AOX1 p.Cys670=
c.2010T>C · rs562776296 · VCV740742
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.189%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.9 | GERP -4.6 |
| Overall | ||
| CADD | 5.253 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.189%
South Asian · 172/91,072 alleles
Filtering AF
0.166%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.157%
Overall
0.0119%
192/1,613,934 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.189% | 529 |
| Middle Eastern | 0.0338% | 2,962 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,248 |
| European (non-Finnish) | 0.000678% | 147,494 |
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.Cys670=
- Coding
- c.2010T>C
- MANE Select
- NM_001159
- dbSNP
- rs562776296
- Type
- single nucleotide variant
- Location
- chr2:200623869 (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-cys670 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown