Sugi Variant

Sugi Variant/PTCD3

PTCD3 — 137 ClinVar variants

All ClinVar germline PTCD3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 98 flagged for review →

5 Pathogenic · 9 Likely pathogenic · 3 Conflicting · 2 Benign · 14 Likely benign · 104 Uncertain significance

Full PTCD3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 98

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 2

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

Predictors lean, ClinVar uncertain 83

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

Predictors split 12

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

All PTCD3 variants

Pathogenic 5

  • p.His232fs Single submitter
  • c.1453-1G>C No assertion criteria combined oxidative phosphorylation deficiency 51
  • c.415-2A>G No assertion criteria combined oxidative phosphorylation deficiency 51
  • p.Phe583fs No assertion criteria combined oxidative phosphorylation deficiency 51
  • p.Thr301Ile No assertion criteria combined oxidative phosphorylation deficiency 51 ⚠

Likely pathogenic 9

  • c.1148-2A>G Single submitter PTCD3-related disorder
  • c.1630-1G>A Single submitter combined oxidative phosphorylation deficiency 51
  • c.1979+1G>A Single submitter combined oxidative phosphorylation deficiency 51
  • c.805-2A>G Single submitter combined oxidative phosphorylation deficiency 51
  • p.Leu95fs Single submitter combined oxidative phosphorylation deficiency 51
  • p.Thr237fs Single submitter combined oxidative phosphorylation deficiency 51
  • p.Trp477Ter Single submitter combined oxidative phosphorylation deficiency 51
  • p.Trp65Ter Single submitter PTCD3-related disorder
  • p.Ser389Ter No assertion criteria PTCD3-related disorder

Conflicting classifications of pathogenicity 3

  • p.Asp682Asn Single submitter Inborn genetic diseases ⚠
  • p.Gln214Ter Single submitter combined oxidative phosphorylation deficiency 51
  • p.Pro640Ala Single submitter combined oxidative phosphorylation deficiency 51 ⚠

Benign 2

Likely benign 14

Uncertain significance 104