DDX53 p.Ala105=
c.315C>T · rs141158062 · VCV765069
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.59%, 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 -2.9 | GERP -3.6 |
| Overall | ||
| CADD | 0.6 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.59%
African / African-American · 336/56,962 alleles
Filtering AF
0.538%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.518%
Overall
0.0321%
387/1,206,541 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.59% | 170 |
| Middle Eastern | 0.0461% | 2,169 |
| Remaining individualsnot grpmax-eligible | 0.04% | 2,499 |
| Admixed American | 0.0311% | 3,220 |
| South Asian | 0.0018% | 55,584 |
| European (non-Finnish) | 0.00168% | 59,619 |
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.Ala105=
- Coding
- c.315C>T
- MANE Select
- NM_182699
- dbSNP
- rs141158062
- Type
- single nucleotide variant
- Location
- chrX:23000372 (GRCh38)
- Structure
- AlphaFold pLDDT 79.66 · 2 PDB
- Residue 105
- the kh domain
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-ala105 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown