DDX41 p.Thr431=
c.1293A>C · rs746693911 · VCV210842
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.387%, 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 -7.8 | GERP -4.2 |
| Overall | ||
| CADD | 0.416 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.387%
East Asian · 169/43,638 alleles
Filtering AF
0.34%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.321%
Overall
0.122%
1,943/1,587,410 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.387% | 258 |
| Finnishnot grpmax-eligible | 0.384% | 261 |
| Middle Eastern | 0.289% | 346 |
| Admixed American | 0.251% | 398 |
| Ashkenazi Jewishnot grpmax-eligible | 0.139% | 721 |
| South Asian | 0.137% | 732 |
| Remaining individualsnot grpmax-eligible | 0.135% | 742 |
| European (non-Finnish) | 0.0935% | 1,070 |
| African / African-American | 0.066% | 1,515 |
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.Thr431=
- Coding
- c.1293A>C
- MANE Select
- NM_016222
- dbSNP
- rs746693911
- Type
- single nucleotide variant
- Location
- chr5:177513020 (GRCh38)
- Gene constraint
- LOEUF 0.768 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 78.38 · 5 PDB
- Residue 431
- the helicase c-terminal domain
Similar variants
- DDX41 p.Thr431Ile 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
- DDX41 p.Arg369Ter Pathogenic/Likely 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-thr431 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown