DDO p.Arg28Gln
c.83G>A · rs138423862 · VCV3080791
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0613%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.02 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -3.1 | GERP -2.4 |
| Regional constraint | o/e 1.02 | unconstrained · MANE · 21 kb · p 0.67 · regional, not allelic |
| Overall | ||
| CADD | 4.402 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0613%
African / African-American · 46/75,026 alleles
Filtering AF
0.0471%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0422%
Overall
0.00657%
106/1,614,102 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0613% | 1,631 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,625 |
| European (non-Finnish) | 0.00466% | 21,455 |
| South Asian | 0.0011% | 91,078 |
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
- DDO
- Protein
- p.Arg28Gln
- Coding
- c.83G>A
- MANE Select
- NM_001372108
- dbSNP
- rs138423862
- Type
- single nucleotide variant
- Location
- chr6:110413380 (GRCh38)
- Gene constraint
- LOEUF 1.282 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.36 · 1 PDB
- Residue 28
- a β-strand
Similar variants
- DDO p.Gly10Arg Likely benign ★★ same type
- DDO c.-11G>A Uncertain significance ★ same type
- DDO c.-18T>G Uncertain significance ★ same type
- DDO c.-20G>C Uncertain significance ★ same type
- DDO c.-36G>C Uncertain significance ★ same type
- DDO c.-56G>C Uncertain significance ★ same type
- DDO c.-71G>A Uncertain significance ★ same type
- DDO p.Ala135Thr 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/ddo-p-arg28gln (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown