AOX1 p.Pro702=
c.2106G>A · rs150316811 · VCV2651812
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0493%, mid)
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 -14 | GERP -4.3 |
| Overall | ||
| CADD | 0.352 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0493%
Middle Eastern · 3/6,080 alleles
Filtering AF
0.0134%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00905%
Overall
0.00539%
87/1,613,972 alleles · ultra-rare
exomes 77/1,461,788 · genomes 10/152,184 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0493% | 2,027 |
| African / African-American | 0.0187% | 5,351 |
| Remaining individualsnot grpmax-eligible | 0.0176% | 5,680 |
| Admixed American | 0.0117% | 8,571 |
| East Asian | 0.00668% | 14,964 |
| European (non-Finnish) | 0.00415% | 24,081 |
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
- AOX1
- Protein
- p.Pro702=
- Coding
- c.2106G>A
- MANE Select
- NM_001159
- dbSNP
- rs150316811
- Type
- single nucleotide variant
- Location
- chr2:200623965 (GRCh38)
- Gene constraint
- LOEUF 1.009 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.13 · 8 PDB
Similar variants
- AOX1 p.Pro702Leu Uncertain significance ★ ⚠ same residue
- AOX1 p.Ala1083Gly Benign ★★ same type
- AOX1 p.Arg130= Benign ★★ same type
- AOX1 p.Gln314Arg Benign ★★ same type
- AOX1 p.Gln737= Benign ★★ same type
- AOX1 p.Ile598Asn Benign ★★ same type
- AOX1 p.Leu553= Benign ★★ same type
- AOX1 p.Pro1245= 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/aox1-p-pro702 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown