Sugi Variant

Sugi Variant/ECHS1

ECHS1 — 370 ClinVar variants

All ClinVar germline ECHS1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 128 flagged for review →

24 Pathogenic · 13 Pathogenic/Likely pathogenic · 23 Likely pathogenic · 28 Conflicting · 37 Benign · 1 Benign/Likely benign · 140 Likely benign · 104 Uncertain significance

Full ECHS1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 128

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 14

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

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 45

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

Predictors split 61

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

All ECHS1 variants

Pathogenic 24

  • p.Ala2Val Multiple submitters mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency ⚠
  • p.Arg54His Multiple submitters mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency
  • p.Gln201Ter Multiple submitters mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency
  • p.Thr124fs Multiple submitters Inborn genetic diseases
  • c.414+2T>C Single submitter
  • c.619+1del Single submitter
  • p.Ala188Val Single submitter mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency
  • p.Ala84Thr Single submitter mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency ⚠
  • p.Arg181fs Single submitter
  • p.Arg25Pro Single submitter mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency ⚠
  • p.Arg41fs Single submitter
  • p.Asn286fs Single submitter mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency
  • p.Asp121fs Single submitter
  • p.Cys225Arg Single submitter mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency ⚠
  • p.Gln71Ter Single submitter
  • p.Ile66fs Single submitter
  • p.Met1Ile Single submitter
  • p.Met1Thr Single submitter
  • p.Met1Val Single submitter
  • c.414+3G>C No assertion criteria mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency
  • p.Ala138Val No assertion criteria mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency ⚠
  • p.Ala158Asp No assertion criteria mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency
  • p.Glu156Gly No assertion criteria mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency ⚠
  • p.Glu77Gln No assertion criteria mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency ⚠

Pathogenic/Likely pathogenic 13

  • c.414+1G>A Multiple submitters mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency
  • c.88+5G>A Multiple submitters mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency
  • p.Ala132Thr Multiple submitters mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency
  • p.Ala173Val Multiple submitters Inborn genetic diseases ⚠
  • p.Ala238Val Multiple submitters mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency ⚠
  • p.Arg54Cys Multiple submitters mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency
  • p.Asn59Ser Multiple submitters mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency
  • p.Gln159Arg Multiple submitters mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency ⚠
  • p.Gly42fs Multiple submitters mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency
  • p.Lys273Glu Multiple submitters Inborn genetic diseases ⚠
  • p.Met1Arg Multiple submitters mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency
  • p.Thr180Ala Multiple submitters mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency ⚠
  • p.Thr277Ile Multiple submitters mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency ⚠

Likely pathogenic 23

  • p.Ala278Thr Multiple submitters mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency
  • p.Ile66Thr Multiple submitters ECHS1-related disorder ⚠
  • p.Val47Met Multiple submitters
  • c.619+1G>T Single submitter mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency
  • c.89-2A>G Single submitter ECHS1-related disorder
  • p.Ala132Val Single submitter
  • p.Ala158Val Single submitter
  • p.Ala222Thr Single submitter ⚠
  • p.Ala226Thr Single submitter mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency
  • p.Ala3Asp Single submitter ⚠
  • p.Ala3Pro Single submitter ⚠
  • p.Ala60Gly Single submitter mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency
  • p.Ala96= Single submitter mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency
  • p.Arg197Trp Single submitter
  • p.Arg25Cys Single submitter mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency ⚠
  • p.Arg283Gly Single submitter mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency
  • p.Arg54Leu Single submitter
  • p.Asp202fs Single submitter mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency
  • p.Gln159His Single submitter ⚠
  • p.Ile167Thr Single submitter ⚠
  • p.Met1Leu Single submitter mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency
  • p.Tyr153Asn Single submitter mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency
  • p.Val19fs Single submitter mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency

Conflicting classifications of pathogenicity 28

  • c.286+4C>T Single submitter mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency
  • c.286+6C>T Single submitter
  • c.89-6C>G Single submitter Inborn genetic diseases
  • p.Ala138= Single submitter
  • p.Ala138Thr Single submitter ⚠
  • p.Ala173= Single submitter
  • p.Ala238Pro Single submitter ⚠
  • p.Ala247Val Single submitter mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency ⚠
  • p.Ala3Val Single submitter Inborn genetic diseases ⚠
  • p.Arg181Cys Single submitter mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency ⚠
  • p.Asn135Ser Single submitter mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency ⚠
  • p.Cys213Arg Single submitter mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency ⚠
  • p.Gln71= Single submitter mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency
  • p.Glu68Lys Single submitter mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency ⚠
  • p.Gly155Ser Single submitter Inborn genetic diseases ⚠
  • p.Gly175Ser Single submitter mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency ⚠
  • p.Gly90Arg Single submitter mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency ⚠
  • p.Leu8= Single submitter
  • p.Leu8Pro Single submitter mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency ⚠
  • p.Lys115Gln Single submitter Inborn genetic diseases ⚠
  • p.Phe279Ser Single submitter mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency ⚠
  • p.Pro163= Single submitter mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency
  • p.Pro163Leu Single submitter mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency ⚠
  • p.Thr266Ala Single submitter Inborn genetic diseases ⚠
  • p.Trp24Ter Single submitter mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency
  • p.Tyr137fs Single submitter Inborn genetic diseases
  • p.Tyr153Cys Single submitter ⚠
  • p.Val130Asp Single submitter mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency ⚠

Benign 37

Benign/Likely benign 1

  • c.808-17G>A Multiple submitters mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency

Likely benign 140

Uncertain significance 104