ITPA — 318 ClinVar variants

All ClinVar germline ITPA variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 96 flagged for review →

19 Pathogenic · 7 Pathogenic/Likely pathogenic · 11 Likely pathogenic · 7 Conflicting · 28 Benign · 5 Benign/Likely benign · 128 Likely benign · 113 Uncertain significance

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

⚑ Evidence disagreements 96

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 5

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

Predictors lean, ClinVar uncertain 62

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

Predictors split 29

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

All ITPA variants

Pathogenic 19

  • c.124+2T>C Multiple submitters inosine triphosphatase deficiency
  • p.Trp151Ter Multiple submitters ITPA-related disorder
  • c.189+1G>A Single submitter developmental and epileptic encephalopathy, 35
  • c.263+583_295+1203del Single submitter developmental and epileptic encephalopathy, 35
  • c.264-1G>C Single submitter inosine triphosphatase deficiency
  • c.264-2A>G Single submitter inosine triphosphatase deficiency
  • p.Gln102Ter Single submitter inosine triphosphatase deficiency
  • p.Gln162Ter Single submitter developmental and epileptic encephalopathy, 35
  • p.Gln25Ter Single submitter inosine triphosphatase deficiency
  • p.Glu48Ter Single submitter developmental and epileptic encephalopathy, 35
  • p.Gly85fs Single submitter inosine triphosphatase deficiency
  • p.Leu120fs Single submitter developmental and epileptic encephalopathy, 35
  • p.Lys94_Leu95insTer Single submitter inosine triphosphatase deficiency
  • p.Phe31fs Single submitter inosine triphosphatase deficiency
  • p.Ser137Ter Single submitter inosine triphosphatase deficiency
  • p.Thr14fs Single submitter developmental and epileptic encephalopathy, 35
  • p.Trp90fs Single submitter inosine triphosphatase deficiency
  • p.Val24fs Single submitter inosine triphosphatase deficiency
  • c.264-607_295+1267del No assertion criteria developmental and epileptic encephalopathy, 35

Pathogenic/Likely pathogenic 7

  • c.124+1G>A Multiple submitters inosine triphosphatase deficiency
  • c.264-1G>A Multiple submitters developmental and epileptic encephalopathy, 35
  • c.411+1del Multiple submitters inosine triphosphatase deficiency
  • p.Arg135fs Multiple submitters Inborn genetic diseases
  • p.Gln156Ter Multiple submitters inosine triphosphatase deficiency
  • p.Gly123fs Multiple submitters tooth agenesis
  • p.Trp90Ter Multiple submitters infantile epileptic-dyskinetic encephalopathy

Likely pathogenic 11

  • c.190-2A>T Single submitter inosine triphosphatase deficiency
  • c.296-2A>C Single submitter inosine triphosphatase deficiency
  • c.489-1G>T Single submitter developmental and epileptic encephalopathy, 35
  • c.49_66+4del Single submitter inosine triphosphatase deficiency
  • c.67-2A>G Single submitter inosine triphosphatase deficiency
  • p.Asp109Tyr Single submitter developmental and epileptic encephalopathy, 35
  • p.Asp124fs Single submitter developmental and epileptic encephalopathy, 35
  • p.Gln46fs Single submitter developmental and epileptic encephalopathy, 35
  • p.Gln46Ter Single submitter developmental and epileptic encephalopathy, 35
  • p.Leu5Ter Single submitter inosine triphosphatase deficiency
  • p.Phe91Leu Single submitter developmental and epileptic encephalopathy, 35

Conflicting classifications of pathogenicity 7

  • c.488+1G>A Single submitter inosine triphosphatase deficiency
  • p.Arg139Gln Single submitter inosine triphosphatase deficiency ⚠
  • p.Arg178Cys Single submitter infantile epileptic-dyskinetic encephalopathy ⚠
  • p.Asn173fs Single submitter infantile epileptic-dyskinetic encephalopathy
  • p.Gly85Ser Single submitter developmental and epileptic encephalopathy, 35 ⚠
  • p.Thr163Met Single submitter developmental and epileptic encephalopathy, 35 ⚠
  • p.Val24Ile Single submitter inosine triphosphatase deficiency ⚠

Benign 28

Benign/Likely benign 5

  • c.264-11_264-8del Multiple submitters inosine triphosphatase deficiency
  • p.Arg180= Multiple submitters inosine triphosphatase deficiency
  • p.Asn78Ser Multiple submitters inosine triphosphatase deficiency
  • p.Glu93Gly Multiple submitters inosine triphosphatase deficiency ⚠
  • p.Pro97= Multiple submitters inosine triphosphatase deficiency

Likely benign 128

  • c.125-25T>C Multiple submitters inosine triphosphatase deficiency
  • c.190-7G>A Multiple submitters inosine triphosphatase deficiency
  • p.Arg178= Multiple submitters inosine triphosphatase deficiency
  • p.Cys74= Multiple submitters inosine triphosphatase deficiency
  • p.Ile140= Multiple submitters inosine triphosphatase deficiency
  • p.Leu42= Multiple submitters inosine triphosphatase deficiency
  • p.Phe132= Multiple submitters inosine triphosphatase deficiency
  • p.Pro32= Multiple submitters inosine triphosphatase deficiency
  • p.Pro67= Multiple submitters inosine triphosphatase deficiency
  • p.Pro86= Multiple submitters inosine triphosphatase deficiency
  • p.Ser53= Multiple submitters inosine triphosphatase deficiency
  • c.124+11G>C Single submitter inosine triphosphatase deficiency
  • c.124+13T>C Single submitter inosine triphosphatase deficiency
  • c.124+16_124+20del Single submitter inosine triphosphatase deficiency
  • c.124+20T>C Single submitter inosine triphosphatase deficiency
  • c.124+7C>T Single submitter inosine triphosphatase deficiency
  • c.125-12T>G Single submitter inosine triphosphatase deficiency
  • c.125-16C>G Single submitter inosine triphosphatase deficiency
  • c.125-17T>A Single submitter inosine triphosphatase deficiency
  • c.125-8C>G Single submitter inosine triphosphatase deficiency
  • c.189+10C>T Single submitter inosine triphosphatase deficiency
  • c.189+11T>G Single submitter inosine triphosphatase deficiency
  • c.189+12G>C Single submitter inosine triphosphatase deficiency
  • c.189+12G>T Single submitter inosine triphosphatase deficiency
  • c.189+16T>C Single submitter inosine triphosphatase deficiency
  • c.189+8C>T Single submitter inosine triphosphatase deficiency
  • c.263+10T>C Single submitter inosine triphosphatase deficiency
  • c.263+13C>G Single submitter inosine triphosphatase deficiency
  • c.263+13C>T Single submitter inosine triphosphatase deficiency
  • c.263+15C>T Single submitter inosine triphosphatase deficiency
  • c.263+16C>T Single submitter inosine triphosphatase deficiency
  • c.263+19C>T Single submitter inosine triphosphatase deficiency
  • c.263+20C>A Single submitter inosine triphosphatase deficiency
  • c.264-13C>A Single submitter inosine triphosphatase deficiency
  • c.295+10G>T Single submitter inosine triphosphatase deficiency
  • c.295+11C>T Single submitter inosine triphosphatase deficiency
  • c.295+16T>C Single submitter inosine triphosphatase deficiency
  • c.296-10C>T Single submitter inosine triphosphatase deficiency
  • c.296-11C>T Single submitter inosine triphosphatase deficiency
  • c.296-18C>G Single submitter inosine triphosphatase deficiency
  • c.296-18C>T Single submitter inosine triphosphatase deficiency
  • c.296-19C>T Single submitter inosine triphosphatase deficiency
  • c.296-20C>T Single submitter inosine triphosphatase deficiency
  • c.296-4G>A Single submitter inosine triphosphatase deficiency
  • c.296-6C>T Single submitter inosine triphosphatase deficiency
  • c.296-8A>G Single submitter inosine triphosphatase deficiency
  • c.411+11A>C Single submitter inosine triphosphatase deficiency
  • c.411+12C>G Single submitter inosine triphosphatase deficiency
  • c.411+13C>A Single submitter inosine triphosphatase deficiency
  • c.411+18T>C Single submitter inosine triphosphatase deficiency
  • c.412-10C>A Single submitter inosine triphosphatase deficiency
  • c.412-15C>A Single submitter
  • c.412-15C>T Single submitter inosine triphosphatase deficiency
  • c.412-16C>A Single submitter inosine triphosphatase deficiency
  • c.412-17C>A Single submitter inosine triphosphatase deficiency
  • c.412-18C>A Single submitter inosine triphosphatase deficiency
  • c.488+11C>G Single submitter inosine triphosphatase deficiency
  • c.488+17_488+21del Single submitter inosine triphosphatase deficiency
  • c.488+20T>A Single submitter inosine triphosphatase deficiency
  • c.488+9C>A Single submitter inosine triphosphatase deficiency
  • c.489-16T>C Single submitter inosine triphosphatase deficiency
  • c.489-18G>T Single submitter inosine triphosphatase deficiency
  • c.489-6C>T Single submitter inosine triphosphatase deficiency
  • c.489-8C>T Single submitter inosine triphosphatase deficiency
  • c.489-9del Single submitter inosine triphosphatase deficiency
  • c.66+10G>A Single submitter inosine triphosphatase deficiency
  • c.66+10G>C Single submitter inosine triphosphatase deficiency
  • c.66+12_66+14dup Single submitter inosine triphosphatase deficiency
  • c.66+15T>C Single submitter inosine triphosphatase deficiency
  • c.66+16T>G Single submitter inosine triphosphatase deficiency
  • c.66+17G>A Single submitter inosine triphosphatase deficiency
  • c.66+18G>A Single submitter inosine triphosphatase deficiency
  • c.67-12_67-8del Single submitter inosine triphosphatase deficiency
  • c.67-19C>T Single submitter inosine triphosphatase deficiency
  • c.67-9T>C Single submitter inosine triphosphatase deficiency
  • c.*46G>T Single submitter
  • c.*98A>G Single submitter
  • p.Ala114= Single submitter inosine triphosphatase deficiency
  • p.Ala119= Single submitter inosine triphosphatase deficiency
  • p.Ala170= Single submitter inosine triphosphatase deficiency
  • p.Ala17Ser Single submitter inosine triphosphatase deficiency
  • p.Ala193= Single submitter inosine triphosphatase deficiency
  • p.Ala2= Single submitter inosine triphosphatase deficiency
  • p.Ala3= Single submitter inosine triphosphatase deficiency
  • p.Arg133= Single submitter inosine triphosphatase deficiency
  • p.Arg135= Single submitter inosine triphosphatase deficiency
  • p.Arg139= Single submitter inosine triphosphatase deficiency
  • p.Arg144= Single submitter inosine triphosphatase deficiency
  • p.Asn16= Single submitter inosine triphosphatase deficiency
  • p.Asn173= Single submitter inosine triphosphatase deficiency
  • p.Asp152= Single submitter inosine triphosphatase deficiency
  • p.Cys33= Single submitter inosine triphosphatase deficiency
  • p.Gln65= Single submitter inosine triphosphatase deficiency
  • p.Glu108= Single submitter inosine triphosphatase deficiency
  • p.Glu161= Single submitter inosine triphosphatase deficiency
  • p.Gly106= Single submitter inosine triphosphatase deficiency
  • p.Gly134= Single submitter inosine triphosphatase deficiency
  • p.Gly159= Single submitter inosine triphosphatase deficiency
  • p.Gly190= Single submitter inosine triphosphatase deficiency
  • p.Gly66= Single submitter inosine triphosphatase deficiency
  • p.Ile52= Single submitter inosine triphosphatase deficiency
  • p.Ile54= Single submitter inosine triphosphatase deficiency
  • p.Leu103= Single submitter inosine triphosphatase deficiency
  • p.Leu115= Single submitter inosine triphosphatase deficiency
  • p.Leu183= Single submitter inosine triphosphatase deficiency
  • p.Leu35= Single submitter inosine triphosphatase deficiency
  • p.Leu5= Single submitter inosine triphosphatase deficiency
  • p.Leu69= Single submitter inosine triphosphatase deficiency
  • p.Leu83= Single submitter inosine triphosphatase deficiency
  • p.Lys172= Single submitter inosine triphosphatase deficiency
  • p.Lys39= Single submitter inosine triphosphatase deficiency
  • p.Phe189= Single submitter inosine triphosphatase deficiency
  • p.Phe31= Single submitter inosine triphosphatase deficiency
  • p.Pro128= Single submitter inosine triphosphatase deficiency
  • p.Pro143= Single submitter inosine triphosphatase deficiency
  • p.Pro43= Single submitter inosine triphosphatase deficiency
  • p.Pro49= Single submitter inosine triphosphatase deficiency
  • p.Pro84= Single submitter inosine triphosphatase deficiency
  • p.Ser126= Single submitter
  • p.Ser126Asn Single submitter
  • p.Ter195= Single submitter inosine triphosphatase deficiency
  • p.Thr122= Single submitter inosine triphosphatase deficiency
  • p.Thr14= Single submitter inosine triphosphatase deficiency
  • p.Thr163= Single submitter
  • p.Tyr164= Single submitter inosine triphosphatase deficiency
  • p.Tyr45= Single submitter inosine triphosphatase deficiency
  • p.Val23= Single submitter inosine triphosphatase deficiency
  • p.Val64= Single submitter inosine triphosphatase deficiency

Uncertain significance 113