DDX41 p.Pro213=
c.639C>T · VCV3838957
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.18 | GERP -4, phastCons 0.7 |
| Overall | ||
| CADD | 4.476 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,890 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000248%
4/1,613,862 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,890 |
| African / African-American | 0.00133% | 74,910 |
| European (non-Finnish) | 0.000169% | 590,012 |
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
- DDX41
- Protein
- p.Pro213=
- Coding
- c.639C>T
- MANE Select
- NM_016222
- Type
- single nucleotide variant
- Location
- chr5:177515191 (GRCh38)
- Gene constraint
- LOEUF 0.768 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 78.38 · 5 PDB
- Residue 213
- the helicase atp-binding domain; an α-helix
Similar variants
- DDX41 p.Pro213Ser Uncertain significance ★★ ⚠ same residue
- DDX41 p.Pro213Arg Uncertain significance ⚠ same residue
- DDX41 c.1303-2A>G Likely pathogenic ★★ same condition
- DDX41 c.27+1G>A Likely pathogenic ★★ same condition
- DDX41 c.434+1G>C Pathogenic/Likely pathogenic ★★ same condition
- DDX41 c.571+1G>A Likely pathogenic ★★ same condition
- DDX41 c.572-1G>A Pathogenic/Likely pathogenic ★★ same condition
- DDX41 p.Arg159Ter Pathogenic ★★ 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/ddx41-p-pro213 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown