AOX1 p.Arg483=
c.1449G>A · rs141842645 · VCV737210
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.481%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.57 · evaluated, not missing |
|---|---|---|
| Pangolin | Δ0.20 | loss · gain 0.00 · SpliceAI below 0.2 · independent |
| Constraint at this position | ||
| Conservation | phyloP 1.2 | GERP 0.024, phastCons 0.66 |
| Overall | ||
| CADD | 6.531 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.481%
African / African-American · 360/74,868 alleles
Filtering AF
0.44%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.424%
Overall
0.0273%
440/1,610,874 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.481% | 208 |
| Remaining individualsnot grpmax-eligible | 0.0674% | 1,483 |
| Admixed American | 0.0586% | 1,707 |
| South Asian | 0.0011% | 90,682 |
| European (non-Finnish) | 0.00017% | 589,550 |
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.Arg483=
- Coding
- c.1449G>A
- MANE Select
- NM_001159
- dbSNP
- rs141842645
- Type
- single nucleotide variant
- Location
- chr2:200613804 (GRCh38)
- Gene constraint
- LOEUF 1.009 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.13 · 8 PDB
Similar variants
- 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
- AOX1 p.Pro702= 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/aox1-p-arg483 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown