Sugi Variant

Sugi Variant/CPA1

CPA1 — 990 ClinVar variants

All ClinVar germline CPA1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 596 flagged for review →

1 Pathogenic · 2 Likely pathogenic · 38 Conflicting · 20 Benign · 13 Benign/Likely benign · 311 Likely benign · 605 Uncertain significance

Full CPA1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 596

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 16

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

Predictors lean, ClinVar uncertain 259

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification. · showing the 150 best-reviewed of 259

Predictors split 321

The independent predictors disagree with each other — read with care. · showing the 150 best-reviewed of 321

All CPA1 variants

Pathogenic 1

Likely pathogenic 2

Conflicting classifications of pathogenicity 38

  • c.65+3A>G Single submitter hereditary chronic pancreatitis
  • c.65+3del Single submitter hereditary chronic pancreatitis
  • c.66-11A>T Single submitter hereditary chronic pancreatitis
  • c.787+1G>A Single submitter hereditary chronic pancreatitis
  • c.788-5C>A Single submitter hereditary chronic pancreatitis
  • p.Ala137Thr Single submitter hereditary chronic pancreatitis ⚠
  • p.Arg169His Single submitter hereditary chronic pancreatitis ⚠
  • p.Arg386His Single submitter hereditary chronic pancreatitis ⚠
  • p.Arg54Gln Single submitter hereditary chronic pancreatitis ⚠
  • p.Arg54Trp Single submitter hereditary chronic pancreatitis ⚠
  • p.Arg66Ter Single submitter hereditary chronic pancreatitis
  • p.Asp130Ala Single submitter hereditary chronic pancreatitis ⚠
  • p.Asp44Asn Single submitter hereditary chronic pancreatitis ⚠
  • p.Gln103Arg Single submitter hereditary chronic pancreatitis ⚠
  • p.Gln103Glu Single submitter hereditary chronic pancreatitis ⚠
  • p.Gln103Ter Single submitter hereditary chronic pancreatitis
  • p.Gln94Arg Single submitter hereditary chronic pancreatitis ⚠
  • p.Glu102fs Single submitter hereditary chronic pancreatitis
  • p.Gly166Asp Single submitter hereditary chronic pancreatitis ⚠
  • p.Gly277Ser Single submitter hereditary chronic pancreatitis ⚠
  • p.Ile209Val Single submitter hereditary chronic pancreatitis ⚠
  • p.Ile249Val Single submitter hereditary chronic pancreatitis ⚠
  • p.Ile303Val Single submitter hereditary chronic pancreatitis ⚠
  • p.Ile357= Single submitter hereditary chronic pancreatitis
  • p.Leu4fs Single submitter hereditary chronic pancreatitis
  • p.Leu5= Single submitter hereditary chronic pancreatitis
  • p.Met1Thr Single submitter hereditary chronic pancreatitis
  • p.Phe105Leu Single submitter hereditary chronic pancreatitis ⚠
  • p.Pro70Ser Single submitter hereditary chronic pancreatitis ⚠
  • p.Ser167Asn Single submitter hereditary chronic pancreatitis ⚠
  • p.Thr212Asn Single submitter hereditary chronic pancreatitis ⚠
  • p.Thr212Ser Single submitter hereditary chronic pancreatitis ⚠
  • p.Thr229Met Single submitter hereditary chronic pancreatitis ⚠
  • p.Tyr200fs Single submitter hereditary chronic pancreatitis
  • p.Tyr318_Lys319delinsTer Single submitter hereditary chronic pancreatitis
  • p.Val14Ala Single submitter hereditary chronic pancreatitis ⚠
  • p.Val14Leu Single submitter hereditary chronic pancreatitis ⚠
  • p.Val67= Single submitter hereditary chronic pancreatitis

Benign 20

Benign/Likely benign 13

  • c.1072+16G>C Multiple submitters
  • c.586-3C>A Multiple submitters hereditary chronic pancreatitis
  • c.788-5C>G Multiple submitters hereditary chronic pancreatitis
  • p.Ala208Thr Multiple submitters hereditary chronic pancreatitis ⚠
  • p.Ala341Thr Multiple submitters hereditary chronic pancreatitis
  • p.Arg2Gln Multiple submitters hereditary chronic pancreatitis ⚠
  • p.Gln202Lys Multiple submitters hereditary chronic pancreatitis
  • p.Ile289= Multiple submitters hereditary chronic pancreatitis
  • p.Leu343= Multiple submitters hereditary chronic pancreatitis
  • p.Phe162= Multiple submitters hereditary chronic pancreatitis
  • p.Thr124Ile Multiple submitters hereditary chronic pancreatitis ⚠
  • p.Thr207= Multiple submitters hereditary chronic pancreatitis
  • p.Thr232Met Multiple submitters hereditary chronic pancreatitis ⚠

Likely benign 311

Showing the top 300 by review status; the full set is in the sitemap.

  • c.148-4C>T Multiple submitters hereditary chronic pancreatitis
  • c.65+174C>T Multiple submitters
  • c.*97A>C Multiple submitters
  • p.Ala137= Multiple submitters hereditary chronic pancreatitis
  • p.Ala137Gly Multiple submitters hereditary chronic pancreatitis ⚠
  • p.Ala171= Multiple submitters hereditary chronic pancreatitis
  • p.Ala31= Multiple submitters hereditary chronic pancreatitis
  • p.Ala341= Multiple submitters hereditary chronic pancreatitis
  • p.Ala406= Multiple submitters hereditary chronic pancreatitis
  • p.Ala74= Multiple submitters hereditary chronic pancreatitis
  • p.Arg27Ter Multiple submitters hereditary chronic pancreatitis
  • p.Arg54= Multiple submitters hereditary chronic pancreatitis
  • p.Asn254= Multiple submitters hereditary chronic pancreatitis
  • p.Asn298= Multiple submitters hereditary chronic pancreatitis
  • p.Asp115= Multiple submitters hereditary chronic pancreatitis
  • p.Asp211= Multiple submitters hereditary chronic pancreatitis
  • p.Asp258= Multiple submitters hereditary chronic pancreatitis
  • p.Asp92= Multiple submitters hereditary chronic pancreatitis
  • p.Glu100= Multiple submitters hereditary chronic pancreatitis
  • p.Glu182= Multiple submitters hereditary chronic pancreatitis
  • p.Glu91= Multiple submitters hereditary chronic pancreatitis
  • p.Glu99= Multiple submitters hereditary chronic pancreatitis
  • p.Gly12= Multiple submitters hereditary chronic pancreatitis
  • p.Gly177= Multiple submitters hereditary chronic pancreatitis
  • p.Gly250= Multiple submitters hereditary chronic pancreatitis
  • p.Gly55= Multiple submitters hereditary chronic pancreatitis
  • p.His242= Multiple submitters hereditary chronic pancreatitis
  • p.His276= Multiple submitters hereditary chronic pancreatitis
  • p.His306= Multiple submitters hereditary chronic pancreatitis
  • p.His47= Multiple submitters hereditary chronic pancreatitis
  • p.Ile174= Multiple submitters hereditary chronic pancreatitis
  • p.Ile219= Multiple submitters hereditary chronic pancreatitis
  • p.Leu11= Multiple submitters hereditary chronic pancreatitis
  • p.Leu217= Multiple submitters hereditary chronic pancreatitis
  • p.Leu381= Multiple submitters hereditary chronic pancreatitis
  • p.Leu391= Multiple submitters hereditary chronic pancreatitis
  • p.Leu97= Multiple submitters hereditary chronic pancreatitis
  • p.Lys194= Multiple submitters hereditary chronic pancreatitis
  • p.Lys278= Multiple submitters hereditary chronic pancreatitis
  • p.Lys287= Multiple submitters hereditary chronic pancreatitis
  • p.Lys334= Multiple submitters hereditary chronic pancreatitis
  • p.Lys401= Multiple submitters hereditary chronic pancreatitis
  • p.Phe105= Multiple submitters hereditary chronic pancreatitis
  • p.Phe216= Multiple submitters hereditary chronic pancreatitis
  • p.Phe302= Multiple submitters hereditary chronic pancreatitis
  • p.Phe377= Multiple submitters hereditary chronic pancreatitis
  • p.Phe379= Multiple submitters hereditary chronic pancreatitis
  • p.Pro253= Multiple submitters hereditary chronic pancreatitis
  • p.Pro68= Multiple submitters hereditary chronic pancreatitis
  • p.Ser163= Multiple submitters hereditary chronic pancreatitis
  • p.Ser246= Multiple submitters hereditary chronic pancreatitis
  • p.Ser264= Multiple submitters hereditary chronic pancreatitis
  • p.Ser363= Multiple submitters hereditary chronic pancreatitis
  • p.Thr114= Multiple submitters hereditary chronic pancreatitis
  • p.Thr176= Multiple submitters hereditary chronic pancreatitis
  • p.Thr185= Multiple submitters hereditary chronic pancreatitis
  • p.Thr229= Multiple submitters hereditary chronic pancreatitis
  • p.Tyr119= Multiple submitters hereditary chronic pancreatitis
  • p.Tyr275= Multiple submitters hereditary chronic pancreatitis
  • p.Tyr316= Multiple submitters hereditary chronic pancreatitis
  • p.Tyr344= Multiple submitters hereditary chronic pancreatitis
  • p.Tyr350= Multiple submitters hereditary chronic pancreatitis
  • p.Tyr369= Multiple submitters hereditary chronic pancreatitis
  • p.Tyr375= Multiple submitters hereditary chronic pancreatitis
  • p.Val25= Multiple submitters hereditary chronic pancreatitis
  • c.1072+10C>T Single submitter
  • c.1072+11G>A Single submitter
  • c.1072+18C>T Single submitter
  • c.1073-11T>C Single submitter
  • c.1073-6C>A Single submitter
  • c.147+5G>C Single submitter
  • c.148-11G>C Single submitter
  • c.148-13_148-12del Single submitter
  • c.148-18G>T Single submitter
  • c.148-6C>G Single submitter
  • c.381+11C>T Single submitter
  • c.381+18G>A Single submitter
  • c.381+20C>T Single submitter
  • c.381+7dup Single submitter
  • c.381+7G>C Single submitter
  • c.381+9G>A Single submitter
  • c.382-4T>A Single submitter hereditary chronic pancreatitis
  • c.484-18C>A Single submitter
  • c.484-20C>A Single submitter
  • c.484-20C>G Single submitter
  • c.585+10G>T Single submitter
  • c.585+7C>T Single submitter
  • c.585+8C>T Single submitter
  • c.585+9G>A Single submitter
  • c.586-20C>T Single submitter
  • c.586-8C>A Single submitter
  • c.586-8C>T Single submitter
  • c.65+14G>A Single submitter
  • c.66-3del Single submitter
  • c.696+14C>A Single submitter
  • c.696+6G>A Single submitter hereditary chronic pancreatitis
  • c.697-20G>C Single submitter
  • c.697-9C>T Single submitter
  • c.787+13G>A Single submitter
  • c.787+17C>G Single submitter
  • c.787+20G>C Single submitter
  • c.787+2T>A Single submitter hereditary chronic pancreatitis
  • c.787+2T>C Single submitter hereditary chronic pancreatitis
  • c.788-10C>A Single submitter
  • c.788-11T>C Single submitter
  • c.788-4A>C Single submitter hereditary chronic pancreatitis
  • c.987+12C>A Single submitter
  • c.987+14T>C Single submitter
  • c.987+15C>T Single submitter
  • c.987+16G>A Single submitter
  • c.988-10T>A Single submitter
  • c.988-14G>C Single submitter
  • c.988-19T>C Single submitter
  • c.988-2A>G Single submitter hereditary chronic pancreatitis
  • c.988-7T>C Single submitter
  • c.*16C>A Single submitter
  • p.Ala106= Single submitter hereditary chronic pancreatitis
  • p.Ala111= Single submitter hereditary chronic pancreatitis
  • p.Ala204= Single submitter hereditary chronic pancreatitis
  • p.Ala205= Single submitter hereditary chronic pancreatitis
  • p.Ala227= Single submitter hereditary chronic pancreatitis
  • p.Ala259Thr Single submitter hereditary chronic pancreatitis ⚠
  • p.Ala266= Single submitter hereditary chronic pancreatitis
  • p.Ala280= Single submitter hereditary chronic pancreatitis
  • p.Ala301= Single submitter hereditary chronic pancreatitis
  • p.Ala336= Single submitter hereditary chronic pancreatitis
  • p.Ala339= Single submitter hereditary chronic pancreatitis
  • p.Ala34= Single submitter hereditary chronic pancreatitis
  • p.Ala356Thr Single submitter hereditary chronic pancreatitis
  • p.Ala393= Single submitter hereditary chronic pancreatitis
  • p.Ala57= Single submitter hereditary chronic pancreatitis
  • p.Arg108= Single submitter hereditary chronic pancreatitis
  • p.Arg110= Single submitter hereditary chronic pancreatitis
  • p.Arg110Gly Single submitter hereditary chronic pancreatitis ⚠
  • p.Arg112= Single submitter hereditary chronic pancreatitis
  • p.Arg112Cys Single submitter hereditary chronic pancreatitis ⚠
  • p.Arg155= Single submitter hereditary chronic pancreatitis
  • p.Arg181= Single submitter hereditary chronic pancreatitis
  • p.Arg27= Single submitter hereditary chronic pancreatitis
  • p.Arg386= Single submitter hereditary chronic pancreatitis
  • p.Arg66= Single submitter hereditary chronic pancreatitis
  • p.Asn150= Single submitter hereditary chronic pancreatitis
  • p.Asn233Asp Single submitter hereditary chronic pancreatitis
  • p.Asn269= Single submitter hereditary chronic pancreatitis
  • p.Asn349= Single submitter hereditary chronic pancreatitis
  • p.Asp115Asn Single submitter hereditary chronic pancreatitis ⚠
  • p.Asp19= Single submitter hereditary chronic pancreatitis
  • p.Asp199= Single submitter hereditary chronic pancreatitis
  • p.Asp19Glu Single submitter hereditary chronic pancreatitis
  • p.Asp252= Single submitter hereditary chronic pancreatitis
  • p.Asp295= Single submitter hereditary chronic pancreatitis
  • p.Asp32= Single submitter hereditary chronic pancreatitis
  • p.Asp32Gly Single submitter hereditary chronic pancreatitis ⚠
  • p.Asp383= Single submitter hereditary chronic pancreatitis
  • p.Asp51Asn Single submitter hereditary chronic pancreatitis ⚠
  • p.Asp98= Single submitter hereditary chronic pancreatitis
  • p.Gln103= Single submitter hereditary chronic pancreatitis
  • p.Gln202= Single submitter
  • p.Gln310= Single submitter hereditary chronic pancreatitis
  • p.Gln94= Single submitter hereditary chronic pancreatitis
  • p.Glu102= Single submitter hereditary chronic pancreatitis
  • p.Glu138= Single submitter hereditary chronic pancreatitis
  • p.Glu153= Single submitter hereditary chronic pancreatitis
  • p.Glu18= Single submitter hereditary chronic pancreatitis
  • p.Glu218= Single submitter hereditary chronic pancreatitis
  • p.Glu285= Single submitter hereditary chronic pancreatitis
  • p.Glu33= Single submitter hereditary chronic pancreatitis
  • p.Glu41= Single submitter hereditary chronic pancreatitis
  • p.Glu412= Single submitter hereditary chronic pancreatitis
  • p.Glu412Gln Single submitter hereditary chronic pancreatitis
  • p.Glu87= Single submitter hereditary chronic pancreatitis
  • p.Gly149= Single submitter hereditary chronic pancreatitis
  • p.Gly154= Single submitter hereditary chronic pancreatitis
  • p.Gly165= Single submitter hereditary chronic pancreatitis
  • p.Gly166= Single submitter hereditary chronic pancreatitis
  • p.Gly177fs Single submitter hereditary chronic pancreatitis
  • p.Gly189= Single submitter hereditary chronic pancreatitis
  • p.Gly262= Single submitter hereditary chronic pancreatitis
  • p.Gly265= Single submitter hereditary chronic pancreatitis
  • p.Gly297= Single submitter hereditary chronic pancreatitis
  • p.Gly3= Single submitter hereditary chronic pancreatitis
  • p.Gly345= Single submitter hereditary chronic pancreatitis
  • p.Gly385= Single submitter hereditary chronic pancreatitis
  • p.Gly388= Single submitter hereditary chronic pancreatitis
  • p.Gly83= Single submitter hereditary chronic pancreatitis
  • p.His123= Single submitter hereditary chronic pancreatitis
  • p.His141= Single submitter hereditary chronic pancreatitis
  • p.His141Gln Single submitter hereditary chronic pancreatitis
  • p.His179= Single submitter hereditary chronic pancreatitis
  • p.His23= Single submitter hereditary chronic pancreatitis
  • p.His230= Single submitter hereditary chronic pancreatitis
  • p.His417= Single submitter hereditary chronic pancreatitis
  • p.His82= Single submitter hereditary chronic pancreatitis
  • p.Ile146= Single submitter hereditary chronic pancreatitis
  • p.Ile157= Single submitter hereditary chronic pancreatitis
  • p.Ile196= Single submitter hereditary chronic pancreatitis
  • p.Ile209= Single submitter hereditary chronic pancreatitis
  • p.Ile28= Single submitter hereditary chronic pancreatitis
  • p.Ile303= Single submitter hereditary chronic pancreatitis
  • p.Ile305= Single submitter hereditary chronic pancreatitis
  • p.Ile396= Single submitter hereditary chronic pancreatitis
  • p.Ile397= Single submitter hereditary chronic pancreatitis
  • p.Ile410= Single submitter hereditary chronic pancreatitis
  • p.Ile72= Single submitter hereditary chronic pancreatitis
  • p.Ile90= Single submitter hereditary chronic pancreatitis
  • p.Leu10= Single submitter hereditary chronic pancreatitis
  • p.Leu125= Single submitter hereditary chronic pancreatitis
  • p.Leu134= Single submitter
  • p.Leu135= Single submitter hereditary chronic pancreatitis
  • p.Leu160= Single submitter hereditary chronic pancreatitis
  • p.Leu210= Single submitter hereditary chronic pancreatitis
  • p.Leu213= Single submitter hereditary chronic pancreatitis
  • p.Leu247= Single submitter hereditary chronic pancreatitis
  • p.Leu263= Single submitter hereditary chronic pancreatitis
  • p.Leu311= Single submitter hereditary chronic pancreatitis
  • p.Leu312= Single submitter hereditary chronic pancreatitis
  • p.Leu329= Single submitter hereditary chronic pancreatitis
  • p.Leu329fs Single submitter hereditary chronic pancreatitis
  • p.Leu390= Single submitter hereditary chronic pancreatitis
  • p.Leu4= Single submitter
  • p.Leu405= Single submitter hereditary chronic pancreatitis
  • p.Leu408= Single submitter hereditary chronic pancreatitis
  • p.Leu415= Single submitter hereditary chronic pancreatitis
  • p.Leu42= Single submitter hereditary chronic pancreatitis
  • p.Leu48= Single submitter hereditary chronic pancreatitis
  • p.Leu48fs Single submitter hereditary chronic pancreatitis
  • p.Leu50= Single submitter hereditary chronic pancreatitis
  • p.Leu7= Single submitter hereditary chronic pancreatitis
  • p.Leu79= Single submitter hereditary chronic pancreatitis
  • p.Leu96= Single submitter hereditary chronic pancreatitis
  • p.Lys145= Single submitter hereditary chronic pancreatitis
  • p.Lys168Asn Single submitter hereditary chronic pancreatitis
  • p.Lys17= Single submitter hereditary chronic pancreatitis
  • p.Lys294= Single submitter hereditary chronic pancreatitis
  • p.Lys300= Single submitter hereditary chronic pancreatitis
  • p.Lys319Arg Single submitter hereditary chronic pancreatitis
  • p.Lys347= Single submitter hereditary chronic pancreatitis
  • p.Lys355= Single submitter hereditary chronic pancreatitis
  • p.Lys374= Single submitter hereditary chronic pancreatitis
  • p.Lys40= Single submitter hereditary chronic pancreatitis
  • p.Lys401Arg Single submitter hereditary chronic pancreatitis ⚠
  • p.Lys401Gln Single submitter hereditary chronic pancreatitis
  • p.Lys401Thr Single submitter hereditary chronic pancreatitis ⚠
  • p.Met1fs Single submitter hereditary chronic pancreatitis
  • p.Met313Leu Single submitter hereditary chronic pancreatitis
  • p.Phe117= Single submitter hereditary chronic pancreatitis
  • p.Phe15= Single submitter hereditary chronic pancreatitis
  • p.Phe20= Single submitter hereditary chronic pancreatitis
  • p.Phe206= Single submitter
  • p.Phe206Leu Single submitter hereditary chronic pancreatitis
  • p.Phe279= Single submitter hereditary chronic pancreatitis
  • p.Phe52= Single submitter hereditary chronic pancreatitis
  • p.Pro140= Single submitter hereditary chronic pancreatitis
  • p.Pro156= Single submitter hereditary chronic pancreatitis
  • p.Pro223= Single submitter
  • p.Pro324= Single submitter hereditary chronic pancreatitis
  • p.Pro392= Single submitter hereditary chronic pancreatitis
  • p.Pro418= Single submitter hereditary chronic pancreatitis
  • p.Pro62= Single submitter hereditary chronic pancreatitis
  • p.Ser109= Single submitter hereditary chronic pancreatitis
  • p.Ser180= Single submitter hereditary chronic pancreatitis
  • p.Ser188= Single submitter hereditary chronic pancreatitis
  • p.Ser267= Single submitter hereditary chronic pancreatitis
  • p.Ser272= Single submitter hereditary chronic pancreatitis
  • p.Ser282= Single submitter hereditary chronic pancreatitis
  • p.Ser288= Single submitter hereditary chronic pancreatitis
  • p.Ser307= Single submitter
  • p.Ser333= Single submitter hereditary chronic pancreatitis
  • p.Ser370Asn Single submitter hereditary chronic pancreatitis ⚠
  • p.Ser394= Single submitter hereditary chronic pancreatitis
  • p.Ser61= Single submitter hereditary chronic pancreatitis
  • p.Ser71= Single submitter hereditary chronic pancreatitis
  • p.Ser81= Single submitter hereditary chronic pancreatitis
  • p.Ser81Tyr Single submitter hereditary chronic pancreatitis ⚠
  • p.Ser95= Single submitter hereditary chronic pancreatitis
  • p.Thr116= Single submitter hereditary chronic pancreatitis
  • p.Thr151= Single submitter hereditary chronic pancreatitis
  • p.Thr164= Single submitter hereditary chronic pancreatitis
  • p.Thr197= Single submitter hereditary chronic pancreatitis
  • p.Thr239= Single submitter hereditary chronic pancreatitis
  • p.Thr338= Single submitter hereditary chronic pancreatitis
  • p.Thr346= Single submitter hereditary chronic pancreatitis
  • p.Thr364= Single submitter hereditary chronic pancreatitis
  • p.Thr378= Single submitter hereditary chronic pancreatitis
  • p.Thr384= Single submitter hereditary chronic pancreatitis
  • p.Thr399= Single submitter hereditary chronic pancreatitis
  • p.Thr403= Single submitter hereditary chronic pancreatitis
  • p.Thr414= Single submitter hereditary chronic pancreatitis
  • p.Thr88Ile Single submitter hereditary chronic pancreatitis
  • p.Trp367Ter Single submitter hereditary chronic pancreatitis
  • p.Tyr119Ter Single submitter hereditary chronic pancreatitis
  • p.Tyr129= Single submitter hereditary chronic pancreatitis
  • p.Tyr152= Single submitter hereditary chronic pancreatitis
  • p.Tyr308= Single submitter hereditary chronic pancreatitis
  • p.Tyr358= Single submitter hereditary chronic pancreatitis
  • p.Tyr387= Single submitter hereditary chronic pancreatitis
  • p.Val136= Single submitter hereditary chronic pancreatitis
  • p.Val14= Single submitter hereditary chronic pancreatitis
  • p.Val143= Single submitter hereditary chronic pancreatitis
  • p.Val184= Single submitter hereditary chronic pancreatitis

Uncertain significance 605

Showing the top 300 by review status; the full set is in the sitemap.