ACOX3 p.Arg149=
c.447G>A · rs753519828 · VCV740183
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0538%, 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 -0.88 | GERP -3.5 |
| Overall | ||
| CADD | 0.514 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0538%
South Asian · 49/91,078 alleles
Filtering AF
0.0418%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0375%
Overall
0.0039%
63/1,614,022 alleles · ultra-rare
exomes 62/1,461,786 · genomes 1/152,236 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0538% | 1,859 |
| Middle Eastern | 0.0164% | 6,084 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,827 |
| East Asian | 0.00445% | 22,453 |
| European (non-Finnish) | 0.000678% | 147,497 |
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
- ACOX3
- Protein
- p.Arg149=
- Coding
- c.447G>A
- MANE Select
- NM_003501
- dbSNP
- rs753519828
- Type
- single nucleotide variant
- Location
- chr4:8414860 (GRCh38)
- Gene constraint
- LOEUF 1.114 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.43
Similar variants
- ACOX3 p.Arg149Gly Benign ★ same residue
- ACOX3 p.Ala28= Benign ★★ same type
- ACOX3 p.Arg75= Likely benign ★★ same type
- ACOX3 p.Ala157Ser Uncertain significance ★ ⚠ same type
- ACOX3 p.Ala207Thr Uncertain significance ★ ⚠ same type
- ACOX3 p.Ala261Ser Uncertain significance ★ ⚠ same type
- ACOX3 p.Ala261Thr Uncertain significance ★ ⚠ same type
- ACOX3 p.Ala2Thr 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/acox3-p-arg149 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown