DDX3X p.Lys255=
c.765G>A · rs2519513487 · VCV2575859
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.90 | donor loss · deltas |
|---|---|---|
| Pangolin | Δ0.86 | loss · gain 0.01 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 2.2, phastCons 1 |
| Overall | ||
| CADD | 22.0 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- DDX3X
- Protein
- p.Lys255=
- Coding
- c.765G>A
- MANE Select
- NM_001356
- dbSNP
- rs2519513487
- Type
- single nucleotide variant
- Location
- chrX:41343822 (GRCh38)
- Structure
- AlphaFold pLDDT 73.24 · 17 PDB
- Residue 255
- the 'involved in stimulation of atpase activity by dna and rna, nucleic acid binding and unwinding and hiv-1 replication' region; an α-helix; the helicase atp-binding 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-lys255 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown