Sugi Variant

Sugi Variant/GNPAT

GNPAT — 558 ClinVar variants

All ClinVar germline GNPAT variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 138 flagged for review →

25 Pathogenic · 4 Pathogenic/Likely pathogenic · 36 Likely pathogenic · 19 Conflicting · 26 Benign · 8 Benign/Likely benign · 276 Likely benign · 164 Uncertain significance

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

⚑ Evidence disagreements 138

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 6

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

Predictors lean, ClinVar uncertain 110

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

Predictors split 22

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

All GNPAT variants

Pathogenic 25

Pathogenic/Likely pathogenic 4

  • p.Leu192fs Multiple submitters rhizomelic chondrodysplasia punctata type 2
  • p.Leu494_Val495insTer Multiple submitters rhizomelic chondrodysplasia punctata type 2
  • p.Trp386Ter Multiple submitters rhizomelic chondrodysplasia punctata type 2
  • p.Tyr60Ter Multiple submitters rhizomelic chondrodysplasia punctata type 2

Likely pathogenic 36

  • p.Arg211Cys Multiple submitters rhizomelic chondrodysplasia punctata type 2
  • p.Arg335Ter Multiple submitters GNPAT-related disorder
  • c.1279+1G>T Single submitter rhizomelic chondrodysplasia punctata type 2
  • c.1280-3T>G Single submitter rhizomelic chondrodysplasia punctata type 2
  • c.1522+2T>G Single submitter
  • c.1603-1G>C Single submitter
  • c.1743+1G>T Single submitter rhizomelic chondrodysplasia punctata type 2
  • c.439-1G>A Single submitter
  • c.696+1G>A Single submitter
  • c.696+2T>C Single submitter
  • c.697-2A>G Single submitter
  • c.773-2A>G Single submitter
  • c.925-2del Single submitter rhizomelic chondrodysplasia punctata type 2
  • p.Arg100Ter Single submitter rhizomelic chondrodysplasia punctata type 2
  • p.Asp97fs Single submitter rhizomelic chondrodysplasia punctata type 2
  • p.Gln148Ter Single submitter rhizomelic chondrodysplasia punctata type 2
  • p.Glu271fs Single submitter rhizomelic chondrodysplasia punctata type 2
  • p.Glu305Ter Single submitter rhizomelic chondrodysplasia punctata type 2
  • p.Glu319fs Single submitter rhizomelic chondrodysplasia punctata type 2
  • p.Glu374fs Single submitter rhizomelic chondrodysplasia punctata type 2
  • p.Glu433Ter Single submitter rhizomelic chondrodysplasia punctata type 2
  • p.Glu463fs Single submitter rhizomelic chondrodysplasia punctata type 2
  • p.Gly571fs Single submitter rhizomelic chondrodysplasia punctata type 2
  • p.Ile280fs Single submitter
  • p.Leu292fs Single submitter rhizomelic chondrodysplasia punctata type 2
  • p.Leu572_Phe573insTer Single submitter rhizomelic chondrodysplasia punctata type 2
  • p.Lys269Ter Single submitter rhizomelic chondrodysplasia punctata type 2
  • p.Lys86Ter Single submitter rhizomelic chondrodysplasia punctata type 2
  • p.Ser512fs Single submitter rhizomelic chondrodysplasia punctata type 2
  • p.Ser9fs Single submitter rhizomelic chondrodysplasia punctata type 2
  • p.Tyr293fs Single submitter rhizomelic chondrodysplasia punctata type 2
  • p.Tyr353Ter Single submitter rhizomelic chondrodysplasia punctata type 2
  • p.Tyr541fs Single submitter rhizomelic chondrodysplasia punctata type 2
  • p.Tyr541Ter Single submitter rhizomelic chondrodysplasia punctata type 2
  • p.Tyr586Ter Single submitter rhizomelic chondrodysplasia punctata type 2
  • p.Val182fs Single submitter rhizomelic chondrodysplasia punctata type 2

Conflicting classifications of pathogenicity 19

  • c.1280-8G>A Single submitter rhizomelic chondrodysplasia punctata type 2
  • c.1744-13C>T Single submitter rhizomelic chondrodysplasia punctata type 2
  • c.569-11del Single submitter rhizomelic chondrodysplasia punctata type 2
  • p.Ala631Val Single submitter rhizomelic chondrodysplasia punctata type 2 ⚠
  • p.Arg210Gln Single submitter Inborn genetic diseases ⚠
  • p.Asn348Ser Single submitter rhizomelic chondrodysplasia punctata type 2 ⚠
  • p.Asn630= Single submitter rhizomelic chondrodysplasia punctata type 2
  • p.Cys584= Single submitter
  • p.Gly460Arg Single submitter ⚠
  • p.Gly571= Single submitter rhizomelic chondrodysplasia punctata type 2
  • p.Ile185= Single submitter rhizomelic chondrodysplasia punctata type 2
  • p.Leu476= Single submitter rhizomelic chondrodysplasia punctata type 2
  • p.Leu485= Single submitter rhizomelic chondrodysplasia punctata type 2
  • p.Phe365= Single submitter rhizomelic chondrodysplasia punctata type 2
  • p.Pro266= Single submitter rhizomelic chondrodysplasia punctata type 2
  • p.Ser19= Single submitter rhizomelic chondrodysplasia punctata type 2
  • p.Ser249= Single submitter rhizomelic chondrodysplasia punctata type 2
  • p.Ser346Pro Single submitter Inborn genetic diseases ⚠
  • p.Val22Ala Single submitter rhizomelic chondrodysplasia punctata type 2 ⚠

Benign 26

Benign/Likely benign 8

  • c.1056-20C>A Multiple submitters rhizomelic chondrodysplasia punctata type 2
  • c.925-16G>A Multiple submitters rhizomelic chondrodysplasia punctata type 2
  • c.-84C>T Multiple submitters rhizomelic chondrodysplasia punctata type 2
  • c.*18T>C Multiple submitters rhizomelic chondrodysplasia punctata type 2
  • p.Asp519Gly Multiple submitters rhizomelic chondrodysplasia punctata type 2
  • p.Pro436= Multiple submitters rhizomelic chondrodysplasia punctata type 2
  • p.Ser459= Multiple submitters
  • p.Val495Ile Multiple submitters rhizomelic chondrodysplasia punctata type 2

Likely benign 276

Uncertain significance 164