Sugi Variant

Sugi Variant/SCO2

SCO2 — 390 ClinVar variants

All ClinVar germline SCO2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 173 flagged for review →

24 Pathogenic · 10 Pathogenic/Likely pathogenic · 14 Likely pathogenic · 24 Conflicting · 4 Benign · 7 Benign/Likely benign · 129 Likely benign · 178 Uncertain significance

Full SCO2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 173

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 11

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

Predictors lean, ClinVar uncertain 136

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

Predictors split 25

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

All SCO2 variants

Pathogenic 24

Pathogenic/Likely pathogenic 10

  • p.Arg6fs Multiple submitters myopia 6
  • p.Arg90Ter Multiple submitters myopia 6
  • p.Gln122Ter Multiple submitters cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1
  • p.Gln161Ter Multiple submitters cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1
  • p.Gln16fs Multiple submitters cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1
  • p.Glu45fs Multiple submitters cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1
  • p.Gly193Ser Multiple submitters myopia 6
  • p.His109fs Multiple submitters cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1
  • p.Leu76fs Multiple submitters cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1
  • p.Pro134fs Multiple submitters cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1

Likely pathogenic 14

  • p.Met1Thr Multiple submitters cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1
  • p.Ser253fs Multiple submitters
  • p.Asp172fs Single submitter cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1
  • p.Glu170Ter Single submitter cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1
  • p.Gly42fs Single submitter cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1
  • p.His203fs Single submitter cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1
  • p.Leu188fs Single submitter cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1
  • p.Leu71fs Single submitter cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1
  • p.Pro169Thr Single submitter
  • p.Ser225fs Single submitter cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1
  • p.Ser251delinsGlyTer Single submitter cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1
  • p.Thr238Arg Single submitter SCO2-related disorder ⚠
  • p.Trp75Ter Single submitter
  • p.Val207fs Single submitter

Conflicting classifications of pathogenicity 24

  • c.-142G>C Single submitter cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1
  • p.Arg112Gln Single submitter Inborn genetic diseases ⚠
  • p.Arg114His Single submitter Inborn genetic diseases ⚠
  • p.Arg149Gln Single submitter Inborn genetic diseases ⚠
  • p.Arg171Gln Single submitter cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1 ⚠
  • p.Arg171Trp Single submitter cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1 ⚠
  • p.Arg255Trp Single submitter myopia 6 ⚠
  • p.Arg256Gln Single submitter Inborn genetic diseases ⚠
  • p.Arg60Trp Single submitter cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1 ⚠
  • p.Arg79= Single submitter mitochondrial DNA depletion syndrome 1
  • p.Asp252fs Single submitter cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1
  • p.Glu154Lys Single submitter Inborn genetic diseases ⚠
  • p.Gly48Arg Single submitter Inborn genetic diseases ⚠
  • p.Leu76= Single submitter cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1
  • p.Leu78_Arg79delinsGln Single submitter cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1
  • p.Leu94Pro Single submitter cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1 ⚠
  • p.Lys82del Single submitter cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1
  • p.Met1Ile Single submitter myopia 6
  • p.Phe67= Single submitter cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1
  • p.Ser246= Single submitter cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1
  • p.Ser251Leu Single submitter ⚠
  • p.Ser39Leu Single submitter Inborn genetic diseases ⚠
  • p.Ter267Ser Single submitter cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1
  • p.Tyr241= Single submitter mitochondrial complex IV deficiency, nuclear type 1

Benign 4

  • c.-14+522A>G Multiple submitters cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1
  • p.Ala211= Multiple submitters myopia 6
  • p.Arg20Pro Multiple submitters myopia 6
  • c.-135_-132dup Single submitter

Benign/Likely benign 7

  • p.Ala259Val Multiple submitters cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1
  • p.Arg179= Multiple submitters
  • p.Arg255= Multiple submitters cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1
  • p.Gln53= Multiple submitters
  • p.Glu152Asp Multiple submitters
  • p.His109= Multiple submitters cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1
  • p.Ser194= Multiple submitters cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1

Likely benign 129

Uncertain significance 178