SPINK1 — 224 ClinVar variants

All ClinVar germline SPINK1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 81 flagged for review →

8 Pathogenic · 1 Pathogenic/Likely pathogenic · 5 Likely pathogenic · 19 Conflicting · 4 Benign · 8 Benign/Likely benign · 73 Likely benign · 106 Uncertain significance

Full SPINK1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 81

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 10

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

Predicted LoF vs a conflicting call 2

ClinVar submitters conflict, and it's a predicted loss-of-function change in a gene where LoF causes disease — flagged for review, not resolved (verify NMD-escape for C-terminal truncations). Non-missense.

Predictors lean, ClinVar uncertain 55

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

All SPINK1 variants

Pathogenic 8

  • p.Glu35Ter Multiple submitters hereditary chronic pancreatitis
  • p.Ser10fs Multiple submitters hereditary chronic pancreatitis
  • c.87+1G>A Single submitter hereditary chronic pancreatitis
  • p.Cys58Ter Single submitter hereditary chronic pancreatitis
  • c.-191-129_56-932del No assertion criteria hereditary chronic pancreatitis
  • c.-191-24G>T No assertion criteria tropical pancreatitis
  • p.Leu14Pro No assertion criteria hereditary chronic pancreatitis
  • p.Met1Thr No assertion criteria hereditary chronic pancreatitis

Pathogenic/Likely pathogenic 1

  • c.194+2T>C Multiple submitters SPINK1-related disorder

Likely pathogenic 5

  • c.55+1G>A Single submitter hereditary chronic pancreatitis
  • c.55+1G>T Single submitter hereditary chronic pancreatitis
  • p.Asn56fs Single submitter hereditary chronic pancreatitis
  • p.Lys41Asn Single submitter hereditary chronic pancreatitis ⚠
  • p.Tyr43Ter Single submitter SPINK1-related disorder

Conflicting classifications of pathogenicity 19

  • c.195-7A>G Single submitter hereditary chronic pancreatitis
  • c.87+26T>C Single submitter hereditary chronic pancreatitis
  • c.-147A>G Single submitter hereditary chronic pancreatitis
  • c.-191-24G>A Single submitter SPINK1-related disorder
  • c.-22C>T Single submitter hereditary chronic pancreatitis
  • c.*27G>T Single submitter hereditary chronic pancreatitis
  • p.Ala13Val Single submitter hereditary chronic pancreatitis ⚠
  • p.Arg28Lys Single submitter hereditary chronic pancreatitis ⚠
  • p.Arg65Leu Single submitter hereditary chronic pancreatitis ⚠
  • p.Arg67His Single submitter hereditary chronic pancreatitis ⚠
  • p.Cys61fs Single submitter hereditary chronic pancreatitis ⚠
  • p.Gln68Arg Single submitter hereditary chronic pancreatitis ⚠
  • p.Gln74Lys Single submitter hereditary chronic pancreatitis ⚠
  • p.Ile42Met Single submitter hereditary chronic pancreatitis ⚠
  • p.Lys31_Tyr33del Single submitter hereditary chronic pancreatitis
  • p.Met1Leu Single submitter hereditary chronic pancreatitis ⚠
  • p.Ser70Thr Single submitter hereditary chronic pancreatitis ⚠
  • p.Thr69Ile Single submitter hereditary chronic pancreatitis ⚠
  • p.Val59Met Single submitter hereditary chronic pancreatitis ⚠

Benign 4

Benign/Likely benign 8

  • c.194+184T>A Multiple submitters hereditary chronic pancreatitis
  • c.194+90A>T Multiple submitters hereditary chronic pancreatitis
  • c.88-23A>T Multiple submitters hereditary chronic pancreatitis
  • c.-41G>A Multiple submitters hereditary chronic pancreatitis
  • c.*32C>T Multiple submitters hereditary chronic pancreatitis
  • p.Cys58= Multiple submitters hereditary chronic pancreatitis
  • p.Leu12Phe Multiple submitters hereditary chronic pancreatitis
  • p.Pro55Ser Multiple submitters tropical pancreatitis

Likely benign 73

  • c.195-21T>A Multiple submitters hereditary chronic pancreatitis
  • c.55+122G>A Multiple submitters
  • c.87+7A>T Multiple submitters hereditary chronic pancreatitis
  • c.*51T>C Multiple submitters hereditary chronic pancreatitis
  • p.Asn37= Multiple submitters hereditary chronic pancreatitis
  • p.Asn37Ser Multiple submitters hereditary chronic pancreatitis
  • p.Asn64= Multiple submitters hereditary chronic pancreatitis
  • p.Asp24= Multiple submitters hereditary chronic pancreatitis
  • p.Gly38= Multiple submitters hereditary chronic pancreatitis
  • p.Leu72= Multiple submitters hereditary chronic pancreatitis
  • p.Phe62= Multiple submitters hereditary chronic pancreatitis
  • p.Ser70= Multiple submitters hereditary chronic pancreatitis
  • p.Tyr54= Multiple submitters hereditary chronic pancreatitis
  • p.Val59= Multiple submitters hereditary chronic pancreatitis
  • c.194+15G>C Single submitter hereditary chronic pancreatitis
  • c.194+19T>G Single submitter hereditary chronic pancreatitis
  • c.195-15T>A Single submitter
  • c.55+11C>A Single submitter hereditary chronic pancreatitis
  • c.55+12A>G Single submitter hereditary chronic pancreatitis
  • c.55+14A>G Single submitter hereditary chronic pancreatitis
  • c.56-15C>T Single submitter hereditary chronic pancreatitis
  • c.56-19A>G Single submitter hereditary chronic pancreatitis
  • c.87+10T>C Single submitter hereditary chronic pancreatitis
  • c.87+18A>G Single submitter hereditary chronic pancreatitis
  • c.87+54C>T Single submitter
  • c.87+7A>G Single submitter hereditary chronic pancreatitis
  • c.88-10C>T Single submitter hereditary chronic pancreatitis
  • c.88-20C>A Single submitter hereditary chronic pancreatitis
  • c.-192+3416G>T Single submitter
  • c.-42C>T Single submitter hereditary chronic pancreatitis
  • p.Ala11= Single submitter hereditary chronic pancreatitis
  • p.Ala13= Single submitter hereditary chronic pancreatitis
  • p.Arg67= Single submitter hereditary chronic pancreatitis
  • p.Asn52= Single submitter hereditary chronic pancreatitis
  • p.Asp44= Single submitter hereditary chronic pancreatitis
  • p.Asp50= Single submitter hereditary chronic pancreatitis
  • p.Cys39= Single submitter hereditary chronic pancreatitis
  • p.Cys61= Single submitter hereditary chronic pancreatitis
  • p.Gln68= Single submitter hereditary chronic pancreatitis
  • p.Gln74= Single submitter hereditary chronic pancreatitis
  • p.Gln74Arg Single submitter hereditary chronic pancreatitis
  • p.Glu29Lys Single submitter hereditary chronic pancreatitis
  • p.Glu35= Single submitter hereditary chronic pancreatitis
  • p.Glu35Asp Single submitter hereditary chronic pancreatitis
  • p.Glu57= Single submitter hereditary chronic pancreatitis
  • p.Gly22Ala Single submitter hereditary chronic pancreatitis
  • p.Gly22Arg Single submitter hereditary chronic pancreatitis
  • p.Gly48= Single submitter hereditary chronic pancreatitis
  • p.Gly77= Single submitter hereditary chronic pancreatitis
  • p.Ile71Val Single submitter hereditary chronic pancreatitis
  • p.Ile73Val Single submitter hereditary chronic pancreatitis
  • p.Leu14= Single submitter hereditary chronic pancreatitis
  • p.Leu17= Single submitter hereditary chronic pancreatitis
  • p.Leu26= Single submitter hereditary chronic pancreatitis
  • p.Leu36= Single submitter hereditary chronic pancreatitis
  • p.Leu60= Single submitter hereditary chronic pancreatitis
  • p.Lys2= Single submitter hereditary chronic pancreatitis
  • p.Lys41= Single submitter hereditary chronic pancreatitis
  • p.Lys66= Single submitter hereditary chronic pancreatitis
  • p.Pro45= Single submitter hereditary chronic pancreatitis
  • p.Pro55= Single submitter hereditary chronic pancreatitis
  • p.Pro78= Single submitter hereditary chronic pancreatitis
  • p.Ser16= Single submitter hereditary chronic pancreatitis
  • p.Ser18= Single submitter hereditary chronic pancreatitis
  • p.Ser25= Single submitter hereditary chronic pancreatitis
  • p.Ter80= Single submitter hereditary chronic pancreatitis
  • p.Thr40= Single submitter hereditary chronic pancreatitis
  • p.Thr49= Single submitter hereditary chronic pancreatitis
  • p.Thr53= Single submitter hereditary chronic pancreatitis
  • p.Tyr33= Single submitter hereditary chronic pancreatitis
  • p.Tyr33Ser Single submitter hereditary chronic pancreatitis
  • p.Val3= Single submitter hereditary chronic pancreatitis
  • p.Val46= Single submitter hereditary chronic pancreatitis

Uncertain significance 106