DDO p.Leu75Phe
c.223C>T · rs1399850662 · VCV3080793
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0022%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.528 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.2 | GERP -1, phastCons 1 |
| Regional constraint | o/e 1.02 | unconstrained · MANE · 21 kb · p 0.67 · regional, not allelic |
| Overall | ||
| CADD | 21.9 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0022%
South Asian · 2/91,082 alleles
Filtering AF
0.000365%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000137%
Overall
0.000137%
2/1,461,864 alleles · very rare
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.Leu75Phe
- Coding
- c.223C>T
- MANE Select
- NM_001372108
- dbSNP
- rs1399850662
- Type
- single nucleotide variant
- Location
- chr6:110408392 (GRCh38)
- Gene constraint
- LOEUF 1.282 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.36 · 1 PDB
- Residue 75
- an α-helix
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-leu75phe (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown