DDO p.Arg5Trp
c.13C>T · rs148048525 · VCV2388725
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0182%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.131 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.8 | GERP 1, phastCons 0.007 |
| Regional constraint | o/e 1.02 | unconstrained · MANE · 21 kb · p 0.67 · regional, not allelic |
| Overall | ||
| CADD | 23.2 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0182%
European (non-Finnish) · 215/1,180,016 alleles
Filtering AF
0.0162%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0154%
Overall
0.0148%
238/1,613,434 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0182% | 5,488 |
| Finnishnot grpmax-eligible | 0.0141% | 7,114 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,918 |
| South Asian | 0.00439% | 22,763 |
| African / African-American | 0.00267% | 37,443 |
| East Asian | 0.00223% | 44,898 |
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.Arg5Trp
- Coding
- c.13C>T
- MANE Select
- NM_001372108
- dbSNP
- rs148048525
- Type
- single nucleotide variant
- Location
- chr6:110413450 (GRCh38)
- Gene constraint
- LOEUF 1.282 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.36 · 1 PDB
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-arg5trp (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown