Sugi Variant

Sugi Variant/PGAP3

PGAP3 — 236 ClinVar variants

All ClinVar germline PGAP3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 84 flagged for review →

23 Pathogenic · 8 Pathogenic/Likely pathogenic · 10 Likely pathogenic · 10 Conflicting · 16 Benign · 3 Benign/Likely benign · 83 Likely benign · 83 Uncertain significance

Full PGAP3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 84

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 agree, ClinVar conflicts 9

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

Predictors lean, ClinVar uncertain 58

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

Predictors split 17

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

All PGAP3 variants

Pathogenic 23

  • c.694+1G>A Multiple submitters hyperphosphatasia with intellectual disability syndrome 4
  • p.Gln89Ter Multiple submitters hyperphosphatasia with intellectual disability syndrome 4
  • p.Glu37Ter Multiple submitters Inborn genetic diseases
  • p.Met135fs Multiple submitters PGAP3-related disorder
  • p.Trp152fs Multiple submitters hyperphosphatasia with intellectual disability syndrome 4
  • c.432+1G>A Single submitter hyperphosphatasia with intellectual disability syndrome 4
  • p.Asp282Gly Single submitter hyperphosphatasia with intellectual disability syndrome 4
  • p.Gln191Ter Single submitter
  • p.Gln247Ter Single submitter
  • p.Leu119fs Single submitter hyperphosphatasia with intellectual disability syndrome 4
  • p.Lys69Ter Single submitter Inborn genetic diseases
  • p.Phe151fs Single submitter
  • p.Trp152Ter Single submitter hyperphosphatasia with intellectual disability syndrome 4
  • p.Trp242Ter Single submitter
  • p.Trp94fs Single submitter hyperphosphatasia with intellectual disability syndrome 4
  • p.Val28fs Single submitter hyperphosphatasia with intellectual disability syndrome 4
  • p.Cys171Arg No assertion criteria hyperphosphatasia with intellectual disability syndrome 4
  • p.Gly92Asp No assertion criteria hyperphosphatasia with intellectual disability syndrome 4
  • p.Leu147fs No assertion criteria hyperphosphatasia with intellectual disability syndrome 4
  • p.Leu281Pro No assertion criteria hyperphosphatasia with intellectual disability syndrome 4
  • p.Pro105Arg No assertion criteria hyperphosphatasia with intellectual disability syndrome 4
  • p.Trp287Cys No assertion criteria hyperphosphatasia with intellectual disability syndrome 4
  • p.Val28Ter No assertion criteria hyperphosphatasia with intellectual disability syndrome 4

Pathogenic/Likely pathogenic 8

  • c.558-10G>A Multiple submitters hyperphosphatasia with intellectual disability syndrome 4
  • p.Asp305Gly Multiple submitters PGAP3-related disorder
  • p.His284Arg Multiple submitters hyperphosphatasia with intellectual disability syndrome 4 ⚠
  • p.His284Tyr Multiple submitters hyperphosphatasia with intellectual disability syndrome 4
  • p.Pro276Leu Multiple submitters hyperphosphatasia with intellectual disability syndrome 4
  • p.Ser107Leu Multiple submitters hyperphosphatasia with intellectual disability syndrome 4
  • p.Tyr213Ter Multiple submitters
  • p.Tyr169Ter No assertion criteria hyperphosphatasia with intellectual disability syndrome 4

Likely pathogenic 10

  • p.Pro105Gln Multiple submitters hyperphosphatasia with intellectual disability syndrome 4
  • c.181+1G>T Single submitter hyperphosphatasia with intellectual disability syndrome 4
  • c.899+2_899+10delinsAGA Single submitter hyperphosphatasia with intellectual disability syndrome 4
  • c.900-1G>A Single submitter hyperphosphatasia with intellectual disability syndrome 4
  • p.Ala15fs Single submitter hyperphosphatasia-intellectual disability syndrome
  • p.Cys68fs Single submitter hyperphosphatasia with intellectual disability syndrome 4
  • p.Leu11fs Single submitter
  • p.Leu17fs Single submitter hyperphosphatasia with intellectual disability syndrome 4
  • p.Ser300fs Single submitter hyperphosphatasia with intellectual disability syndrome 4
  • p.Trp62Ter Single submitter hyperphosphatasia with intellectual disability syndrome 4

Conflicting classifications of pathogenicity 10

  • c.*559C>T Single submitter hyperphosphatasia with intellectual disability syndrome 4
  • p.Arg159Ser Single submitter hyperphosphatasia with intellectual disability syndrome 4 ⚠
  • p.Arg186Thr Single submitter hyperphosphatasia with intellectual disability syndrome 4 ⚠
  • p.Arg218His Single submitter Inborn genetic diseases ⚠
  • p.Glu270Lys Single submitter hyperphosphatasia with intellectual disability syndrome 4 ⚠
  • p.Gly3Asp Single submitter ⚠
  • p.His284Asp Single submitter hyperphosphatasia with intellectual disability syndrome 4 ⚠
  • p.Leu59Val Single submitter Inborn genetic diseases ⚠
  • p.Thr174Ile Single submitter Inborn genetic diseases ⚠
  • p.Val257Met Single submitter Inborn genetic diseases ⚠

Benign 16

Benign/Likely benign 3

Likely benign 83

Uncertain significance 83