DDX59 p.Pro41=
c.123C>T · rs533727818 · VCV3043217
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.015%, amr)
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 -4.4 | GERP -3 |
| Overall | ||
| CADD | 0.37 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.015%
Admixed American · 9/60,008 alleles
Filtering AF
0.00773%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00578%
Overall
0.00217%
35/1,614,112 alleles · ultra-rare
exomes 31/1,461,890 · genomes 4/152,222 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.015% | 6,668 |
| European (non-Finnish) | 0.00212% | 47,201 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,508 |
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.Pro41=
- Coding
- c.123C>T
- MANE Select
- NM_001031725
- dbSNP
- rs533727818
- Type
- single nucleotide variant
- Location
- chr1:200666618 (GRCh38)
- Gene constraint
- LOEUF 0.864 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.71 · 1 PDB
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-pro41 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown