AGO1 p.Arg504=
c.1512G>T · rs764770945 · VCV739538
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0667%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 5 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 11.39 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0667%
Admixed American · 40/60,012 alleles
Filtering AF
0.0502%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0446%
Overall
0.00254%
41/1,614,046 alleles · ultra-rare
exomes 38/1,461,858 · genomes 3/152,188 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0667% | 1,500 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,508 |
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
- AGO1
- Protein
- p.Arg504=
- Coding
- c.1512G>T
- MANE Select
- NM_012199
- dbSNP
- rs764770945
- Type
- single nucleotide variant
- Location
- chr1:35907049 (GRCh38)
- Gene constraint
- LOEUF 0.164 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 91.45 · 8 PDB
- Residue 504
- an α-helix
Similar variants
- AGO1 p.Asp356Asn Likely pathogenic ★★ same type
- AGO1 p.Gly199Ser Pathogenic/Likely pathogenic ★★ same type
- AGO1 p.Pro189Leu Likely pathogenic ★★ same type
- AGO1 p.Ala103Val Uncertain significance ★★ ⚠ same type
- AGO1 p.Ala413Val Uncertain significance ★★ ⚠ same type
- AGO1 p.Ala479Val Uncertain significance ★★ ⚠ same type
- AGO1 p.Arg26Gln Uncertain significance ★★ ⚠ same type
- AGO1 p.Arg284His 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/ago1-p-arg504 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown