Sugi Variant

Sugi Variant/PPM1D

PPM1D — 369 ClinVar variants

All ClinVar germline PPM1D variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 127 flagged for review →

18 Pathogenic · 4 Pathogenic/Likely pathogenic · 26 Likely pathogenic · 23 Conflicting · 21 Benign · 9 Benign/Likely benign · 116 Likely benign · 152 Uncertain significance

Full PPM1D gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 127

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 97

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

Predictors split 18

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

All PPM1D variants

Pathogenic 18

  • p.Gln404Ter Multiple submitters Inborn genetic diseases
  • p.Glu423Ter Multiple submitters hereditary breast carcinoma
  • p.Trp427Ter Multiple submitters intellectual developmental disorder with gastrointestinal difficulties and high pain threshold
  • p.Arg429_Val430insTer Single submitter intellectual developmental disorder with gastrointestinal difficulties and high pain threshold
  • p.Cys414Ter Single submitter
  • p.Glu405Ter Single submitter Inborn genetic diseases
  • p.Ile486fs Single submitter intellectual developmental disorder with gastrointestinal difficulties and high pain threshold
  • p.Leu422fs Single submitter Neurodevelopmental delay
  • p.Leu484Ter Single submitter
  • p.Phe449_Leu450insTer Single submitter
  • p.Pro426fs Single submitter
  • p.Pro437fs Single submitter autosomal dominant non-syndromic intellectual disability
  • p.Ser412fs Single submitter
  • p.Ser503fs Single submitter intellectual developmental disorder with gastrointestinal difficulties and high pain threshold
  • p.Thr406fs Single submitter intellectual developmental disorder with gastrointestinal difficulties and high pain threshold
  • p.Trp427fs Single submitter intellectual developmental disorder with gastrointestinal difficulties and high pain threshold
  • p.Pro418fs No assertion criteria intellectual developmental disorder with gastrointestinal difficulties and high pain threshold
  • p.Ser421fs No assertion criteria intellectual developmental disorder with gastrointestinal difficulties and high pain threshold

Pathogenic/Likely pathogenic 4

  • p.Cys407Ter Multiple submitters PPM1D-related disorder
  • p.Glu424fs Multiple submitters intellectual developmental disorder with gastrointestinal difficulties and high pain threshold
  • p.Ser421Ter Multiple submitters PPM1D-related disorder
  • p.Tyr401fs Multiple submitters intellectual developmental disorder with gastrointestinal difficulties and high pain threshold

Likely pathogenic 26

  • p.Arg536fs Multiple submitters intellectual developmental disorder with gastrointestinal difficulties and high pain threshold
  • p.Gln462Ter Multiple submitters PPM1D-related disorder
  • p.Leu484fs Multiple submitters intellectual developmental disorder with gastrointestinal difficulties and high pain threshold
  • p.Pro413fs Multiple submitters intellectual developmental disorder with gastrointestinal difficulties and high pain threshold
  • p.Asn431_Ser432insTer Single submitter intellectual developmental disorder with gastrointestinal difficulties and high pain threshold
  • p.Asp425fs Single submitter
  • p.Cys407fs Single submitter
  • p.Cys478fs Single submitter
  • p.Gln524Ter Single submitter
  • p.Glu405fs Single submitter
  • p.Glu475fs Single submitter
  • p.Gly83Trp Single submitter ovarian cancer ⚠
  • p.His435fs Single submitter PPM1D-related disorder
  • p.Leu546fs Single submitter
  • p.Lys433fs Single submitter
  • p.Lys480Ter Single submitter
  • p.Met409fs Single submitter intellectual developmental disorder with gastrointestinal difficulties and high pain threshold
  • p.Phe534_Lys535delinsTer Single submitter
  • p.Pro417fs Single submitter intellectual developmental disorder with gastrointestinal difficulties and high pain threshold
  • p.Pro471fs Single submitter intellectual developmental disorder with gastrointestinal difficulties and high pain threshold
  • p.Pro518fs Single submitter intellectual developmental disorder with gastrointestinal difficulties and high pain threshold
  • p.Thr416fs Single submitter intellectual developmental disorder with gastrointestinal difficulties and high pain threshold
  • p.Thr483fs Single submitter PPM1D-related disorder
  • p.Val408fs Single submitter intellectual developmental disorder with gastrointestinal difficulties and high pain threshold
  • p.Val419fs Single submitter Inborn genetic diseases
  • p.Gln404fs No assertion criteria intellectual developmental disorder with gastrointestinal difficulties and high pain threshold

Conflicting classifications of pathogenicity 23

  • p.Arg458Ter Single submitter intellectual developmental disorder with gastrointestinal difficulties and high pain threshold
  • p.Arg552Ter Single submitter Inborn genetic diseases
  • p.Arg572Ter Single submitter intellectual developmental disorder with gastrointestinal difficulties and high pain threshold
  • p.Asn460Thr Single submitter Inborn genetic diseases ⚠
  • p.Asn512fs Single submitter PPM1D-related disorder
  • p.Asn533Lys Single submitter ⚠
  • p.Asp397fs Single submitter intellectual developmental disorder with gastrointestinal difficulties and high pain threshold
  • p.Cys478Ter Single submitter intellectual developmental disorder with gastrointestinal difficulties and high pain threshold
  • p.Glu476Ter Single submitter intellectual developmental disorder with gastrointestinal difficulties and high pain threshold
  • p.Glu525Ter Single submitter Inborn genetic diseases
  • p.Glu539Ter Single submitter intellectual developmental disorder with gastrointestinal difficulties and high pain threshold
  • p.Ile27Met Single submitter Inborn genetic diseases ⚠
  • p.Ile436fs Single submitter intellectual developmental disorder with gastrointestinal difficulties and high pain threshold
  • p.Ile486Thr Single submitter ⚠
  • p.Leu393Val Single submitter Inborn genetic diseases ⚠
  • p.Leu58Val Single submitter Inborn genetic diseases ⚠
  • p.Lys38Gln Single submitter Inborn genetic diseases ⚠
  • p.Lys38Glu Single submitter Inborn genetic diseases ⚠
  • p.Lys469Glu Single submitter hereditary breast carcinoma ⚠
  • p.Ser313Thr Single submitter ⚠
  • p.Ser446Ter Single submitter
  • p.Ser44Trp Single submitter intellectual developmental disorder with gastrointestinal difficulties and high pain threshold ⚠
  • p.Val271Ile Single submitter ⚠

Benign 21

Benign/Likely benign 9

Likely benign 116

Uncertain significance 152