathogenic/Likely pathogenic ★★ same condition
- AMT p.Arg222Cys Pathogenic ★★ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/amt-p-ala53 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown