DDX59 p.Phe443=
c.1329T>C · rs115960805 · VCV749322
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.158%, afr)
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 -0.6 | GERP -4.8 |
| Overall | ||
| CADD | 2.439 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.158%
African / African-American · 114/72,052 alleles
Filtering AF
0.135%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.126%
Overall
0.0134%
211/1,569,558 alleles · rare
exomes 126/1,417,224 · genomes 85/152,334 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.158% | 632 |
| Admixed American | 0.0594% | 1,684 |
| Middle Eastern | 0.0503% | 1,987 |
| Remaining individualsnot grpmax-eligible | 0.0313% | 3,196 |
| South Asian | 0.0259% | 3,862 |
| European (non-Finnish) | 0.00223% | 44,873 |
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
- DDX59
- Protein
- p.Phe443=
- Coding
- c.1329T>C
- MANE Select
- NM_001031725
- dbSNP
- rs115960805
- Type
- single nucleotide variant
- Location
- chr1:200649212 (GRCh38)
- Gene constraint
- LOEUF 0.864 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.71 · 1 PDB
- Residue 443
- the helicase c-terminal domain
Similar variants
- DDX59 p.Val367Gly Pathogenic/Likely pathogenic ★★ same type
- DDX59 p.Arg318His Uncertain significance ★★ ⚠ same type
- DDX59 p.Glu179Gly Uncertain significance ★★ ⚠ same type
- DDX59 p.Glu30Lys Uncertain significance ★★ ⚠ same type
- DDX59 p.His171Tyr Uncertain significance ★★ ⚠ same type
- DDX59 p.His400Gln Uncertain significance ★★ ⚠ same type
- DDX59 p.Ile609Asn Uncertain significance ★★ ⚠ same type
- DDX59 p.Ile9Met Uncertain significance ★★ ⚠ 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/ddx59-p-phe443 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown