Sugi Variant

Sugi Variant/TYMP

TYMP — 566 ClinVar variants

All ClinVar germline TYMP variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 132 flagged for review →

51 Pathogenic · 15 Pathogenic/Likely pathogenic · 46 Likely pathogenic · 33 Conflicting · 21 Benign · 4 Benign/Likely benign · 266 Likely benign · 130 Uncertain significance

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

⚑ Evidence disagreements 132

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 3

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

Predictors agree, ClinVar conflicts 17

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

Predictors lean, ClinVar uncertain 82

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

Predictors split 30

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

All TYMP variants

Pathogenic 51

Pathogenic/Likely pathogenic 15

  • c.646+1G>A Multiple submitters mitochondrial DNA depletion syndrome 1
  • c.647-1G>A Multiple submitters mitochondrial DNA depletion syndrome 1
  • p.Ala135fs Multiple submitters mitochondrial neurogastrointestinal encephalomyopathy
  • p.Ala268fs Multiple submitters mitochondrial neurogastrointestinal encephalomyopathy
  • p.Ala297fs Multiple submitters mitochondrial neurogastrointestinal encephalomyopathy
  • p.Ala3_Leu4insTer Multiple submitters mitochondrial DNA depletion syndrome 1
  • p.Ala333fs Multiple submitters mitochondrial neurogastrointestinal encephalomyopathy
  • p.Gln100Ter Multiple submitters mitochondrial DNA depletion syndrome 1
  • p.Gln174Ter Multiple submitters mitochondrial DNA depletion syndrome 1
  • p.Gln247Ter Multiple submitters mitochondrial DNA depletion syndrome 1
  • p.Glu21Ter Multiple submitters mitochondrial neurogastrointestinal encephalomyopathy
  • p.Gly145Arg Multiple submitters mitochondrial neurogastrointestinal encephalomyopathy
  • p.Gly153Ser Multiple submitters mitochondrial neurogastrointestinal encephalomyopathy
  • p.Trp108Ter Multiple submitters mitochondrial DNA depletion syndrome 1
  • p.Val208Met Multiple submitters TYMP-related disorder

Likely pathogenic 46

  • c.1301-1G>A Multiple submitters mitochondrial DNA depletion syndrome 1
  • c.214+1G>T Multiple submitters mitochondrial DNA depletion syndrome 1
  • c.418-1G>A Multiple submitters mitochondrial DNA depletion syndrome 1
  • p.Ala216Val Multiple submitters TYMP-related disorder
  • p.Asp114Asn Multiple submitters TYMP-related disorder
  • p.Cys183fs Multiple submitters mitochondrial neurogastrointestinal encephalomyopathy
  • p.Gly298Asp Multiple submitters mitochondrial DNA depletion syndrome 1
  • p.Leu270Pro Multiple submitters mitochondrial DNA depletion syndrome 1
  • p.Lys222Arg Multiple submitters mitochondrial neurogastrointestinal encephalomyopathy ⚠
  • p.Met173Arg Multiple submitters mitochondrial DNA depletion syndrome 1 ⚠
  • p.Met173fs Multiple submitters TYMP-related disorder
  • p.Pro131Ser Multiple submitters mitochondrial DNA depletion syndrome 1
  • c.207_214+6del Single submitter mitochondrial DNA depletion syndrome 1
  • c.214+1G>C Single submitter mitochondrial DNA depletion syndrome 1
  • c.214+2T>C Single submitter mitochondrial DNA depletion syndrome 1
  • c.418-1G>T Single submitter mitochondrial neurogastrointestinal encephalomyopathy
  • c.516+1G>C Single submitter
  • c.516+1G>T Single submitter
  • c.646+2T>C Single submitter
  • c.765+1G>C Single submitter mitochondrial DNA depletion syndrome 1
  • c.765+2T>C Single submitter mitochondrial DNA depletion syndrome 1
  • c.766-1G>A Single submitter
  • c.766-1G>C Single submitter
  • c.766-2A>T Single submitter mitochondrial neurogastrointestinal encephalomyopathy
  • p.Arg202Thr Single submitter mitochondrial DNA depletion syndrome 1
  • p.Arg55fs Single submitter mitochondrial neurogastrointestinal encephalomyopathy
  • p.Asp114Glu Single submitter mitochondrial DNA depletion syndrome 1
  • p.Cys182fs Single submitter mitochondrial DNA depletion syndrome 1
  • p.Gln179Ter Single submitter mitochondrial DNA depletion syndrome 1
  • p.Gln245Ter Single submitter mitochondrial neurogastrointestinal encephalomyopathy
  • p.Gln24fs Single submitter mitochondrial neurogastrointestinal encephalomyopathy
  • p.Glu159Val Single submitter
  • p.Glu246Ter Single submitter mitochondrial DNA depletion syndrome 1
  • p.Glu250Ter Single submitter mitochondrial DNA depletion syndrome 1
  • p.Gly152Ter Single submitter mitochondrial DNA depletion syndrome 1
  • p.Leu277fs Single submitter mitochondrial DNA depletion syndrome 1
  • p.Leu285Arg Single submitter ⚠
  • p.Ser160Pro Single submitter mitochondrial DNA depletion syndrome 1
  • p.Ter483Gln Single submitter mitochondrial DNA depletion syndrome 1
  • p.Thr9fs Single submitter mitochondrial DNA depletion syndrome 1
  • p.Val185fs Single submitter mitochondrial DNA depletion syndrome 1
  • p.Val204fs Single submitter mitochondrial neurogastrointestinal encephalomyopathy
  • p.Val208Ala Single submitter ⚠
  • p.Val232fs Single submitter mitochondrial DNA depletion syndrome 1
  • p.Ala11fs No assertion criteria mitochondrial DNA depletion syndrome 1
  • p.Met173Lys No assertion criteria mitochondrial DNA depletion syndrome 1

Conflicting classifications of pathogenicity 33

  • c.516+10G>A Single submitter mitochondrial DNA depletion syndrome 1
  • c.516+14C>T Single submitter mitochondrial DNA depletion syndrome 1
  • c.516+4C>T Single submitter
  • c.517-14G>A Single submitter
  • c.517-15G>A Single submitter mitochondrial DNA depletion syndrome 1
  • c.646+8G>A Single submitter mitochondrial DNA depletion syndrome 1
  • c.647-8C>T Single submitter mitochondrial DNA depletion syndrome 1
  • c.647-9C>G Single submitter mitochondrial DNA depletion syndrome 1
  • c.*3C>T Single submitter mitochondrial DNA depletion syndrome 1
  • p.Ala201Asp Single submitter ⚠
  • p.Ala252= Single submitter mitochondrial DNA depletion syndrome 1
  • p.Ala272Thr Single submitter ⚠
  • p.Ala2Val Single submitter Inborn genetic diseases ⚠
  • p.Arg146His Single submitter mitochondrial DNA depletion syndrome 1 ⚠
  • p.Gln481= Single submitter mitochondrial DNA depletion syndrome 1
  • p.Glu286= Single submitter mitochondrial DNA depletion syndrome 1
  • p.Glu289Lys Single submitter mitochondrial DNA depletion syndrome 1 ⚠
  • p.Glu379= Single submitter mitochondrial DNA depletion syndrome 1
  • p.Gly10Arg Single submitter Inborn genetic diseases ⚠
  • p.Gly119Arg Single submitter ⚠
  • p.Gly120Ser Single submitter ⚠
  • p.Gly137= Single submitter
  • p.Gly137Val Single submitter Inborn genetic diseases ⚠
  • p.Gly226Arg Single submitter Inborn genetic diseases ⚠
  • p.Gly64Arg Single submitter Inborn genetic diseases ⚠
  • p.Leu285Pro Single submitter mitochondrial neurogastrointestinal encephalomyopathy ⚠
  • p.Leu292Val Single submitter Inborn genetic diseases ⚠
  • p.Leu447fs Single submitter mitochondrial DNA depletion syndrome 1
  • p.Lys43Thr Single submitter mitochondrial DNA depletion syndrome 1 ⚠
  • p.Pro131Thr Single submitter mitochondrial DNA depletion syndrome 1 ⚠
  • p.Ser144= Single submitter mitochondrial DNA depletion syndrome 1
  • p.Ser65Asn Single submitter mitochondrial DNA depletion syndrome 1 ⚠
  • p.Ser65Gly Single submitter mitochondrial DNA depletion syndrome 1 ⚠

Benign 21

Benign/Likely benign 4

  • c.1301-12dup Multiple submitters
  • c.516+9C>T Multiple submitters mitochondrial neurogastrointestinal encephalomyopathy
  • p.Gln245= Multiple submitters mitochondrial neurogastrointestinal encephalomyopathy
  • p.Thr207= Multiple submitters

Likely benign 266

Uncertain significance 130