Sugi Variant

Sugi Variant/DPYD

DPYD — 541 ClinVar variants

All ClinVar germline DPYD variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 219 flagged for review →

10 Pathogenic · 13 Pathogenic/Likely pathogenic · 122 Likely pathogenic · 23 Conflicting · 45 Benign · 5 Benign/Likely benign · 66 Likely benign · 257 Uncertain significance

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

⚑ Evidence disagreements 219

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 2

ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.

Predictors agree, ClinVar conflicts 11

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

Predictors lean, ClinVar uncertain 98

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

Predictors split 108

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

All DPYD variants

Pathogenic 10

  • p.Phe100fs Multiple submitters dihydropyrimidine dehydrogenase deficiency
  • c.151-2A>C Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Asn668fs Single submitter Inborn genetic diseases
  • p.Asn736fs Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Glu884Ter Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Leu155Ter Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Leu5fs Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Phe607fs Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Thr270_Leu271insTer Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Asp974Val No assertion criteria 5-fluorouracil toxicity ⚠

Pathogenic/Likely pathogenic 13

  • c.1905+1G>C Multiple submitters dihydropyrimidine dehydrogenase deficiency
  • p.Arg21Ter Multiple submitters dihydropyrimidine dehydrogenase deficiency
  • p.Arg561Ter Multiple submitters dihydropyrimidine dehydrogenase deficiency
  • p.Arg70Ter Multiple submitters dihydropyrimidine dehydrogenase deficiency
  • p.Arg759Ter Multiple submitters dihydropyrimidine dehydrogenase deficiency
  • p.Gln860fs Multiple submitters dihydropyrimidine dehydrogenase deficiency
  • p.Glu221Ter Multiple submitters dihydropyrimidine dehydrogenase deficiency
  • p.Glu69Ter Multiple submitters dihydropyrimidine dehydrogenase deficiency
  • p.Ile370fs Multiple submitters dihydropyrimidine dehydrogenase deficiency
  • p.Leu461fs Multiple submitters Neurodevelopmental delay
  • p.Lys42_Arg43insTer Multiple submitters dihydropyrimidine dehydrogenase deficiency
  • p.Pro86Leu Multiple submitters dihydropyrimidine dehydrogenase deficiency
  • p.Ser492Leu Multiple submitters dihydropyrimidine dehydrogenase deficiency

Likely pathogenic 122

  • c.1340-2A>C Multiple submitters DPYD-related disorder
  • c.1977_1983del Multiple submitters dihydropyrimidine dehydrogenase deficiency
  • c.233+1G>T Multiple submitters dihydropyrimidine dehydrogenase deficiency
  • c.2622+1G>A Multiple submitters dihydropyrimidine dehydrogenase deficiency
  • c.2767-1G>A Multiple submitters dihydropyrimidine dehydrogenase deficiency
  • c.680+1G>T Multiple submitters dihydropyrimidine dehydrogenase deficiency
  • p.Arg589fs Multiple submitters dihydropyrimidine dehydrogenase deficiency
  • p.Arg916fs Multiple submitters dihydropyrimidine dehydrogenase deficiency
  • p.Cys385_Glu386delinsTer Multiple submitters dihydropyrimidine dehydrogenase deficiency
  • p.Gln299Ter Multiple submitters dihydropyrimidine dehydrogenase deficiency
  • p.Gln470Ter Multiple submitters DPYD-related disorder
  • p.Glu415Ter Multiple submitters dihydropyrimidine dehydrogenase deficiency
  • p.Leu682fs Multiple submitters dihydropyrimidine dehydrogenase deficiency
  • p.Met1Ile Multiple submitters dihydropyrimidine dehydrogenase deficiency
  • p.Ser201Arg Multiple submitters dihydropyrimidine dehydrogenase deficiency
  • p.Trp621Ter Multiple submitters dihydropyrimidine dehydrogenase deficiency
  • c.1340-1G>A Single submitter dihydropyrimidine dehydrogenase deficiency
  • c.1525-1G>C Single submitter dihydropyrimidine dehydrogenase deficiency
  • c.1525-2A>G Single submitter dihydropyrimidine dehydrogenase deficiency
  • c.1905+2dup Single submitter dihydropyrimidine dehydrogenase deficiency
  • c.2059-1G>T Single submitter dihydropyrimidine dehydrogenase deficiency
  • c.2059-2A>G Single submitter dihydropyrimidine dehydrogenase deficiency
  • c.2179+1G>A Single submitter dihydropyrimidine dehydrogenase deficiency
  • c.2299+1G>A Single submitter dihydropyrimidine dehydrogenase deficiency
  • c.2300-1G>C Single submitter
  • c.2442+1G>C Single submitter dihydropyrimidine dehydrogenase deficiency
  • c.2442+1G>T Single submitter
  • c.2766+1G>A Single submitter dihydropyrimidine dehydrogenase deficiency
  • c.2907+1G>C Single submitter dihydropyrimidine dehydrogenase deficiency
  • c.40-6_42del Single submitter dihydropyrimidine dehydrogenase deficiency
  • c.484-1G>A Single submitter dihydropyrimidine dehydrogenase deficiency
  • c.484-2A>G Single submitter dihydropyrimidine dehydrogenase deficiency
  • c.680+1G>A Single submitter dihydropyrimidine dehydrogenase deficiency
  • c.763-1G>A Single submitter dihydropyrimidine dehydrogenase deficiency
  • c.850+23455_1128+8811del Single submitter dihydropyrimidine dehydrogenase deficiency
  • c.958+2T>C Single submitter dihydropyrimidine dehydrogenase deficiency
  • c.959-2A>G Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Ala72fs Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Ala946fs Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Arg208Ter Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Arg235Gln Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Arg332fs Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Asp346Ter Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Asp716fs Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Asp850fs Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Cys257Ter Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Cys322Ter Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Cys911fs Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Gln170Ter Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Gln220Ter Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Gln233Ter Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Gln498Ter Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Gln814Ter Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Gln852Ter Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Gln885Ter Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Gln930Ter Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Glu463fs Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Glu689Ter Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Glu892Ter Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Gly439fs Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.His40fs Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Ile435fs Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Ile454fs Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Ile591fs Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Ile948Thr Single submitter dihydropyrimidine dehydrogenase deficiency ⚠
  • p.Leu192fs Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Leu206fs Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Leu523fs Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Leu572fs Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Met182fs Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Met1Leu Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Phe117_Ser118insTer Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Phe438fs Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Pro149fs Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Pro393fs Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Pro633fs Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Pro712fs Single submitter
  • p.Ser32Ter Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Ser534fs Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Ser780fs Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Thr594fs Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Thr737fs Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Trp459fs Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Trp501Ter Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Trp568Ter Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Trp697Ter Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Tyr525Ter Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Tyr645Ter Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Tyr830Ter Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Val945fs Single submitter dihydropyrimidine dehydrogenase deficiency
  • c.1128+1G>C No assertion criteria dihydropyrimidine dehydrogenase deficiency
  • c.1339+1G>T No assertion criteria dihydropyrimidine dehydrogenase deficiency
  • c.1340-2A>G No assertion criteria dihydropyrimidine dehydrogenase deficiency
  • c.150+2T>A No assertion criteria dihydropyrimidine dehydrogenase deficiency
  • c.1524+1G>A No assertion criteria dihydropyrimidine dehydrogenase deficiency
  • c.2058+1G>C No assertion criteria dihydropyrimidine dehydrogenase deficiency
  • c.2177_2179+1del No assertion criteria dihydropyrimidine dehydrogenase deficiency
  • c.321+2T>C No assertion criteria dihydropyrimidine dehydrogenase deficiency
  • c.322-1G>C No assertion criteria dihydropyrimidine dehydrogenase deficiency
  • c.483+1G>T No assertion criteria dihydropyrimidine dehydrogenase deficiency
  • c.762+2T>C No assertion criteria dihydropyrimidine dehydrogenase deficiency
  • c.763-2A>G No assertion criteria dihydropyrimidine dehydrogenase deficiency
  • c.851-1G>C No assertion criteria dihydropyrimidine dehydrogenase deficiency
  • p.Ala348fs No assertion criteria dihydropyrimidine dehydrogenase deficiency
  • p.Arg358Cys No assertion criteria ⚠
  • p.Arg78Ter No assertion criteria dihydropyrimidine dehydrogenase deficiency
  • p.Glu611Ter No assertion criteria dihydropyrimidine dehydrogenase deficiency
  • p.Gly727fs No assertion criteria dihydropyrimidine dehydrogenase deficiency
  • p.Gly763fs No assertion criteria dihydropyrimidine dehydrogenase deficiency
  • p.Lys505_Tyr506insTer No assertion criteria dihydropyrimidine dehydrogenase deficiency
  • p.Lys894Ter No assertion criteria dihydropyrimidine dehydrogenase deficiency
  • p.Lys908Ter No assertion criteria dihydropyrimidine dehydrogenase deficiency
  • p.Met680fs No assertion criteria dihydropyrimidine dehydrogenase deficiency
  • p.Phe576fs No assertion criteria dihydropyrimidine dehydrogenase deficiency
  • p.Pro374fs No assertion criteria dihydropyrimidine dehydrogenase deficiency
  • p.Pro864fs No assertion criteria dihydropyrimidine dehydrogenase deficiency
  • p.Pro919fs No assertion criteria dihydropyrimidine dehydrogenase deficiency
  • p.Ser175fs No assertion criteria dihydropyrimidine dehydrogenase deficiency
  • p.Ser558fs No assertion criteria dihydropyrimidine dehydrogenase deficiency
  • p.Ser657fs No assertion criteria dihydropyrimidine dehydrogenase deficiency
  • p.Thr779fs No assertion criteria dihydropyrimidine dehydrogenase deficiency
  • p.Tyr304fs No assertion criteria dihydropyrimidine dehydrogenase deficiency

Conflicting classifications of pathogenicity 23

  • c.1974+1G>A Single submitter dihydropyrimidine dehydrogenase deficiency
  • c.321+1G>A Single submitter dihydropyrimidine dehydrogenase deficiency
  • c.484-4G>A Single submitter Inborn genetic diseases
  • p.Ala551Thr Single submitter DPYD-related disorder ⚠
  • p.Ala683= Single submitter Inborn genetic diseases
  • p.Arg74Ter Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Asn151Asp Single submitter dihydropyrimidine dehydrogenase deficiency ⚠
  • p.Asn635= Single submitter Inborn genetic diseases
  • p.Asn893Ser Single submitter DPYD-related disorder ⚠
  • p.Asp829Asn Single submitter dihydropyrimidine dehydrogenase deficiency ⚠
  • p.Cys29= Single submitter
  • p.Gln972Arg Single submitter ⚠
  • p.Gly539Arg Single submitter dihydropyrimidine dehydrogenase deficiency ⚠
  • p.Leu16= Single submitter dihydropyrimidine dehydrogenase deficiency
  • p.Lys259Glu Single submitter Inborn genetic diseases ⚠
  • p.Lys63Glu Single submitter dihydropyrimidine dehydrogenase deficiency ⚠
  • p.Met406Ile Single submitter dihydropyrimidine dehydrogenase deficiency ⚠
  • p.Met599Thr Single submitter dihydropyrimidine dehydrogenase deficiency ⚠
  • p.Pro1023Thr Single submitter dihydropyrimidine dehydrogenase deficiency ⚠
  • p.Thr760Ile Single submitter dihydropyrimidine dehydrogenase deficiency ⚠
  • p.Thr962= Single submitter
  • p.Tyr211Cys Single submitter Inborn genetic diseases ⚠
  • p.Val1021Ala Single submitter Inborn genetic diseases ⚠

Benign 45

Benign/Likely benign 5

  • c.1525-11G>A Multiple submitters dihydropyrimidine dehydrogenase deficiency
  • c.2180-3T>C Multiple submitters dihydropyrimidine dehydrogenase deficiency
  • c.681-8C>T Multiple submitters dihydropyrimidine dehydrogenase deficiency
  • p.Asn457= Multiple submitters Inborn genetic diseases
  • p.Gln498= Multiple submitters dihydropyrimidine dehydrogenase deficiency

Likely benign 66

Uncertain significance 257