ATG2A p.Pro291=
c.873G>C · rs77225736 · VCV785813
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.55%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| REVEL | 0.003 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | Δ0.64 | acceptor gain · deltas |
| Pangolin | Δ0.23 | gain · loss 0.09 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -5.6 | GERP -3.1 |
| Overall | ||
| CADD | 12.17 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.55%
African / African-American · 2,608/73,506 alleles
Filtering AF
3.43%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.39%
Overall
0.202%
3,165/1,564,252 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.55% | 28 |
| Admixed American | 0.283% | 353 |
| Remaining individualsnot grpmax-eligible | 0.256% | 391 |
| Middle Eastern | 0.0934% | 1,070 |
| European (non-Finnish) | 0.0208% | 4,811 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0174% | 5,756 |
| South Asian | 0.00349% | 28,671 |
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
- ATG2A
- Protein
- p.Pro291=
- Coding
- c.873G>C
- MANE Select
- NM_015104
- dbSNP
- rs77225736
- Type
- single nucleotide variant
- Location
- chr11:64912376 (GRCh38)
- Gene constraint
- LOEUF 0.614 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.38 · 7 PDB
- Residue 291
- a turn
Similar variants
- ATG2A p.Ala857Val Benign ★★ same type
- ATG2A p.Val1825Ile Benign ★★ same type
- ATG2A p.Val664Met Benign ★★ same type
- ATG2A p.Ala1033Gly Uncertain significance ★ ⚠ same type
- ATG2A p.Ala1162Val Uncertain significance ★ same type
- ATG2A p.Ala1367Val Uncertain significance ★ ⚠ same type
- ATG2A p.Ala1505Glu Uncertain significance ★ ⚠ same type
- ATG2A p.Ala1904Thr 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/atg2a-p-pro291 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown