AGO2 p.Thr657=
c.1971G>A · rs745418916 · VCV2658861
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0273%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -14 | GERP -3.8 |
| Overall | ||
| CADD | 6.747 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0273%
Admixed American · 16/58,580 alleles
Filtering AF
0.0171%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0139%
Overall
0.00342%
55/1,607,556 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0273% | 3,661 |
| African / African-American | 0.00668% | 14,974 |
| South Asian | 0.00556% | 17,995 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,133 |
| European (non-Finnish) | 0.00229% | 43,605 |
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
- AGO2
- Protein
- p.Thr657=
- Coding
- c.1971G>A
- MANE Select
- NM_012154
- dbSNP
- rs745418916
- Type
- single nucleotide variant
- Location
- chr8:140541227 (GRCh38)
- Gene constraint
- LOEUF 0.102 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 92.82 · 71 PDB
- Residue 657
- an α-helix; the piwi domain; the 'interaction with gw182 family members' region
Similar variants
- AGO2 p.Arg714Trp Pathogenic/Likely pathogenic ★★ same type
- AGO2 p.Cys751Tyr Pathogenic/Likely pathogenic ★★ same type
- AGO2 p.Gly201Val Pathogenic/Likely pathogenic ★★ same type
- AGO2 p.Gly604Arg Pathogenic/Likely pathogenic ★★ same type
- AGO2 p.Thr357Met Pathogenic/Likely pathogenic ★★ same type
- AGO2 p.Ala142Thr Uncertain significance ★★ ⚠ same type
- AGO2 p.Ala372Val Uncertain significance ★★ ⚠ same type
- AGO2 p.Arg630His Uncertain significance ★★ ⚠ 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/ago2-p-thr657 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown