Sugi Variant

Sugi Variant/DPH1

DPH1 — 154 ClinVar variants

All ClinVar germline DPH1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 76 flagged for review →

6 Pathogenic · 3 Pathogenic/Likely pathogenic · 6 Likely pathogenic · 3 Conflicting · 8 Benign · 2 Benign/Likely benign · 25 Likely benign · 101 Uncertain significance

Full DPH1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 76

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 1

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

Predictors agree, ClinVar conflicts 1

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

Predictors lean, ClinVar uncertain 70

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

Predictors split 4

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

All DPH1 variants

Pathogenic 6

  • p.Arg307Ter Single submitter developmental delay with short stature, dysmorphic facial features, and sparse hair 1
  • p.Cys203fs Single submitter
  • p.Glu305fs Single submitter
  • p.Glu35Ter Single submitter developmental delay with short stature, dysmorphic facial features, and sparse hair 1
  • p.Tyr107Cys Single submitter developmental delay with short stature, dysmorphic facial features, and sparse hair 1
  • p.Leu159Pro No assertion criteria developmental delay with short stature, dysmorphic facial features, and sparse hair 1

Pathogenic/Likely pathogenic 3

  • p.Glu92fs Multiple submitters developmental delay with short stature, dysmorphic facial features, and sparse hair 1
  • p.Leu229Pro Multiple submitters developmental delay with short stature, dysmorphic facial features, and sparse hair 1
  • p.Met1Lys No assertion criteria developmental delay with short stature, dysmorphic facial features, and sparse hair 1 ⚠

Likely pathogenic 6

  • c.1007+1G>A Single submitter
  • c.400+1G>A Single submitter developmental delay with short stature, dysmorphic facial features, and sparse hair 1
  • p.Arg153fs Single submitter developmental delay with short stature, dysmorphic facial features, and sparse hair
  • p.Arg218Ter Single submitter developmental delay with short stature, dysmorphic facial features, and sparse hair 1
  • p.Pro169fs Single submitter developmental delay with short stature, dysmorphic facial features, and sparse hair 1
  • p.Tyr128His Single submitter developmental delay with short stature, dysmorphic facial features, and sparse hair

Conflicting classifications of pathogenicity 3

  • c.1086+2dup Single submitter developmental delay with short stature, dysmorphic facial features, and sparse hair 1
  • p.Leu120Pro Single submitter developmental delay with short stature, dysmorphic facial features, and sparse hair ⚠
  • c.749+39G>A No assertion criteria developmental delay with short stature, dysmorphic facial features, and sparse hair 1

Benign 8

  • c.1228-21A>G Multiple submitters developmental delay with short stature, dysmorphic facial features, and sparse hair
  • c.400+117G>A Multiple submitters developmental delay with short stature, dysmorphic facial features, and sparse hair
  • c.*19-155C>T Multiple submitters
  • c.*19-205C>T Multiple submitters
  • c.*19-278G>T Multiple submitters
  • p.Pro332= Multiple submitters developmental delay with short stature, dysmorphic facial features, and sparse hair
  • c.1227+33C>G Single submitter
  • p.Ser183= No assertion criteria DPH1-related disorder

Benign/Likely benign 2

Likely benign 25

Uncertain significance 101