DDX3X — 899 ClinVar variants

All ClinVar germline DDX3X variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 200 flagged for review →

189 Pathogenic · 28 Pathogenic/Likely pathogenic · 125 Likely pathogenic · 24 Conflicting · 64 Benign · 18 Benign/Likely benign · 228 Likely benign · 223 Uncertain significance

Full DDX3X gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 200

Variants where the independent computational evidence doesn't line up with the clinical picture — a QC signal for a second look, not a reclassification.

Predictors vs ClinVar 4

ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.

Predictors agree, ClinVar conflicts 9

ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.

Predicted LoF vs a conflicting call 1

ClinVar submitters conflict, and it's a predicted loss-of-function change in a gene where LoF causes disease — flagged for review, not resolved (verify NMD-escape for C-terminal truncations). Non-missense.

Predictors lean, ClinVar uncertain 95

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.

Predictors split 91

The independent predictors disagree with each other — read with care.

All DDX3X variants

Pathogenic 189

Pathogenic/Likely pathogenic 28

  • c.1071_1170+24del Multiple submitters Inborn genetic diseases
  • p.Ala349Thr Multiple submitters intellectual disability, X-linked 102
  • p.Ala497Val Multiple submitters intellectual disability, X-linked 102
  • p.Arg292Ter Multiple submitters intellectual disability, X-linked 102
  • p.Arg326Cys Multiple submitters Inborn genetic diseases
  • p.Arg376Cys Multiple submitters Inborn genetic diseases
  • p.Arg475Cys Multiple submitters intellectual disability, X-linked 102
  • p.Arg475Gly Multiple submitters Inborn genetic diseases
  • p.Arg480Gly Multiple submitters intellectual disability, X-linked 102
  • p.Arg488Cys Multiple submitters intellectual disability, X-linked 102
  • p.Arg488His Multiple submitters intellectual disability, X-linked 102
  • p.Arg534Cys Multiple submitters intellectual disability, X-linked 102
  • p.Cys298Ter Multiple submitters intellectual disability, X-linked 102
  • p.Gln27Ter Multiple submitters
  • p.Gly193Ter Multiple submitters intellectual disability, X-linked 102
  • p.Gly248= Multiple submitters intellectual disability, X-linked 102
  • p.His472Pro Multiple submitters Inborn genetic diseases
  • p.Ile214Thr Multiple submitters intellectual disability, X-linked 102
  • p.Ile514Thr Multiple submitters intellectual disability, X-linked 102
  • p.Leu560del Multiple submitters intellectual disability
  • p.Phe402del Multiple submitters intellectual disability, X-linked 102
  • p.Pro324Arg Multiple submitters intellectual disability, X-linked 102
  • p.Pro41del Multiple submitters intellectual disability, X-linked 102
  • p.Pro41Ser Multiple submitters DDX3X-related disorder
  • p.Ser58Ter Multiple submitters intellectual disability, X-linked 102
  • p.Ser590Asn Multiple submitters intellectual disability, X-linked 102 ⚠
  • p.Thr532Met Multiple submitters intellectual disability, X-linked 102
  • p.Tyr38Cys Multiple submitters intellectual disability, X-linked 102

Likely pathogenic 125

Conflicting classifications of pathogenicity 24

Benign 64

Benign/Likely benign 18

Likely benign 228

Uncertain significance 223