DDX59 p.Pro103=
c.309A>G · rs3795633 · VCV1530773
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 40.2%, eas) — too common for a highly-penetrant pathogenic allele
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 -3.8 | GERP -4.1 |
| Overall | ||
| CADD | 0.145 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
40.2%
East Asian · 18,031/44,850 alleles
Filtering AF
39.7%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 39.5%
Overall
8.49%
137,088/1,614,008 alleles · common
exomes 119,082/1,461,858 · genomes 18,006/152,150 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 40.2% | 2 |
| Admixed American | 23.4% | 4 |
| South Asian | 16% | 6 |
| African / African-American | 15.1% | 7 |
| Amishnot grpmax-eligible | 13.6% | 7 |
| Finnishnot grpmax-eligible | 12.1% | 8 |
| Ashkenazi Jewishnot grpmax-eligible | 11.6% | 9 |
| Middle Eastern | 11.3% | 9 |
| Remaining individualsnot grpmax-eligible | 9.98% | 10 |
| European (non-Finnish) | 5.16% | 19 |
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.Pro103=
- Coding
- c.309A>G
- MANE Select
- NM_001031725
- dbSNP
- rs3795633
- Type
- single nucleotide variant
- Location
- chr1:200666432 (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-pro103 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown