DAO p.Ile11=
c.33C>T · rs146543709 · VCV730134
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.036%, 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 -20 | GERP -4.6 |
| Overall | ||
| CADD | 0.611 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.036%
African / African-American · 27/75,018 alleles
Filtering AF
0.0254%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0219%
Overall
0.0122%
197/1,614,122 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.036% | 2,778 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,945 |
| European (non-Finnish) | 0.0131% | 7,613 |
| Admixed American | 0.005% | 20,004 |
| South Asian | 0.00329% | 30,361 |
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
- DAO
- Protein
- p.Ile11=
- Coding
- c.33C>T
- MANE Select
- NM_001917
- dbSNP
- rs146543709
- Type
- single nucleotide variant
- Location
- chr12:108885039 (GRCh38)
- Gene constraint
- LOEUF 1.222 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.26 · 22 PDB
- Residue 11
- the 'required for protein stability' region; an α-helix; a binding site
Similar variants
- DAO p.Ile318Ser Uncertain significance ★★ ⚠ same type
- DAO c.195-99C>T Benign ★★ same type
- DAO c.387-258A>G Benign ★★ same type
- DAO c.453-182G>C Benign ★★ same type
- DAO c.507+98G>A Benign ★★ same type
- DAO c.508-55A>G Benign ★★ same type
- DAO c.696-25C>T Benign ★★ same type
- DAO c.912+166C>T 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/dao-p-ile11 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown