DDX41 p.Val34=
c.102G>A · VCV3500499
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0022%, sas)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.7 | GERP -4 |
| Overall | ||
| CADD | 3.688 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0022%
South Asian · 2/90,806 alleles
Filtering AF
0.000366%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000211%
Overall
0.000621%
10/1,611,422 alleles · very rare
exomes 10/1,459,086 · genomes 0/152,336 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0022% | 45,403 |
| European (non-Finnish) | 0.000678% | 147,409 |
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.Val34=
- Coding
- c.102G>A
- MANE Select
- NM_016222
- Type
- single nucleotide variant
- Location
- chr5:177516761 (GRCh38)
- Gene constraint
- LOEUF 0.768 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 78.38 · 5 PDB
- Residue 34
- the 'disordered' region
Similar variants
- DDX41 p.Val34Met Uncertain significance ★ ⚠ same residue
- DDX41 p.Val34fs Likely pathogenic ★ 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-val34 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown