DDX3X p.Arg531=
c.1593T>C · rs761401204 · VCV1204023
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0741%, sas)
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 0.15 | GERP -0.96, phastCons 0.99 |
| Overall | ||
| CADD | 7.905 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0741%
South Asian · 41/55,345 alleles
Filtering AF
0.0561%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0498%
Overall
0.00367%
44/1,199,641 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0741% | 1,350 |
| Middle Eastern | 0.0232% | 4,313 |
| Remaining individualsnot grpmax-eligible | 0.00423% | 23,636 |
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.Arg531=
- Coding
- c.1593T>C
- MANE Select
- NM_001356
- dbSNP
- rs761401204
- Type
- single nucleotide variant
- Location
- chrX:41346600 (GRCh38)
- Structure
- AlphaFold pLDDT 73.24 · 17 PDB
- Residue 531
- the 'interaction with hcv core protein' region; 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-arg531 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown