Sugi Variant

Sugi Variant/PDK3

PDK3 — 228 ClinVar variants

All ClinVar germline PDK3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 78 flagged for review →

10 Conflicting · 37 Benign · 6 Benign/Likely benign · 78 Likely benign · 97 Uncertain significance

Full PDK3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 78

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 48

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

Predictors split 22

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

All PDK3 variants

Conflicting classifications of pathogenicity 10

  • c.249-15T>C Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Ala227Val Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Arg158His Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Arg162His Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Asn224Ser Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Asp175Asn Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Lys114Thr Single submitter Charcot-Marie-Tooth disease ⚠
  • p.Lys14Asn Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Met126Val Single submitter Charcot-Marie-Tooth disease ⚠
  • p.Pro102Ser Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠

Benign 37

Benign/Likely benign 6

  • c.1077+8G>A Multiple submitters Charcot-Marie-Tooth disease X-linked dominant 6
  • c.249-9dup Multiple submitters Charcot-Marie-Tooth disease
  • c.674-11T>C Multiple submitters Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Lys410Gln Multiple submitters Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Pro68= Multiple submitters Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Tyr94= Multiple submitters Charcot-Marie-Tooth disease X-linked dominant 6

Likely benign 78

  • c.751-10A>G Multiple submitters Charcot-Marie-Tooth disease
  • c.963+16T>C Multiple submitters Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Arg158= Multiple submitters Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Gly266= Multiple submitters Charcot-Marie-Tooth disease X-linked dominant 6
  • p.His379= Multiple submitters Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Ile187= Multiple submitters Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Leu112= Multiple submitters Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Leu361= Multiple submitters Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Ser375= Multiple submitters Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Thr176= Multiple submitters Charcot-Marie-Tooth disease X-linked dominant 6
  • c.106+11G>A Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.106+14C>G Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.106+18G>A Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.106+18G>C Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.107-12A>T Single submitter
  • c.1077+13_1077+16del Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.1077+217C>T Single submitter
  • c.1077+7C>A Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.1077+7C>T Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.1078-3_1078-2dup Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.249-14T>G Single submitter Charcot-Marie-Tooth disease
  • c.249-8C>T Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.321-11C>T Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.321-8T>A Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.506-142C>T Single submitter
  • c.506-6G>C Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.506-7C>T Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.595+11C>T Single submitter
  • c.595+12G>A Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.595+20G>A Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.596-4G>A Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.596-7C>T Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.673+10A>G Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.674-13T>C Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.674-18T>C Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.750+18A>G Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.750+20C>T Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.751-13C>A Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.852+18A>G Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.853-4G>A Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.963+14A>C Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.964-12T>C Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.964-13C>G Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.964-250A>T Single submitter
  • c.*5C>T Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.*7A>G Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.*9C>G Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Ala194= Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Ala255= Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Ala386= Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Ala399= Single submitter
  • p.Arg162= Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Arg332His Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Asn192= Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Asp229= Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Asp387= Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Gly173Trp Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Ile285= Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Leu109= Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Leu273= Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Leu333= Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Leu344= Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Leu66= Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Lys134= Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Ser365= Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Thr145= Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Thr156= Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Thr203= Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Thr272= Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Thr44= Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Thr60= Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Tyr260= Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Tyr345fs Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Tyr46= Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Val193= Single submitter
  • p.Val355= Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Val77= Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.249-11_249-9del No assertion criteria PDK3-related disorder

Uncertain significance 97

  • c.320+6T>C Multiple submitters Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Ala360Val Multiple submitters Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Arg378Cys Multiple submitters Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Asp188Asn Multiple submitters Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Ile113Thr Multiple submitters Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Leu112Pro Multiple submitters Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Pro141Leu Multiple submitters Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Pro231Arg Multiple submitters Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Ser98Asn Multiple submitters Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Thr156Ile Multiple submitters Charcot-Marie-Tooth disease ⚠
  • p.Tyr236Cys Multiple submitters Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • c.106+14_106+15dup Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.1077+2T>G Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.1077+4C>T Single submitter Charcot-Marie-Tooth disease
  • c.248+3A>G Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.321-3C>T Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.505+3A>T Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.595+3A>G Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.674-5T>G Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.964-4A>G Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • c.*2A>G Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Ala255Val Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Ala376Thr Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Ala404Val Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Arg158Gly Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Arg295= Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Arg299Cys Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Arg299His Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Arg50Gln Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Arg5Trp Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Arg62Gly Single submitter ⚠
  • p.Arg74Cys Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Arg74His Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Asn73fs Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Asp101Gly Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Asp106Asn Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Asp199fs Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Asp199Gly Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Asp387Asn Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Asp398Gly Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Gln103Arg Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Gln128Glu Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Gln128Lys Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Gln406fs Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Glu17Gln Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Glu247Ala Single submitter ⚠
  • p.Glu279Gly Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Glu314Ter Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Gly174fs Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Gly185Glu Single submitter ⚠
  • p.Gly325Val Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.His119Tyr Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Ile131Thr Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Ile143Val Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Ile232Thr Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Ile29Asn Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Ile356Val Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Ile409Met Single submitter
  • p.Leu288Pro Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Leu369Pro Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Leu66Arg Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Leu66Val Single submitter ⚠
  • p.Leu8Pro Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Lys114Glu Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Lys271Glu Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Lys343Thr Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Lys401Arg Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Lys405Glu Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Met163Val Single submitter ⚠
  • p.Met347Val Single submitter ⚠
  • p.Phe366Cys Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Phe372Ter Single submitter Charcot-Marie-Tooth disease
  • p.Pro181Leu Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Pro26Leu Single submitter ⚠
  • p.Pro396Leu Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Pro54fs Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Pro54Ser Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Pro68Leu Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Pro75Leu Single submitter
  • p.Pro75Thr Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Ser363fs Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Ser45del Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Ter407ValextTer? Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Thr145Ser Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Thr203Arg Single submitter Charcot-Marie-Tooth disease X-linked dominant 6
  • p.Thr316Ala Single submitter ⚠
  • p.Thr383Met Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Trp389Ter Single submitter
  • p.Trp6Cys Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Tyr260Cys Single submitter ⚠
  • p.Tyr402Cys Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Tyr46Cys Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Val193Leu Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Val193Met Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Val234Ala Single submitter ⚠
  • p.Val274Ile Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠
  • p.Val274Phe Single submitter Charcot-Marie-Tooth disease X-linked dominant 6 ⚠