AOX1 p.Val1040=
c.3120C>T · rs114924183 · VCV773128
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.707%, nfe)
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 1.3 | GERP 4.1, phastCons 1 |
| Overall | ||
| CADD | 8.378 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.707%
European (non-Finnish) · 8,232/1,164,682 alleles
Filtering AF
0.694%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.689%
Overall
0.564%
8,943/1,584,816 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.707% | 141 |
| Remaining individualsnot grpmax-eligible | 0.422% | 237 |
| Finnishnot grpmax-eligible | 0.367% | 272 |
| Amishnot grpmax-eligible | 0.219% | 456 |
| Admixed American | 0.154% | 648 |
| African / African-American | 0.105% | 949 |
| South Asian | 0.0577% | 1,734 |
| Middle Eastern | 0.0167% | 6,006 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00343% | 29,134 |
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.Val1040=
- Coding
- c.3120C>T
- MANE Select
- NM_001159
- dbSNP
- rs114924183
- Type
- single nucleotide variant
- Location
- chr2:200656886 (GRCh38)
- Gene constraint
- LOEUF 1.009 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.13 · 8 PDB
- Residue 1040
- a β-strand
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-val1040 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown