DDX3X p.Phe16=
c.48T>C · VCV4691675
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0266%, eas)
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 · T>A here scores Δ0.66 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 7.8 | GERP 2.1, phastCons 1 |
| Overall | ||
| CADD | 17.06 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0266%
East Asian · 9/33,809 alleles
Filtering AF
0.0139%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0103%
Overall
0.000822%
9/1,095,258 alleles · ultra-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.Phe16=
- Coding
- c.48T>C
- MANE Select
- NM_001356
- Type
- single nucleotide variant
- Location
- chrX:41337410 (GRCh38)
- Structure
- AlphaFold pLDDT 73.24 · 17 PDB
- Residue 16
- the 'required for tbk1 and ikbke-dependent ifnb1 activation' 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-phe16 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown