DDX50 p.Ser239=
c.717C>T · rs61743410 · VCV710605
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.7%, 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 -6.9 | GERP -4.3 |
| Overall | ||
| CADD | 1.044 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.7%
African / African-American · 1,272/74,964 alleles
Filtering AF
1.62%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.59%
Overall
0.0912%
1,472/1,613,242 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.7% | 59 |
| Admixed American | 0.115% | 867 |
| Remaining individualsnot grpmax-eligible | 0.11% | 906 |
| Middle Eastern | 0.0661% | 1,514 |
| European (non-Finnish) | 0.00492% | 20,342 |
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
- DDX50
- Protein
- p.Ser239=
- Coding
- c.717C>T
- MANE Select
- NM_024045
- dbSNP
- rs61743410
- Type
- single nucleotide variant
- Location
- chr10:68913239 (GRCh38)
- Gene constraint
- LOEUF 0.778 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.89 · 1 PDB
- Residue 239
- the helicase atp-binding domain
Similar variants
- DDX50 p.Ala659Thr Benign ★★ same type
- DDX50 p.Ala138Asp Uncertain significance ★ ⚠ same type
- DDX50 p.Ala138Gly Uncertain significance ★ ⚠ same type
- DDX50 p.Ala241Val Uncertain significance ★ ⚠ same type
- DDX50 p.Ala392Ser Uncertain significance ★ ⚠ same type
- DDX50 p.Ala406Gly Uncertain significance ★ ⚠ same type
- DDX50 p.Arg132His Uncertain significance ★ ⚠ same type
- DDX50 p.Arg182Gln 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/ddx50-p-ser239 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown