DDX3X p.Ala499=
c.1497A>G · rs1467805850 · VCV2027655
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000224%, nfe)
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 3.5 | GERP 1.2, phastCons 1 |
| Overall | ||
| CADD | 12.56 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000224%
European (non-Finnish) · 2/892,852 alleles
Filtering AF
3.7e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.4e-05%
Overall
0.000166%
2/1,206,275 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.Ala499=
- Coding
- c.1497A>G
- MANE Select
- NM_001356
- dbSNP
- rs1467805850
- Type
- single nucleotide variant
- Location
- chrX:41346410 (GRCh38)
- Structure
- AlphaFold pLDDT 73.24 · 17 PDB
- Residue 499
- the 'interaction with hcv core protein' region; a turn; 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-ala499 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown