DDX3X p.Pro142=
c.426A>C · rs779721240 · VCV1185840
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.024%, amr)
Conditions
1
Inborn genetic diseases
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 2.2 | GERP -1.1, phastCons 1 |
| Overall | ||
| CADD | 9.59 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.024%
Admixed American · 11/45,766 alleles
Filtering AF
0.0134%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0104%
Overall
0.00149%
18/1,210,333 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.024% | 4,161 |
| Remaining individualsnot grpmax-eligible | 0.0126% | 7,936 |
| African / African-American | 0.00175% | 57,299 |
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.Pro142=
- Coding
- c.426A>C
- MANE Select
- NM_001356
- dbSNP
- rs779721240
- Type
- single nucleotide variant
- Location
- chrX:41342636 (GRCh38)
- Structure
- AlphaFold pLDDT 73.24 · 17 PDB
- Residue 142
- the 'interaction with chuk' region; an α-helix; the 'disordered' region; the 'interaction with gsk3b' region
Similar variants
- DDX3X c.1498-2A>G Pathogenic ★★ same condition
- DDX3X c.151+1G>A Pathogenic ★★ same condition
- DDX3X c.1769+1G>A Pathogenic ★★ same condition
- DDX3X c.865-1G>C Pathogenic ★★ same condition
- DDX3X p.Ala497Val Pathogenic/Likely pathogenic ★★ same condition
- DDX3X p.Arg292Ter Pathogenic/Likely pathogenic ★★ same condition
- DDX3X p.Arg326Cys Pathogenic/Likely pathogenic ★★ same condition
- DDX3X p.Arg376Cys Pathogenic/Likely pathogenic ★★ same condition
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-pro142 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown