Sugi Variant

Sugi Variant/PGAP2

PGAP2 — 147 ClinVar variants

All ClinVar germline PGAP2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 50 flagged for review →

7 Pathogenic · 1 Pathogenic/Likely pathogenic · 10 Likely pathogenic · 6 Conflicting · 18 Benign · 1 Benign/Likely benign · 33 Likely benign · 71 Uncertain significance

Full PGAP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 50

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 3

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 25

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

Predictors split 21

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

All PGAP2 variants

Pathogenic 7

  • c.-60_-57del Single submitter hyperphosphatasia with intellectual disability syndrome 3
  • p.Glu131Ter Single submitter hyperphosphatasia with intellectual disability syndrome 3
  • p.Met1Arg Single submitter hyperphosphatasia with intellectual disability syndrome 3
  • p.Tyr160Cys Single submitter hyperphosphatasia with intellectual disability syndrome 3
  • p.Val84fs Single submitter hyperphosphatasia with intellectual disability syndrome 1
  • p.Arg16Trp No assertion criteria hyperphosphatasia with intellectual disability syndrome 3
  • p.Thr164Ile No assertion criteria hyperphosphatasia with intellectual disability syndrome 3 ⚠

Pathogenic/Likely pathogenic 1

  • p.Arg238Pro Multiple submitters hyperphosphatasia with intellectual disability syndrome 3 ⚠

Likely pathogenic 10

  • p.Ala127Val Multiple submitters hyperphosphatasia with intellectual disability syndrome 3
  • p.Thr294Met Multiple submitters hyperphosphatasia with intellectual disability syndrome 3
  • c.166-1G>C Single submitter hyperphosphatasia with intellectual disability syndrome 3
  • p.Arg246Gln Single submitter hyperphosphatasia with intellectual disability syndrome 3 ⚠
  • p.Arg246Leu Single submitter hyperphosphatasia with intellectual disability syndrome 3 ⚠
  • p.Gln245fs Single submitter Inborn genetic diseases
  • p.Leu215fs Single submitter hyperphosphatasia with intellectual disability syndrome 3
  • p.Met1Val Single submitter hyperphosphatasia with intellectual disability syndrome 3
  • p.Phe150Ser Single submitter hyperphosphatasia with intellectual disability syndrome 3
  • p.Tyr170Cys Single submitter genetic developmental and epileptic encephalopathy ⚠

Conflicting classifications of pathogenicity 6

  • c.-30A>G Single submitter Inborn genetic diseases
  • p.Ala290Val Single submitter Inborn genetic diseases ⚠
  • p.Arg18Cys Single submitter ⚠
  • p.Asn177Ser Single submitter hyperphosphatasia with intellectual disability syndrome 3 ⚠
  • p.Gly216Arg Single submitter hyperphosphatasia with intellectual disability syndrome 3 ⚠
  • p.Thr49Ile Single submitter hyperphosphatasia with intellectual disability syndrome 3 ⚠

Benign 18

Benign/Likely benign 1

  • p.Val182Ile Multiple submitters Inborn genetic diseases

Likely benign 33

Uncertain significance 71