DDX11 p.Lys897del
c.2689_2691del · rs730880280 · VCV8370
Pathogenic
No assertion criteria
Classification
Pathogenic
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00203%, nfe)
Conditions
1
Warsaw breakage syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.43 | GERP -1.9, phastCons 0.009 |
| Region caveats | ||
| Repeat context | seg dup | · reads may not map uniquely · confidence, not pathogenicity |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00203%
European (non-Finnish) · 24/1,179,928 alleles
Filtering AF
0.00138%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00116%
Overall
0.00171%
25/1,461,426 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00203% | 49,164 |
| Admixed American | 0.00167% | 60,022 |
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.Lys897del
- Coding
- c.2689_2691del
- MANE Select
- NM_030653
- dbSNP
- rs730880280
- Type
- Deletion
- Location
- chr12:31103727 (GRCh38)
- Gene constraint
- LOEUF 0.781 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.77
Similar variants
- DDX11 c.394-2_394-1del Likely pathogenic ★ same condition
- DDX11 p.Arg630fs Likely pathogenic ★ same condition
- DDX11 p.Asn464fs Likely pathogenic ★ same condition
- DDX11 p.Asp816fs Likely pathogenic ★ same condition
- DDX11 p.Gly261fs Likely pathogenic ★ same condition
- DDX11 p.Lys303fs Likely pathogenic ★ same condition
- DDX11 c.481-2del Conflicting classifications of pathogenicity ★ same condition
- DDX11 p.Ala769fs Conflicting classifications of pathogenicity ★ same condition
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-lys897del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown