Sugi Variant

Sugi Variant/USP9X

USP9X — 1214 ClinVar variants

All ClinVar germline USP9X variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 547 flagged for review →

74 Pathogenic · 3 Pathogenic/Likely pathogenic · 60 Likely pathogenic · 21 Conflicting · 130 Benign · 34 Benign/Likely benign · 283 Likely benign · 609 Uncertain significance

Full USP9X gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 547

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 5

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 349

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification. · showing the 150 best-reviewed of 349

Predictors split 182

The independent predictors disagree with each other — read with care. · showing the 150 best-reviewed of 182

All USP9X variants

Pathogenic 74

  • p.Arg592Ter Multiple submitters intellectual disability, X-linked 99, syndromic, female-restricted
  • p.Arg916Ter Multiple submitters intellectual disability, X-linked 99, syndromic, female-restricted
  • p.Gln605fs Multiple submitters intellectual disability, X-linked 99, syndromic, female-restricted
  • p.Leu28fs Multiple submitters Inborn genetic diseases
  • c.1763+1G>A Single submitter Inborn genetic diseases
  • c.2637-2A>G Single submitter
  • c.2877+1G>A Single submitter Inborn genetic diseases
  • p.Ala1587fs Single submitter intellectual disability, X-linked 99, syndromic, female-restricted
  • p.Arg1658Ter Single submitter
  • p.Arg1799Ter Single submitter
  • p.Arg2085Cys Single submitter
  • p.Arg215Ter Single submitter
  • p.Arg401Ter Single submitter
  • p.Arg742Ter Single submitter
  • p.Arg750Ter Single submitter
  • p.Arg879Lys Single submitter ⚠
  • p.Arg882fs Single submitter intellectual disability, X-linked 99, syndromic, female-restricted
  • p.Asn15fs Single submitter intellectual disability, X-linked 99, syndromic, female-restricted
  • p.Asn2397Ter Single submitter
  • p.Asn716fs Single submitter
  • p.Asp1685Asn Single submitter
  • p.Asp49fs Single submitter
  • p.Cys2306fs Single submitter USP9X-related disorder
  • p.Gln18Ter Single submitter intellectual disability, X-linked 99, syndromic, female-restricted
  • p.Gln2324fs Single submitter
  • p.Gln2403Ter Single submitter
  • p.Gln2436Ter Single submitter intellectual disability, X-linked 99, syndromic, female-restricted
  • p.Gln676Ter Single submitter intellectual disability, X-linked 99
  • p.Glu1093fs Single submitter
  • p.Glu1851fs Single submitter intellectual disability, X-linked 99, syndromic, female-restricted
  • p.Glu653Ter Single submitter Inborn genetic diseases
  • p.Gly1008Ter Single submitter intellectual disability, X-linked 99, syndromic, female-restricted
  • p.Gly1373fs Single submitter
  • p.Gly770Ter Single submitter
  • p.His1347fs Single submitter
  • p.His1879fs Single submitter Inborn genetic diseases
  • p.Leu1431fs Single submitter intellectual disability
  • p.Leu174del Single submitter
  • p.Leu2016fs Single submitter intellectual disability, X-linked 99, syndromic, female-restricted
  • p.Lys2060_Lys2061insTer Single submitter
  • p.Phe1020fs Single submitter
  • p.Phe2122fs Single submitter
  • p.Phe2182_Val2183insTer Single submitter intellectual disability, X-linked 99, syndromic, female-restricted
  • p.Pro2258fs Single submitter intellectual disability, X-linked 99, syndromic, female-restricted
  • p.Pro87fs Single submitter intellectual disability, X-linked 99
  • p.Ser480fs Single submitter
  • p.Ser839fs Single submitter
  • p.Ser959Ter Single submitter
  • p.Thr2204fs Single submitter Inborn genetic diseases
  • p.Thr267fs Single submitter
  • p.Thr327_Val328insTer Single submitter Inborn genetic diseases
  • p.Trp1022Ter Single submitter
  • p.Trp2070Ter Single submitter intellectual disability, X-linked 99, syndromic, female-restricted
  • p.Trp2308fs Single submitter USP9X-related disorder
  • p.Trp380Ter Single submitter intellectual disability, X-linked 99, syndromic, female-restricted
  • p.Trp458Ter Single submitter
  • p.Tyr2009fs Single submitter intellectual disability, X-linked 99, syndromic, female-restricted
  • p.Tyr2220Ter Single submitter
  • p.Tyr2331fs Single submitter intellectual disability, X-linked 99, syndromic, female-restricted
  • p.Tyr2402Ter Single submitter intellectual disability, X-linked 99, syndromic, female-restricted
  • p.Val1870fs Single submitter
  • c.3028-2A>G No assertion criteria intellectual disability, X-linked 99, syndromic, female-restricted
  • p.Arg2002Ter No assertion criteria intellectual disability, X-linked 99, syndromic, female-restricted
  • p.Arg371Ter No assertion criteria intellectual disability, X-linked 99, syndromic, female-restricted
  • p.Arg852Ter No assertion criteria intellectual disability, X-linked 99, syndromic, female-restricted
  • p.Gln1255Ter No assertion criteria intellectual disability, X-linked 99, syndromic, female-restricted
  • p.Gln2509fs No assertion criteria intellectual disability, X-linked 99
  • p.Leu1379fs No assertion criteria intellectual disability, X-linked 99, syndromic, female-restricted
  • p.Leu2093His No assertion criteria intellectual disability, X-linked 99
  • p.Lys2227_Tyr2229delinsSerTer No assertion criteria intellectual disability, X-linked 99, syndromic, female-restricted
  • p.Ser2153fs No assertion criteria intellectual disability, X-linked 99, syndromic, female-restricted
  • p.Thr614fs No assertion criteria intellectual disability, X-linked 99, syndromic, female-restricted
  • p.Tyr761fs No assertion criteria intellectual disability, X-linked 99, syndromic, female-restricted
  • p.Val1758Asp No assertion criteria ⚠

Pathogenic/Likely pathogenic 3

  • c.323-1G>A Multiple submitters intellectual disability, X-linked 99, syndromic, female-restricted
  • p.Arg2085His Multiple submitters intellectual disability, X-linked 99
  • p.Arg2366Ter Multiple submitters intellectual disability, X-linked 99, syndromic, female-restricted

Likely pathogenic 60

Conflicting classifications of pathogenicity 21

Benign 130

Benign/Likely benign 34

Likely benign 283

Uncertain significance 609

Showing the top 300 by review status; the full set is in the sitemap.