AGTPBP1 p.Arg309=
c.927G>A · rs201333759 · VCV3043439
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.284%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.074 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 2.2 | GERP 1.3, phastCons 1 |
| Overall | ||
| CADD | 11.28 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.284%
European (non-Finnish) · 3,255/1,145,088 alleles
Filtering AF
0.276%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.273%
Overall
0.232%
3,584/1,544,416 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.284% | 352 |
| Remaining individualsnot grpmax-eligible | 0.247% | 404 |
| Admixed American | 0.216% | 463 |
| Middle Eastern | 0.203% | 493 |
| African / African-American | 0.0456% | 2,193 |
| Finnishnot grpmax-eligible | 0.0397% | 2,519 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0106% | 9,403 |
| South Asian | 0.00366% | 27,335 |
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
- AGTPBP1
- Protein
- p.Arg309=
- Coding
- c.927G>A
- MANE Select
- NM_001330701
- dbSNP
- rs201333759
- Type
- single nucleotide variant
- Location
- chr9:85655303 (GRCh38)
- Gene constraint
- LOEUF 0.556 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.95
Similar variants
- AGTPBP1 c.-206G>A Uncertain significance ★★ same type
- AGTPBP1 p.Ala461Gly Uncertain significance ★★ ⚠ same type
- AGTPBP1 p.Arg1136His Uncertain significance ★★ ⚠ same type
- AGTPBP1 p.Arg174His Uncertain significance ★★ ⚠ same type
- AGTPBP1 p.Cys1069Phe Uncertain significance ★★ ⚠ same type
- AGTPBP1 p.Glu1176Gly Uncertain significance ★★ ⚠ same type
- AGTPBP1 c.-87T>C Benign/Likely benign ★★ same type
- AGTPBP1 p.Lys822= Likely benign ★★ 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/agtpbp1-p-arg309 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown