L2HGDH — 336 ClinVar variants

All ClinVar germline L2HGDH variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 149 flagged for review →

25 Pathogenic · 7 Pathogenic/Likely pathogenic · 12 Likely pathogenic · 18 Conflicting · 20 Benign · 12 Benign/Likely benign · 90 Likely benign · 152 Uncertain significance

Full L2HGDH gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 149

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 12

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

Predictors lean, ClinVar uncertain 113

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

Predictors split 24

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

All L2HGDH variants

Pathogenic 25

  • p.Arg251Ter Multiple submitters L-2-hydroxyglutaric aciduria
  • p.Arg277Ter Multiple submitters L2HGDH-related disorders
  • p.Arg70Ter Multiple submitters L-2-hydroxyglutaric aciduria
  • p.Asp320fs Multiple submitters L-2-hydroxyglutaric aciduria
  • p.Met1Val Multiple submitters Inborn genetic diseases
  • p.Met372fs Multiple submitters L-2-hydroxyglutaric aciduria
  • p.Pro177fs Multiple submitters L-2-hydroxyglutaric aciduria
  • p.Tyr301Ter Multiple submitters L-2-hydroxyglutaric aciduria
  • c.1065-13_1196+207del Single submitter L-2-hydroxyglutaric aciduria
  • c.256+2T>A Single submitter L-2-hydroxyglutaric aciduria
  • c.408+1G>C Single submitter L-2-hydroxyglutaric aciduria
  • p.Ala361fs Single submitter L-2-hydroxyglutaric aciduria
  • p.Arg339fs Single submitter L-2-hydroxyglutaric aciduria
  • p.Gln143Ter Single submitter L-2-hydroxyglutaric aciduria
  • p.Gln237Ter Single submitter L-2-hydroxyglutaric aciduria
  • p.Glu268Ter Single submitter L-2-hydroxyglutaric aciduria
  • p.Gly156fs Single submitter L-2-hydroxyglutaric aciduria
  • p.Gly55Asp Single submitter L-2-hydroxyglutaric aciduria
  • p.Gly57Arg Single submitter L-2-hydroxyglutaric aciduria
  • p.Gly60Arg Single submitter L-2-hydroxyglutaric aciduria
  • p.Lys81fs Single submitter L-2-hydroxyglutaric aciduria
  • p.Lys81Glu Single submitter L-2-hydroxyglutaric aciduria
  • p.Phe315fs Single submitter L-2-hydroxyglutaric aciduria
  • c.140+726del No assertion criteria L-2-hydroxyglutaric aciduria
  • c.906+1G>T No assertion criteria L-2-hydroxyglutaric aciduria

Pathogenic/Likely pathogenic 7

  • c.256+1G>A Multiple submitters L-2-hydroxyglutaric aciduria
  • p.Ala140Pro Multiple submitters L-2-hydroxyglutaric aciduria
  • p.Arg335Ter Multiple submitters L-2-hydroxyglutaric aciduria
  • p.Glu176Asp Multiple submitters L-2-hydroxyglutaric aciduria
  • p.His98Arg Multiple submitters L-2-hydroxyglutaric aciduria
  • p.Pro302Leu Multiple submitters L-2-hydroxyglutaric aciduria
  • p.Tyr285fs Multiple submitters L-2-hydroxyglutaric aciduria

Likely pathogenic 12

Conflicting classifications of pathogenicity 18

Benign 20

Benign/Likely benign 12

  • c.409-15dup Multiple submitters L-2-hydroxyglutaric aciduria
  • c.409-5del Multiple submitters L-2-hydroxyglutaric aciduria
  • c.703+12T>C Multiple submitters L-2-hydroxyglutaric aciduria
  • p.Arg33Ser Multiple submitters L-2-hydroxyglutaric aciduria
  • p.Glu170= Multiple submitters L-2-hydroxyglutaric aciduria
  • p.Gly451= Multiple submitters L-2-hydroxyglutaric aciduria
  • p.Ile53= Multiple submitters L-2-hydroxyglutaric aciduria
  • p.Leu112= Multiple submitters L-2-hydroxyglutaric aciduria
  • p.Leu18Arg Multiple submitters L-2-hydroxyglutaric aciduria
  • p.Pro280= Multiple submitters L-2-hydroxyglutaric aciduria
  • p.Tyr367Cys Multiple submitters L-2-hydroxyglutaric aciduria ⚠
  • p.Val2= Multiple submitters L-2-hydroxyglutaric aciduria

Likely benign 90

  • c.1064+5C>T Multiple submitters L-2-hydroxyglutaric aciduria
  • c.1065-14T>G Multiple submitters L-2-hydroxyglutaric aciduria
  • p.Ala20= Multiple submitters
  • p.Ala329= Multiple submitters L-2-hydroxyglutaric aciduria
  • p.Asp284= Multiple submitters L-2-hydroxyglutaric aciduria
  • p.Cys252= Multiple submitters L-2-hydroxyglutaric aciduria
  • p.Gly221= Multiple submitters L-2-hydroxyglutaric aciduria
  • p.Gly400= Multiple submitters L-2-hydroxyglutaric aciduria
  • p.Ile240= Multiple submitters L-2-hydroxyglutaric aciduria
  • p.Leu200= Multiple submitters L-2-hydroxyglutaric aciduria
  • p.Ser23= Multiple submitters L-2-hydroxyglutaric aciduria
  • p.Thr245= Multiple submitters L-2-hydroxyglutaric aciduria
  • p.Thr46Ile Multiple submitters L-2-hydroxyglutaric aciduria
  • p.Val213= Multiple submitters L-2-hydroxyglutaric aciduria
  • c.1064+13_1064+16del Single submitter L-2-hydroxyglutaric aciduria
  • c.1064+19A>G Single submitter
  • c.1196+16A>C Single submitter L-2-hydroxyglutaric aciduria
  • c.1196+20A>C Single submitter L-2-hydroxyglutaric aciduria
  • c.1197-11T>C Single submitter L-2-hydroxyglutaric aciduria
  • c.1197-17A>T Single submitter L-2-hydroxyglutaric aciduria
  • c.1197-20C>T Single submitter L-2-hydroxyglutaric aciduria
  • c.140+11G>A Single submitter L-2-hydroxyglutaric aciduria
  • c.140+17C>G Single submitter L-2-hydroxyglutaric aciduria
  • c.140+570C>T Single submitter
  • c.141-14A>G Single submitter L-2-hydroxyglutaric aciduria
  • c.141-15G>T Single submitter L-2-hydroxyglutaric aciduria
  • c.141-16T>A Single submitter L-2-hydroxyglutaric aciduria
  • c.257-9G>C Single submitter L-2-hydroxyglutaric aciduria
  • c.408+13del Single submitter L-2-hydroxyglutaric aciduria
  • c.408+15T>C Single submitter L-2-hydroxyglutaric aciduria
  • c.408+7C>T Single submitter L-2-hydroxyglutaric aciduria
  • c.409-13T>A Single submitter
  • c.409-19T>C Single submitter
  • c.409-20T>C Single submitter L-2-hydroxyglutaric aciduria
  • c.409-4G>T Single submitter L-2-hydroxyglutaric aciduria
  • c.409-6_409-5del Single submitter Inborn genetic diseases
  • c.540+19G>A Single submitter L-2-hydroxyglutaric aciduria
  • c.540+20A>G Single submitter L-2-hydroxyglutaric aciduria
  • c.541-12A>C Single submitter L-2-hydroxyglutaric aciduria
  • c.541-15A>G Single submitter L-2-hydroxyglutaric aciduria
  • c.703+13del Single submitter L-2-hydroxyglutaric aciduria
  • c.738+16C>A Single submitter L-2-hydroxyglutaric aciduria
  • c.739-12A>G Single submitter L-2-hydroxyglutaric aciduria
  • c.739-20_739-19del Single submitter L-2-hydroxyglutaric aciduria
  • c.739-5A>G Single submitter L-2-hydroxyglutaric aciduria
  • c.906+18C>T Single submitter L-2-hydroxyglutaric aciduria
  • c.906+7A>G Single submitter L-2-hydroxyglutaric aciduria
  • c.907-13G>A Single submitter L-2-hydroxyglutaric aciduria
  • c.907-22_907-20del Single submitter L-2-hydroxyglutaric aciduria
  • c.*2413G>A Single submitter
  • c.*4056C>T Single submitter
  • p.Ala118= Single submitter L-2-hydroxyglutaric aciduria
  • p.Ala151= Single submitter L-2-hydroxyglutaric aciduria
  • p.Ala26= Single submitter L-2-hydroxyglutaric aciduria
  • p.Ala30= Single submitter L-2-hydroxyglutaric aciduria
  • p.Asp410= Single submitter L-2-hydroxyglutaric aciduria
  • p.Cys12= Single submitter L-2-hydroxyglutaric aciduria
  • p.Cys179= Single submitter L-2-hydroxyglutaric aciduria
  • p.Cys272= Single submitter L-2-hydroxyglutaric aciduria
  • p.Gln126= Single submitter L-2-hydroxyglutaric aciduria
  • p.Gln133= Single submitter L-2-hydroxyglutaric aciduria
  • p.Gly135= Single submitter L-2-hydroxyglutaric aciduria
  • p.Gly211= Single submitter
  • p.Gly326= Single submitter L-2-hydroxyglutaric aciduria
  • p.Gly413= Single submitter
  • p.Gly56= Single submitter L-2-hydroxyglutaric aciduria
  • p.His88= Single submitter L-2-hydroxyglutaric aciduria
  • p.Ile250= Single submitter L-2-hydroxyglutaric aciduria
  • p.Leu152= Single submitter
  • p.Leu166= Single submitter L-2-hydroxyglutaric aciduria
  • p.Leu269= Single submitter L-2-hydroxyglutaric aciduria
  • p.Leu37= Single submitter L-2-hydroxyglutaric aciduria
  • p.Leu69= Single submitter L-2-hydroxyglutaric aciduria
  • p.Lys174= Single submitter L-2-hydroxyglutaric aciduria
  • p.Phe461= Single submitter L-2-hydroxyglutaric aciduria
  • p.Pro105= Single submitter L-2-hydroxyglutaric aciduria
  • p.Pro162= Single submitter L-2-hydroxyglutaric aciduria
  • p.Pro177= Single submitter L-2-hydroxyglutaric aciduria
  • p.Pro3= Single submitter
  • p.Pro304= Single submitter L-2-hydroxyglutaric aciduria
  • p.Pro72= Single submitter L-2-hydroxyglutaric aciduria
  • p.Ser201= Single submitter L-2-hydroxyglutaric aciduria
  • p.Ser23Phe Single submitter Inborn genetic diseases
  • p.Ser41= Single submitter L-2-hydroxyglutaric aciduria
  • p.Thr316= Single submitter L-2-hydroxyglutaric aciduria
  • p.Thr381= Single submitter L-2-hydroxyglutaric aciduria
  • p.Thr46= Single submitter L-2-hydroxyglutaric aciduria
  • p.Tyr178= Single submitter L-2-hydroxyglutaric aciduria
  • p.Tyr338= Single submitter L-2-hydroxyglutaric aciduria
  • p.Tyr373= Single submitter L-2-hydroxyglutaric aciduria

Uncertain significance 152