DDX53 p.Pro353=
c.1059T>C · rs146090889 · VCV2660164
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.206%, 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 -4.2 | GERP -3.9 |
| Overall | ||
| CADD | 0.982 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.206%
African / African-American · 117/56,830 alleles
Filtering AF
0.176%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.164%
Overall
0.0107%
129/1,207,732 alleles · rare
exomes 70/1,096,923 · genomes 59/110,809 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.206% | 486 |
| Admixed American | 0.0197% | 5,064 |
| Remaining individualsnot grpmax-eligible | 0.0021% | 47,543 |
| European (non-Finnish) | 0.000224% | 447,089 |
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
- DDX53
- Protein
- p.Pro353=
- Coding
- c.1059T>C
- MANE Select
- NM_182699
- dbSNP
- rs146090889
- Type
- single nucleotide variant
- Location
- chrX:23001116 (GRCh38)
- Structure
- AlphaFold pLDDT 79.66 · 2 PDB
- Residue 353
- the helicase atp-binding domain; an α-helix
Similar variants
- DDX53 p.Ala107Ser Benign ★★ same type
- DDX53 p.Gly499Val Benign ★★ ⚠ same type
- DDX53 p.Ile134Val Likely benign ★★ same type
- DDX53 p.Ser326Asn Likely pathogenic ★ ⚠ same type
- DDX53 p.Ala11Gly Uncertain significance ★ ⚠ same type
- DDX53 p.Ala437Val Uncertain significance ★ ⚠ same type
- DDX53 p.Ala480Ser Uncertain significance ★ ⚠ same type
- DDX53 p.Ala579Val 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/ddx53-p-pro353 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown