Sugi Variant

Sugi Variant/SPINT2

SPINT2 — 198 ClinVar variants

All ClinVar germline SPINT2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 57 flagged for review →

10 Pathogenic · 1 Pathogenic/Likely pathogenic · 7 Likely pathogenic · 2 Conflicting · 9 Benign · 4 Benign/Likely benign · 104 Likely benign · 61 Uncertain significance

Full SPINT2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 57

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 46

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

Predictors split 8

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

All SPINT2 variants

Pathogenic 10

  • p.Asn57fs Multiple submitters congenital secretory sodium diarrhea 3
  • p.Tyr163Cys Multiple submitters SPINT2-related disorder
  • p.Met1Ile Single submitter
  • p.Met1Val Single submitter
  • c.337+2T>C No assertion criteria congenital secretory sodium diarrhea 3
  • c.553+2T>A No assertion criteria congenital secretory sodium diarrhea 3
  • c.593-1G>A No assertion criteria congenital secretory sodium diarrhea 3
  • p.Gly168Ser No assertion criteria congenital secretory sodium diarrhea 3
  • p.Met1Leu No assertion criteria congenital secretory sodium diarrhea 3
  • p.Trp149Ter No assertion criteria congenital secretory sodium diarrhea 3

Pathogenic/Likely pathogenic 1

  • p.Arg115fs Multiple submitters congenital secretory sodium diarrhea 3

Likely pathogenic 7

Conflicting classifications of pathogenicity 2

Benign 9

Benign/Likely benign 4

Likely benign 104

Uncertain significance 61