AOC3 p.Asp673=
c.2019T>C · VCV4641381
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.044%, afr)
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 -0.13 | GERP -2.6, phastCons 0.008 |
| Overall | ||
| CADD | 12.08 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.044%
African / African-American · 33/75,010 alleles
Filtering AF
0.0321%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0281%
Overall
0.00782%
126/1,612,014 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.044% | 2,273 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0203% | 4,915 |
| East Asian | 0.0111% | 8,976 |
| Remaining individualsnot grpmax-eligible | 0.00641% | 15,612 |
| European (non-Finnish) | 0.0062% | 16,141 |
| Admixed American | 0.005% | 19,997 |
| South Asian | 0.0022% | 45,527 |
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
- AOC3
- Protein
- p.Asp673=
- Coding
- c.2019T>C
- MANE Select
- NM_003734
- Type
- single nucleotide variant
- Location
- chr17:42856277 (GRCh38)
- Gene constraint
- LOEUF 1.056 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.15 · 11 PDB
- Residue 673
- a β-strand; a binding site
Similar variants
- AOC3 p.Asp673Gly Uncertain significance ★ ⚠ same residue
- AOC3 p.Arg73Cys Uncertain significance ★★ ⚠ same type
- AOC3 p.Ala582Thr Benign ★★ same type
- AOC3 p.Arg329Gln Benign/Likely benign ★★ same type
- AOC3 p.Arg441Trp Benign ★★ ⚠ same type
- AOC3 p.Arg566Gln Likely benign ★★ same type
- AOC3 p.Ile371Thr Benign ★★ same type
- AOC3 p.Tyr271= 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/aoc3-p-asp673 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown