DDX3X p.Arg548=
c.1644G>A · rs1303918534 · VCV1983388
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00123%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.27 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.08 | GERP -4.8, phastCons 0.13 |
| Overall | ||
| CADD | 3.843 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00123%
European (non-Finnish) · 11/894,472 alleles
Filtering AF
0.00066%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000482%
Overall
0.001%
11/1,096,687 alleles · very rare
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
- DDX3X
- Protein
- p.Arg548=
- Coding
- c.1644G>A
- MANE Select
- NM_001356
- dbSNP
- rs1303918534
- Type
- single nucleotide variant
- Location
- chrX:41346887 (GRCh38)
- Structure
- AlphaFold pLDDT 73.24 · 17 PDB
- Residue 548
- the 'interaction with hcv core protein' region; the 'interaction with nxf1' region; an α-helix; the helicase c-terminal domain; the 'interaction with gsk3b' region
Similar variants
- DDX3X c.1497+1G>A Likely pathogenic ★★ same type
- DDX3X c.1498-2A>G Pathogenic ★★ same type
- DDX3X c.151+1G>A Pathogenic ★★ same type
- DDX3X c.1769+1G>A Pathogenic ★★ same type
- DDX3X c.765+1G>A Pathogenic ★★ same type
- DDX3X c.865-1G>A Pathogenic ★★ same type
- DDX3X c.865-1G>C Pathogenic ★★ same type
- DDX3X c.865-2A>G Pathogenic ★★ 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/ddx3x-p-arg548 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown