DDX11 p.Phe13=
c.39T>C · rs150002506 · VCV741411
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.206%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · T>A here scores Δ0.29 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.19 | GERP -0.6, phastCons 0.97 |
| Overall | ||
| CADD | 10.37 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.206%
African / African-American · 154/74,912 alleles
Filtering AF
0.179%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.169%
Overall
0.0103%
166/1,610,316 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.206% | 486 |
| Admixed American | 0.01% | 9,991 |
| Remaining individualsnot grpmax-eligible | 0.00482% | 20,765 |
| European (non-Finnish) | 0.000255% | 392,747 |
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
- DDX11
- Protein
- p.Phe13=
- Coding
- c.39T>C
- MANE Select
- NM_030653
- dbSNP
- rs150002506
- Type
- single nucleotide variant
- Location
- chr12:31078432 (GRCh38)
- Gene constraint
- LOEUF 0.781 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.77
- Residue 13
- the helicase atp-binding domain
Similar variants
- DDX11 c.1763-1G>C Pathogenic ★★ same type
- DDX11 c.1949-1G>A Pathogenic/Likely pathogenic ★★ same type
- DDX11 c.792+1G>A Likely pathogenic ★★ same type
- DDX11 p.Arg140Ter Likely pathogenic ★★ same type
- DDX11 p.Arg263Gln Pathogenic/Likely pathogenic ★★ same type
- DDX11 p.Arg558Ter Pathogenic/Likely pathogenic ★★ same type
- DDX11 p.Arg75Ter Pathogenic/Likely pathogenic ★★ same type
- DDX11 p.Cys649Ter Pathogenic/Likely pathogenic ★★ 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/ddx11-p-phe13 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown