Sugi Variant

Sugi Variant/SETD1B

SETD1B — 890 ClinVar variants

All ClinVar germline SETD1B variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 432 flagged for review →

56 Pathogenic · 9 Pathogenic/Likely pathogenic · 42 Likely pathogenic · 26 Conflicting · 13 Benign · 8 Benign/Likely benign · 278 Likely benign · 458 Uncertain significance

Full SETD1B gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 432

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 2

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

Predictors agree, ClinVar conflicts 24

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

Predictors lean, ClinVar uncertain 293

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 293

Predictors split 113

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

All SETD1B variants

Pathogenic 56

  • p.Arg1329Ter Multiple submitters intellectual developmental disorder with seizures and language delay
  • p.Asp458fs Multiple submitters intellectual developmental disorder with seizures and language delay
  • p.His8fs Multiple submitters neurodevelopmental disorder
  • c.5337+1G>A Single submitter
  • c.545-372A>G Single submitter intellectual developmental disorder with seizures and language delay
  • p.Ala1776fs Single submitter intellectual developmental disorder with seizures and language delay
  • p.Arg1523fs Single submitter
  • p.Arg1524Ter Single submitter
  • p.Arg1538Ter Single submitter
  • p.Arg1735fs Single submitter intellectual developmental disorder with seizures and language delay
  • p.Arg1748His Single submitter
  • p.Arg1748Ser Single submitter intellectual developmental disorder with seizures and language delay
  • p.Arg1792Leu Single submitter ⚠
  • p.Arg1885Gln Single submitter
  • p.Arg511fs Single submitter intellectual developmental disorder with seizures and language delay
  • p.Arg555Trp Single submitter ⚠
  • p.Arg72fs Single submitter intellectual developmental disorder with seizures and language delay
  • p.Arg996Ter Single submitter
  • p.Arg998Ter Single submitter intellectual developmental disorder with seizures and language delay
  • p.Asp1123fs Single submitter Inborn genetic diseases
  • p.Gln1322Ter Single submitter intellectual developmental disorder with seizures and language delay
  • p.Gln1589fs Single submitter SETD1B-related disorder
  • p.Gln1786Ter Single submitter intellectual developmental disorder with seizures and language delay
  • p.Gln1801fs Single submitter
  • p.Gln200fs Single submitter intellectual developmental disorder with seizures and language delay
  • p.Gln527Ter Single submitter intellectual developmental disorder with seizures and language delay
  • p.Gln776Ter Single submitter intellectual developmental disorder with seizures and language delay
  • p.Gln978Ter Single submitter intellectual developmental disorder with seizures and language delay
  • p.Glu1191Ter Single submitter intellectual developmental disorder with seizures and language delay
  • p.Glu1851Lys Single submitter
  • p.Glu412fs Single submitter intellectual developmental disorder with seizures and language delay
  • p.Glu995Ter Single submitter
  • p.Gly1621fs Single submitter intellectual developmental disorder with seizures and language delay
  • p.Leu1321fs Single submitter
  • p.Leu1508fs Single submitter
  • p.Leu752_Phe753insTer Single submitter intellectual developmental disorder with seizures and language delay
  • p.Phe1408fs Single submitter intellectual developmental disorder with seizures and language delay
  • p.Pro694fs Single submitter
  • p.Pro99fs Single submitter intellectual developmental disorder with seizures and language delay
  • p.Ser1162fs Single submitter Developmental delay
  • p.Ser1335fs Single submitter Inborn genetic diseases
  • p.Ser1729_Ala1730insTer Single submitter intellectual developmental disorder with seizures and language delay
  • p.Ser1795Leu Single submitter intellectual developmental disorder with seizures and language delay ⚠
  • p.Ser21Ter Single submitter intellectual developmental disorder with seizures and language delay
  • p.Ser349fs Single submitter
  • p.Thr787fs Single submitter intellectual developmental disorder with seizures and language delay
  • p.Tyr258fs Single submitter Inborn genetic diseases
  • p.Val161fs Single submitter
  • p.Ala1129Val No assertion criteria intellectual developmental disorder with seizures and language delay ⚠
  • p.Ala1901Glu No assertion criteria intellectual developmental disorder with seizures and language delay
  • p.Arg1301Ter No assertion criteria intellectual developmental disorder with seizures and language delay
  • p.Asn113_Asp121delinsValProGlnGluValPheThrAspVal No assertion criteria intellectual developmental disorder with seizures and language delay
  • p.Glu1034fs No assertion criteria SETD1B-related disorder
  • p.Ile1925fs No assertion criteria intellectual developmental disorder with seizures and language delay
  • p.Phe95_Tyr96delinsTer No assertion criteria intellectual developmental disorder with seizures and language delay
  • p.Tyr1873Ter No assertion criteria intellectual developmental disorder with seizures and language delay

Pathogenic/Likely pathogenic 9

  • p.Arg1703Ter Multiple submitters intellectual developmental disorder with seizures and language delay
  • p.Arg1748Cys Multiple submitters intellectual developmental disorder with seizures and language delay
  • p.Arg1792Gln Multiple submitters Neurodevelopmental delay ⚠
  • p.Arg1902Cys Multiple submitters intellectual developmental disorder with seizures and language delay
  • p.Asp1942_Tyr1943del Multiple submitters neurodevelopmental disorder
  • p.Gln780Ter Multiple submitters intellectual developmental disorder with seizures and language delay
  • p.Glu1948Lys Multiple submitters intellectual developmental disorder with seizures and language delay
  • p.Gly1392fs Multiple submitters intellectual developmental disorder with seizures and language delay
  • p.Tyr1943Cys Multiple submitters SETD1B-associated disorder

Likely pathogenic 42

  • p.Arg1825Trp Multiple submitters intellectual developmental disorder with seizures and language delay
  • c.2978-2A>G Single submitter
  • c.3418+2_3418+3del Single submitter
  • c.544+1G>A Single submitter SETD1B-related disorder
  • c.544+2T>C Single submitter intellectual developmental disorder with seizures and language delay
  • p.Ala320fs Single submitter
  • p.Arg1885Trp Single submitter intellectual developmental disorder with seizures and language delay
  • p.Arg196Ter Single submitter intellectual developmental disorder with seizures and language delay
  • p.Arg982fs Single submitter intellectual developmental disorder with seizures and language delay
  • p.Asn1709fs Single submitter intellectual developmental disorder with seizures and language delay
  • p.Asp1736fs Single submitter intellectual developmental disorder with seizures and language delay
  • p.Asp1815Asn Single submitter neurodevelopmental disorder
  • p.Asp1893Asn Single submitter SETD1B-related disorder
  • p.Asp1893His Single submitter SETD1B-related disorder
  • p.Cys1954Arg Single submitter intellectual developmental disorder with seizures and language delay
  • p.Cys1954Tyr Single submitter intellectual developmental disorder with seizures and language delay
  • p.Glu1068Ter Single submitter
  • p.Glu1199fs Single submitter intellectual developmental disorder with seizures and language delay
  • p.Glu509fs Single submitter epilepsy
  • p.Glu919_Asp926del Single submitter
  • p.Glu94fs Single submitter intellectual developmental disorder with seizures and language delay
  • p.Gly362fs Single submitter intellectual developmental disorder with seizures and language delay
  • p.His720fs Single submitter intellectual developmental disorder with seizures and language delay
  • p.Ile1933fs Single submitter intellectual developmental disorder with seizures and language delay
  • p.Leu1586fs Single submitter SETD1B-related disorder
  • p.Lys1896Glu Single submitter intellectual developmental disorder with seizures and language delay
  • p.Met705fs Single submitter
  • p.Phe1903Val Single submitter intellectual developmental disorder with seizures and language delay
  • p.Pro1351fs Single submitter intellectual developmental disorder with seizures and language delay
  • p.Pro1584fs Single submitter intellectual developmental disorder with seizures and language delay
  • p.Pro715fs Single submitter intellectual developmental disorder with seizures and language delay
  • p.Pro749fs Single submitter intellectual developmental disorder with seizures and language delay
  • p.Ser1283fs Single submitter SETD1B-related disorder
  • p.Ser1414Tyr Single submitter intellectual developmental disorder with seizures and language delay ⚠
  • p.Ser1770fs Single submitter SETD1B-related disorder
  • p.Ser1880fs Single submitter intellectual developmental disorder with seizures and language delay
  • p.Ser913Ter Single submitter intellectual developmental disorder with seizures and language delay
  • p.Tyr1701fs Single submitter intellectual developmental disorder with seizures and language delay
  • p.Tyr48fs Single submitter
  • p.Val1088fs Single submitter SETD1B-related disorder
  • p.Val129Gly Single submitter intellectual developmental disorder with seizures and language delay
  • p.Tyr1943_Lys1944delinsTer No assertion criteria intellectual developmental disorder with seizures and language delay

Conflicting classifications of pathogenicity 26

Benign 13

Benign/Likely benign 8

Likely benign 278

Uncertain significance 458

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