DDX41 p.Lys115=
c.345G>A · rs1761221426 · VCV1937437
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00833%, amr)
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 2.2 | GERP -1.5, phastCons 1 |
| Overall | ||
| CADD | 12.08 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00833%
Admixed American · 5/60,012 alleles
Filtering AF
0.00323%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00207%
Overall
0.00031%
5/1,613,946 alleles · very rare
exomes 2/1,461,714 · genomes 3/152,232 · joint denominator
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.Lys115=
- Coding
- c.345G>A
- MANE Select
- NM_016222
- dbSNP
- rs1761221426
- Type
- single nucleotide variant
- Location
- chr5:177516147 (GRCh38)
- Gene constraint
- LOEUF 0.768 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 78.38 · 5 PDB
- Residue 115
- a cross-link site
Similar variants
- DDX41 p.Lys115Arg Likely benign ★ same residue
- DDX41 c.1098+2T>G Likely pathogenic ★★ same type
- DDX41 c.1303-2A>G Likely pathogenic ★★ same type
- DDX41 c.27+1G>A Likely pathogenic ★★ same type
- DDX41 c.434+1G>A Pathogenic/Likely pathogenic ★★ same type
- DDX41 c.434+1G>C Pathogenic/Likely pathogenic ★★ same type
- DDX41 c.571+1G>A Likely pathogenic ★★ same type
- DDX41 c.572-1G>A 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/ddx41-p-lys115 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown