BCKDK — 188 ClinVar variants

All ClinVar germline BCKDK variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 86 flagged for review →

7 Pathogenic · 9 Likely pathogenic · 8 Conflicting · 5 Benign · 2 Benign/Likely benign · 63 Likely benign · 94 Uncertain significance

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

⚑ Evidence disagreements 86

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 1

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

Predictors lean, ClinVar uncertain 58

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

Predictors split 26

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

All BCKDK variants

Pathogenic 7

  • p.Arg156Ter Multiple submitters branched-chain keto acid dehydrogenase kinase deficiency
  • p.Asn119fs Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • p.Ile116Asn Single submitter BCKDK-related disorder
  • p.Leu17fs Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • c.264+1G>C No assertion criteria branched-chain keto acid dehydrogenase kinase deficiency
  • p.Arg224Pro No assertion criteria branched-chain keto acid dehydrogenase kinase deficiency
  • p.Met74fs No assertion criteria branched-chain keto acid dehydrogenase kinase deficiency

Likely pathogenic 9

  • c.543+1G>A Single submitter maple syrup urine disease type 1A
  • p.Arg312Ser Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • p.Arg327Trp Single submitter branched-chain keto acid dehydrogenase kinase deficiency ⚠
  • p.Gln145Ter Single submitter
  • p.Thr35fs Single submitter BCKDK-related disorder
  • p.Tyr151Ter Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • p.Tyr293Ter Single submitter
  • p.Asp216fs No assertion criteria intellectual disability
  • p.Leu389fs No assertion criteria branched-chain keto acid dehydrogenase kinase deficiency

Conflicting classifications of pathogenicity 8

  • p.Arg374Trp Single submitter BCKDK-related disorder ⚠
  • p.Arg406= Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • p.Asp395= Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • p.Gln387Ter Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • p.Leu241= Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • p.Phe368= Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • p.Ser356Cys Single submitter branched-chain keto acid dehydrogenase kinase deficiency ⚠
  • p.Thr223= Single submitter

Benign 5

  • c.716+147C>T Multiple submitters
  • c.845+10C>T Multiple submitters branched-chain keto acid dehydrogenase kinase deficiency
  • c.845+31C>T Multiple submitters
  • p.Thr205= Multiple submitters branched-chain keto acid dehydrogenase kinase deficiency
  • p.Asp83= Single submitter branched-chain keto acid dehydrogenase kinase deficiency

Benign/Likely benign 2

  • c.544-10C>T Multiple submitters branched-chain keto acid dehydrogenase kinase deficiency
  • p.Ala61Ser Multiple submitters branched-chain keto acid dehydrogenase kinase deficiency

Likely benign 63

  • c.196-14del Multiple submitters branched-chain keto acid dehydrogenase kinase deficiency
  • c.717-15C>T Multiple submitters branched-chain keto acid dehydrogenase kinase deficiency
  • c.717-4G>A Multiple submitters branched-chain keto acid dehydrogenase kinase deficiency
  • p.Arg187= Multiple submitters branched-chain keto acid dehydrogenase kinase deficiency
  • p.Gly22= Multiple submitters branched-chain keto acid dehydrogenase kinase deficiency
  • p.His211= Multiple submitters branched-chain keto acid dehydrogenase kinase deficiency
  • p.Ile320= Multiple submitters branched-chain keto acid dehydrogenase kinase deficiency
  • p.Ser196= Multiple submitters branched-chain keto acid dehydrogenase kinase deficiency
  • p.Val218= Multiple submitters branched-chain keto acid dehydrogenase kinase deficiency
  • p.Val307= Multiple submitters
  • p.Val40= Multiple submitters branched-chain keto acid dehydrogenase kinase deficiency
  • c.1094+7C>A Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • c.195+10G>A Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • c.195+20G>A Single submitter
  • c.195+6dup Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • c.196-4C>T Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • c.196-8del Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • c.375+14G>A Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • c.376-13C>T Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • c.423+16G>C Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • c.423+9_423+10insCTTCCCTCC Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • c.424-18T>C Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • c.424-20C>T Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • c.543+7G>T Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • c.544-8C>G Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • c.716+18C>T Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • c.716+19_716+20del Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • c.717-14G>A Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • c.717-5C>T Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • c.846-8C>T Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • c.936-10A>G Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • c.936-11C>A Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • p.Ala24Thr Single submitter Inborn genetic diseases
  • p.Ala26= Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • p.Ala377= Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • p.Arg18= Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • p.Arg399= Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • p.Arg411= Single submitter
  • p.Asp324= Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • p.Asp404= Single submitter
  • p.Cys152= Single submitter
  • p.Gly172= Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • p.Gly357= Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • p.His124= Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • p.His355= Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • p.Ile403= Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • p.Leu128= Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • p.Leu173= Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • p.Leu185= Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • p.Leu76= Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • p.Leu88= Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • p.Pro11= Single submitter
  • p.Pro113= Single submitter
  • p.Pro215= Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • p.Pro274= Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • p.Ser356= Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • p.Ser5= Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • p.Thr372= Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • p.Thr394= Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • p.Thr73= Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • p.Val299= Single submitter branched-chain keto acid dehydrogenase kinase deficiency
  • c.642+10T>A No assertion criteria BCKDK-related disorder
  • c.845+6G>A No assertion criteria BCKDK-related disorder

Uncertain significance 94