AGXT p.Gln65=
c.195G>A · rs890310872 · VCV1115616
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0042%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.33 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 7 | GERP 1.3, phastCons 1 |
| Overall | ||
| CADD | 13.2 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0042%
African / African-American · 3/71,354 alleles
Filtering AF
0.00112%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00061%
Overall
0.000326%
5/1,532,026 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0042% | 23,785 |
| Remaining individualsnot grpmax-eligible | 0.00343% | 29,148 |
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.Gln65=
- Coding
- c.195G>A
- MANE Select
- NM_000030
- dbSNP
- rs890310872
- Type
- single nucleotide variant
- Location
- chr2:240869199 (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 65
- an α-helix
Similar variants
- AGXT p.Gln65Ter Pathogenic ★ same residue
- AGXT p.Gln65Arg Uncertain significance ★ ⚠ 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-gln65 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown