Sugi Variant

Sugi Variant/LDHA

LDHA — 249 ClinVar variants

All ClinVar germline LDHA variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 81 flagged for review →

6 Pathogenic · 2 Pathogenic/Likely pathogenic · 5 Likely pathogenic · 10 Conflicting · 32 Benign · 3 Benign/Likely benign · 75 Likely benign · 116 Uncertain significance

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

⚑ Evidence disagreements 81

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 1

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

Predictors agree, ClinVar conflicts 2

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

Predictors lean, ClinVar uncertain 63

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

Predictors split 15

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

All LDHA variants

Pathogenic 6

  • p.Ser137Ter Multiple submitters glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Arg169Ter Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Asn156fs Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Gln100Ter Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Leu211_Lys212insTer Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Leu254fs No assertion criteria glycogen storage disease due to lactate dehydrogenase M-subunit deficiency

Pathogenic/Likely pathogenic 2

  • p.Glu229fs Multiple submitters glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Leu214fs Multiple submitters glycogen storage disease due to lactate dehydrogenase M-subunit deficiency

Likely pathogenic 5

  • c.126+2T>C Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.419-1G>C Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.593-1del Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.710+1del Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Asp82Asn Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠

Conflicting classifications of pathogenicity 10

  • p.Ala147Ser Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Glu61= Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Lys232Asn Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Lys90Arg Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Thr74= Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Thr95= Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Tyr281= Single submitter Inborn genetic diseases
  • p.Tyr83= Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Val136Ile Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Val270= Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency

Benign 32

Benign/Likely benign 3

  • c.*243C>G Multiple submitters glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Leu259= Multiple submitters glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Lys317= Multiple submitters glycogen storage disease due to lactate dehydrogenase M-subunit deficiency

Likely benign 75

  • c.126+170A>G Multiple submitters
  • c.126+213G>A Multiple submitters
  • c.127-14T>C Multiple submitters glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.419-17T>C Multiple submitters
  • c.419-277G>C Multiple submitters
  • c.711-275G>A Multiple submitters
  • c.711-8T>A Multiple submitters glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.835-14C>T Multiple submitters glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.-24-10C>G Multiple submitters glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.His186= Multiple submitters glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Ile54= Multiple submitters glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Val198= Multiple submitters glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.126+10_126+11del Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.126+17C>T Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.127-6T>C Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.245-11C>T Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.245-17A>G Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.418+13A>C Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.419-16T>G Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.592+17T>G Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.592+7A>C Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.593-11A>G Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.593-20G>A Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.593-302G>A Single submitter
  • c.593-7C>A Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.710+11T>G Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.710+14C>G Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.710+16A>T Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.710+19T>C Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.711-13del Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.711-19A>G Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.711-276T>C Single submitter
  • c.711-8T>C Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.834+15T>C Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.834+20C>T Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.835-14_835-11del Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.835-19_835-15dup Single submitter
  • c.835-8A>C Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.-24-17T>C Single submitter
  • c.-24-608G>T Single submitter
  • c.-24-640A>T Single submitter
  • c.*15A>G Single submitter
  • c.*582C>T Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.*89T>C Single submitter
  • p.Ala314= Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Arg269= Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Asn113= Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Asp46= Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Gln100= Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Glu311= Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Gly325= Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Gly97= Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.His181= Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Ile294= Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Ile77= Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Leu109= Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Leu13= Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Leu218= Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Leu244= Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Leu254= Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Leu58= Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Leu91= Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Lys224= Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Phe332_Ter333insTer Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Pro19= Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Pro272= Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Ser105= Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Thr322= Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Tyr145= Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Val241= Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Val256= Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Val287= Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Val31= Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.835-15del No assertion criteria
  • c.*41C>T No assertion criteria LDHA-related disorder

Uncertain significance 116

  • c.126+3_126+6del Multiple submitters glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.*660C>T Multiple submitters glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Arg112Cys Multiple submitters glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Arg157His Multiple submitters glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Asp285Val Multiple submitters glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Asp46Val Multiple submitters glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Ile159Asn Multiple submitters glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Lys149Glu Multiple submitters glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Ser274Phe Multiple submitters Inborn genetic diseases ⚠
  • p.Thr18Ala Multiple submitters Inborn genetic diseases ⚠
  • p.Thr18Ile Multiple submitters glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Thr18Ser Multiple submitters glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Thr322Ile Multiple submitters Inborn genetic diseases ⚠
  • p.Thr3Ile Multiple submitters glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Thr95Met Multiple submitters ⚠
  • p.Val124Ala Multiple submitters glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Val146Met Multiple submitters Inborn genetic diseases ⚠
  • p.Val256Ile Multiple submitters Inborn genetic diseases ⚠
  • c.592+7A>G Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.710+5T>C Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.711-3C>T Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.711-6A>T Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.-64T>C Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.*129A>G Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.*175C>T Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.*18T>C Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.*228G>A Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.*253G>A Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.*311C>T Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.*312G>A Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.*48C>T Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.*501C>A Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.*52G>T Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.*586A>G Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.*604A>T Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.*666C>T Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.*694C>T Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.*706G>A Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.*725T>G Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.*745T>C Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.*762T>G Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.*817A>C Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.*835A>G Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • c.*914A>G Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Ala260Pro Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Ala314Pro Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Ala314Val Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Ala320Thr Single submitter ⚠
  • p.Ala49Asp Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Arg112His Single submitter Inborn genetic diseases ⚠
  • p.Arg112Pro Single submitter ⚠
  • p.Arg171His Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Arg171Pro Single submitter ⚠
  • p.Arg268Lys Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Arg315Cys Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Arg315His Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Arg73Gly Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Arg99His Single submitter Inborn genetic diseases ⚠
  • p.Asn11Ser Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Asn266His Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Asn88Asp Single submitter ⚠
  • p.Asp46Leu Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Cys131Ser Single submitter Inborn genetic diseases
  • p.Gln111Arg Single submitter Inborn genetic diseases ⚠
  • p.Gln111Glu Single submitter Inborn genetic diseases ⚠
  • p.Glu16Gly Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Glu240Gly Single submitter Inborn genetic diseases ⚠
  • p.Glu55Lys Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Gly103Arg Single submitter Inborn genetic diseases ⚠
  • p.Gly103Glu Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Gly152Arg Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Gly162Ser Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Gly208Arg Single submitter Inborn genetic diseases ⚠
  • p.Gly282Arg Single submitter Inborn genetic diseases ⚠
  • p.Gly60Arg Single submitter Inborn genetic diseases ⚠
  • p.His186Tyr Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Ile159Thr Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Ile39Met Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Ile94Phe Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Leu165Met Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Lys132Asn Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Lys278Thr Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Lys318Thr Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Lys328= Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Lys42= Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Lys57Arg Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Met41Val Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Met63Ile Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Pro129Arg Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Pro129Leu Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Pro139Leu Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Pro154Ser Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Ser184Gly Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Ser255fs Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Ser69Arg Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Thr275Ala Single submitter Inborn genetic diseases ⚠
  • p.Thr275Ile Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Thr275Ser Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Thr309Pro Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Thr3Ala Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Tyr10= Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Tyr145Asn Single submitter Inborn genetic diseases ⚠
  • p.Tyr83Cys Single submitter Inborn genetic diseases ⚠
  • p.Val110Ile Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Val114Met Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Val125del Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Val180Phe Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Val256Leu Single submitter Inborn genetic diseases ⚠
  • p.Val270Ala Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Val270Leu Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Val28Ala Single submitter glycogen storage disease due to lactate dehydrogenase M-subunit deficiency ⚠
  • p.Val306Glu Single submitter Inborn genetic diseases ⚠
  • c.-24-260dup No assertion criteria
  • p.Gln226_Trp227insTer No assertion criteria
  • p.Glu329Ter No assertion criteria glycogen storage disease due to lactate dehydrogenase M-subunit deficiency
  • p.Leu190Phe No assertion criteria ⚠