AGXT p.Phe152Ser
c.455T>C · rs765812098 · VCV1356728
Computational evidence
| Protein change | ||
| AlphaMissense | 0.8999 | likely pathogenic · top 6% in AGXT |
|---|---|---|
| REVEL | 0.818 | moderately pathogenic-leaning |
| SaProt | LLR -7.13 | tolerated |
| ⇒ AlphaMissense and REVEL call this damaging; SaProt does not. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 4.8 | GERP 1, phastCons 1 |
| Regional constraint | o/e 1.00 | unconstrained · MANE · 9,952 bp · p 0.92 · regional, not allelic |
| Overall | ||
| CADD | 27.2 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Finnishnot grpmax-eligible | 0.00322% | 31,042 |
| European (non-Finnish)grpmax | 0.000341% | 293,191 |
Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- AGXT
- Protein
- p.Phe152Ser
- Coding
- c.455T>C
- MANE Select
- NM_000030
- dbSNP
- rs765812098
- Type
- single nucleotide variant
- Location
- chr2:240871380 (GRCh38)
- Gene constraint
- LOEUF 1.251 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 98.30 · 17 PDB
- Residue 152
- a UniProt-annotated variant site (in hp1; associated in cis with l-11 and m-340; results in protein destabilization; no loss of dimerization; decreased alanine--glyoxylate aminotransferase activity; loss of alanine--glyoxylate aminotransferase activity when associated with l-11 and m-340; mitochondrial mistargeting when associated with l-11 and m-340); a β-strand
Similar variants
- AGXT p.Phe152Ile Pathogenic ★★ same residue
- AGXT p.Phe152Cys Likely pathogenic ★ same residue
- AGXT c.358+1G>A Pathogenic ★★ same type
- AGXT c.359-2A>G Likely pathogenic ★★ same type
- AGXT c.423+1G>A Pathogenic/Likely pathogenic ★★ same type
- AGXT c.524+2T>A Likely pathogenic ★★ same type
- AGXT c.525-1G>A Pathogenic ★★ same type
- AGXT c.525-2A>T Pathogenic/Likely pathogenic ★★ same type
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/agxt-p-phe152ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown