PDHX — 379 ClinVar variants

All ClinVar germline PDHX variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 143 flagged for review →

15 Pathogenic · 6 Pathogenic/Likely pathogenic · 12 Likely pathogenic · 20 Conflicting · 55 Benign · 11 Benign/Likely benign · 94 Likely benign · 166 Uncertain significance

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

⚑ Evidence disagreements 143

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 8

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

Predictors lean, ClinVar uncertain 105

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 PDHX variants

Pathogenic 15

  • p.Arg284Ter Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • p.Gln248Ter Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • c.1182+2T>C Single submitter pyruvate dehydrogenase E3-binding protein deficiency
  • c.965-1G>A Single submitter
  • p.Ala83_Val84insTer Single submitter
  • p.Cys307_Asp308delinsTer Single submitter
  • p.Cys438fs Single submitter
  • p.Gly148fs Single submitter
  • p.Gly71Ter Single submitter
  • p.Pro376fs Single submitter pyruvate dehydrogenase E3-binding protein deficiency
  • c.1024-1G>A No assertion criteria pyruvate dehydrogenase E3-binding protein deficiency
  • c.1183-3088_1247+760del No assertion criteria pyruvate dehydrogenase E3-binding protein deficiency
  • c.641+1G>A No assertion criteria pyruvate dehydrogenase E3-binding protein deficiency
  • p.Asp322fs No assertion criteria pyruvate dehydrogenase E3-binding protein deficiency
  • p.Pro207fs No assertion criteria pyruvate dehydrogenase E3-binding protein deficiency

Pathogenic/Likely pathogenic 6

  • p.Arg446Ter Multiple submitters PDHX-related disorders
  • p.Gln411Ter Multiple submitters PDHX-related disorders
  • p.His140fs Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • p.Pro186fs Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • p.Thr238fs Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • p.Thr265fs Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency

Likely pathogenic 12

  • p.Arg476Ter Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • c.161-2A>G Single submitter
  • c.542+1G>C Single submitter
  • c.816+1G>A Single submitter
  • p.Gln436fs Single submitter Inborn genetic diseases
  • p.Ser264Ter Single submitter pyruvate dehydrogenase E3-binding protein deficiency
  • p.Ser63Ter Single submitter pyruvate dehydrogenase E3-binding protein deficiency
  • p.Val220fs Single submitter pyruvate dehydrogenase E3-binding protein deficiency
  • p.Val298fs Single submitter mitochondrial disease
  • p.Val338fs Single submitter pyruvate dehydrogenase E3-binding protein deficiency
  • p.Val431Ala Single submitter pyruvate dehydrogenase E3-binding protein deficiency
  • c.-48del No assertion criteria pyruvate dehydrogenase E1-alpha deficiency

Conflicting classifications of pathogenicity 20

  • c.161-6T>C Single submitter pyruvate dehydrogenase E3-binding protein deficiency
  • c.242-4G>A Single submitter pyruvate dehydrogenase E3-binding protein deficiency
  • c.343-7A>C Single submitter
  • c.542+10T>C Single submitter pyruvate dehydrogenase E3-binding protein deficiency
  • p.Arg464His Single submitter Inborn genetic diseases ⚠
  • p.Arg499Gln Single submitter Inborn genetic diseases ⚠
  • p.Asn270Ser Single submitter Inborn genetic diseases ⚠
  • p.Asn419Ser Single submitter ⚠
  • p.Gln248Glu Single submitter pyruvate dehydrogenase E3-binding protein deficiency ⚠
  • p.Glu134= Single submitter pyruvate dehydrogenase E3-binding protein deficiency
  • p.Glu193= Single submitter pyruvate dehydrogenase E3-binding protein deficiency
  • p.Glu214Gln Single submitter Inborn genetic diseases ⚠
  • p.Gly273fs Single submitter pyruvate dehydrogenase E3-binding protein deficiency
  • p.Gly413= Single submitter
  • p.Leu197Met Single submitter pyruvate dehydrogenase E3-binding protein deficiency ⚠
  • p.Lys488Glu Single submitter Inborn genetic diseases ⚠
  • p.Ser245Leu Single submitter ⚠
  • p.Thr225Met Single submitter pyruvate dehydrogenase E3-binding protein deficiency ⚠
  • p.Thr234= Single submitter pyruvate dehydrogenase E3-binding protein deficiency
  • p.Thr250Ile Single submitter pyruvate dehydrogenase E3-binding protein deficiency ⚠

Benign 55

  • c.1023+132G>A Multiple submitters
  • c.1023+16C>G Multiple submitters
  • c.1023+18A>G Multiple submitters
  • c.1024-53C>T Multiple submitters
  • c.1182+190A>T Multiple submitters
  • c.1182+245A>G Multiple submitters
  • c.160+189A>G Multiple submitters
  • c.241+24C>A Multiple submitters
  • c.241+3G>A Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • c.241+57G>T Multiple submitters
  • c.343-39G>A Multiple submitters
  • c.641+4T>C Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • c.641+76G>A Multiple submitters
  • c.641+81T>G Multiple submitters
  • c.641+83C>A Multiple submitters
  • c.965-187G>T Multiple submitters
  • c.-124G>C Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • c.-129C>T Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • c.-202A>G Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • c.-272G>A Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • c.-302A>G Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • c.-319G>A Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • c.-390G>A Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • c.-505G>A Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • c.-506T>C Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • c.-717G>C Multiple submitters
  • c.-787G>A Multiple submitters
  • c.-840C>T Multiple submitters
  • c.-88C>A Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • c.*123A>G Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • c.*173G>A Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • c.*200T>C Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • c.*486G>T Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • c.*644C>A Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • c.*890T>C Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • p.Arg189His Multiple submitters ⚠
  • p.Asp146= Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • p.Ile113= Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • p.Ile169= Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • p.Leu319= Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • p.Leu396= Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • p.Pro177= Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • p.Pro266= Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • p.Thr101Ala Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • p.Val286= Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • c.1024-215A>T Single submitter
  • c.161-10del Single submitter
  • c.241+56dup Single submitter
  • c.241+68dup Single submitter
  • c.342+119dup Single submitter
  • c.542+157del Single submitter
  • c.542+192C>T Single submitter
  • c.641+168A>G Single submitter
  • c.965-319A>T Single submitter
  • c.-131_-129delGGC Single submitter

Benign/Likely benign 11

  • c.161-10dup Multiple submitters
  • c.343-15_343-13del Multiple submitters
  • c.642-19A>G Multiple submitters
  • c.*27A>C Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • p.Ala501= Multiple submitters
  • p.Ala83= Multiple submitters
  • p.Arg444Lys Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • p.Glu158= Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • p.Gly206= Multiple submitters
  • p.Phe445Val Multiple submitters pyruvate dehydrogenase E3-binding protein deficiency
  • p.Val326Leu Multiple submitters pyruvate dehydrogenase E1-alpha deficiency

Likely benign 94

Uncertain significance 166