Sugi Variant

Sugi Variant/USP53

USP53 — 254 ClinVar variants

All ClinVar germline USP53 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 138 flagged for review →

20 Pathogenic · 2 Pathogenic/Likely pathogenic · 20 Likely pathogenic · 7 Conflicting · 20 Benign · 2 Benign/Likely benign · 47 Likely benign · 136 Uncertain significance

Full USP53 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 138

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 7

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

Predictors lean, ClinVar uncertain 109

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

Predictors split 21

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

All USP53 variants

Pathogenic 20

  • p.Arg338Ter Multiple submitters cholestasis
  • p.Arg520Ter Multiple submitters cholestasis, progressive familial intrahepatic, 7, with or without hearing loss
  • p.Ser563fs Multiple submitters cholestasis, progressive familial intrahepatic, 7, with or without hearing loss
  • c.373-1G>A Single submitter cholestasis, progressive familial intrahepatic, 7, with or without hearing loss
  • c.569+2T>C Single submitter cholestasis
  • p.Arg195fs Single submitter cholestasis
  • p.Arg57Ter Single submitter cholestasis
  • p.Arg8fs Single submitter
  • p.Arg99Ser Single submitter cholestasis
  • p.Gly37fs Single submitter
  • p.Gly70fs Single submitter
  • p.Ile650fs Single submitter
  • p.Lys407Ter Single submitter cholestasis, progressive familial intrahepatic, 7, with or without hearing loss
  • p.Phe317fs Single submitter cholestasis, progressive familial intrahepatic, 7, with or without hearing loss
  • p.Ser171fs Single submitter cholestasis, progressive familial intrahepatic, 7, with or without hearing loss
  • p.Ser357fs Single submitter cholestasis, progressive familial intrahepatic, 7, with or without hearing loss
  • p.Ser690fs Single submitter
  • p.Trp51Ter Single submitter cholestasis, progressive familial intrahepatic, 7, with or without hearing loss
  • p.Val279fs Single submitter cholestasis
  • p.Pro242Leu No assertion criteria cholestasis, progressive familial intrahepatic, 7, with or without hearing loss

Pathogenic/Likely pathogenic 2

  • p.Arg476Ter Multiple submitters cholestasis, progressive familial intrahepatic, 7, with or without hearing loss
  • p.Arg582Ter Multiple submitters cholestasis, progressive familial intrahepatic, 7, with or without hearing loss

Likely pathogenic 20

  • c.145-10_168del Multiple submitters cholestasis, progressive familial intrahepatic, 7, with or without hearing loss
  • c.822+1del Multiple submitters cholestasis, progressive familial intrahepatic, 7, with or without hearing loss
  • p.Arg111Ter Multiple submitters cholestasis, progressive familial intrahepatic, 7, with or without hearing loss
  • c.237+1G>A Single submitter cholestasis, progressive familial intrahepatic, 7, with or without hearing loss
  • c.570-1G>A Single submitter cholestasis, progressive familial intrahepatic, 7, with or without hearing loss
  • c.676-1G>C Single submitter USP53-related disorder
  • c.823-2del Single submitter
  • c.972+3_972+6del Single submitter cholestasis, progressive familial intrahepatic, 7, with or without hearing loss
  • c.973-1G>A Single submitter cholestasis, progressive familial intrahepatic, 7, with or without hearing loss
  • p.Ala27fs Single submitter cholestasis, progressive familial intrahepatic, 7, with or without hearing loss
  • p.Ala46Ser Single submitter cholestasis, progressive familial intrahepatic, 7, with or without hearing loss ⚠
  • p.Gln113fs Single submitter cholestasis, progressive familial intrahepatic, 7, with or without hearing loss
  • p.Gln69Ter Single submitter cholestasis, progressive familial intrahepatic, 7, with or without hearing loss
  • p.Gly293Val Single submitter cholestasis
  • p.His132Arg Single submitter cholestasis
  • p.Ile546fs Single submitter USP53-related disorder
  • p.Leu432fs Single submitter cholestasis, progressive familial intrahepatic, 7, with or without hearing loss
  • p.Leu53Ter Single submitter cholestasis, progressive familial intrahepatic, 7, with or without hearing loss
  • p.Trp3Ter Single submitter cholestasis, progressive familial intrahepatic, 7, with or without hearing loss
  • p.Tyr277fs Single submitter cholestasis, progressive familial intrahepatic, 7, with or without hearing loss

Conflicting classifications of pathogenicity 7

  • p.Asp568Tyr Single submitter cholestasis, progressive familial intrahepatic, 7, with or without hearing loss ⚠
  • p.Gly668Ser Single submitter cholestasis, progressive familial intrahepatic, 7, with or without hearing loss ⚠
  • p.Ile1014Thr Single submitter Inborn genetic diseases ⚠
  • p.Leu485Pro Single submitter Inborn genetic diseases ⚠
  • p.Lys427Arg Single submitter Inborn genetic diseases ⚠
  • p.Lys647Arg Single submitter Inborn genetic diseases ⚠
  • p.Val550Asp Single submitter Inborn genetic diseases ⚠

Benign 20

Benign/Likely benign 2

Likely benign 47

Uncertain significance 136