Sugi Variant

Sugi Variant/PIDD1

PIDD1 — 328 ClinVar variants

All ClinVar germline PIDD1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 220 flagged for review →

10 Pathogenic · 1 Pathogenic/Likely pathogenic · 6 Likely pathogenic · 8 Conflicting · 12 Benign · 1 Benign/Likely benign · 68 Likely benign · 222 Uncertain significance

Full PIDD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 220

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 5

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

Predictors lean, ClinVar uncertain 166

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 166

Predictors split 48

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

All PIDD1 variants

Pathogenic 10

  • p.Arg862Trp Multiple submitters intellectual developmental disorder, autosomal recessive 75, with neuropsychiatric features and variant lissencephaly
  • c.1917+1G>T Single submitter intellectual developmental disorder, autosomal recessive 75, with neuropsychiatric features and variant lissencephaly
  • p.Ala607fs Single submitter intellectual developmental disorder, autosomal recessive 75, with neuropsychiatric features and variant lissencephaly
  • p.Gln331fs Single submitter Inborn genetic diseases
  • p.Leu547fs Single submitter
  • c.2275-1G>A No assertion criteria intellectual developmental disorder, autosomal recessive 75, with neuropsychiatric features and variant lissencephaly
  • p.Arg815Trp No assertion criteria intellectual developmental disorder, autosomal recessive 75, with neuropsychiatric features and variant lissencephaly ⚠
  • p.Gln863Ter No assertion criteria intellectual developmental disorder, autosomal recessive 75, with neuropsychiatric features and variant lissencephaly
  • p.Gly602fs No assertion criteria intellectual developmental disorder, autosomal recessive 75, with neuropsychiatric features and variant lissencephaly
  • p.Val706fs No assertion criteria intellectual developmental disorder, autosomal recessive 75, with neuropsychiatric features and variant lissencephaly

Pathogenic/Likely pathogenic 1

  • p.Arg637Ter Multiple submitters intellectual developmental disorder, autosomal recessive 75, with neuropsychiatric features and variant lissencephaly

Likely pathogenic 6

  • c.1302+1G>A Single submitter intellectual developmental disorder, autosomal recessive 75, with neuropsychiatric features and variant lissencephaly
  • c.296-1G>A Single submitter intellectual developmental disorder, autosomal recessive 75, with neuropsychiatric features and variant lissencephaly
  • p.Ala739fs Single submitter intellectual developmental disorder, autosomal recessive 75, with neuropsychiatric features and variant lissencephaly
  • p.Gln504Ter Single submitter intellectual developmental disorder, autosomal recessive 75, with neuropsychiatric features and variant lissencephaly
  • p.Glu574fs Single submitter intellectual disability
  • p.Pro280fs Single submitter intellectual developmental disorder, autosomal recessive 75, with neuropsychiatric features and variant lissencephaly

Conflicting classifications of pathogenicity 8

  • c.2042-2A>G Single submitter PIDD1-associated neurodevelopmental disorder
  • p.Arg103Gln Single submitter Inborn genetic diseases ⚠
  • p.Arg37Trp Single submitter Inborn genetic diseases ⚠
  • p.Arg682Cys Single submitter developmental and epileptic encephalopathy, 3 ⚠
  • p.Arg68fs Single submitter intellectual developmental disorder, autosomal recessive 75, with neuropsychiatric features and variant lissencephaly
  • p.Gln391= Single submitter PIDD1-associated neurodevelopmental disorder
  • p.Pro482Ala Single submitter ⚠
  • p.Ser299Leu Single submitter Inborn genetic diseases ⚠

Benign 12

Benign/Likely benign 1

Likely benign 68

Uncertain significance 222