Sugi Variant

Sugi Variant/PHF21A

PHF21A — 397 ClinVar variants

All ClinVar germline PHF21A variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 166 flagged for review →

27 Pathogenic · 6 Pathogenic/Likely pathogenic · 13 Likely pathogenic · 16 Conflicting · 38 Benign · 6 Benign/Likely benign · 115 Likely benign · 176 Uncertain significance

Full PHF21A gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 166

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 agree, ClinVar conflicts 14

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

Predicted LoF vs a conflicting call 1

ClinVar submitters conflict, and it's a predicted loss-of-function change in a gene where LoF causes disease — flagged for review, not resolved (verify NMD-escape for C-terminal truncations). Non-missense.

Predictors lean, ClinVar uncertain 122

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

Predictors split 29

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

All PHF21A variants

Pathogenic 27

  • p.Gln75Ter Multiple submitters
  • p.Lys392Ter Multiple submitters intellectual developmental disorder with behavioral abnormalities and craniofacial dysmorphism with or without seizures
  • p.Thr345fs Multiple submitters intellectual developmental disorder with behavioral abnormalities and craniofacial dysmorphism with or without seizures
  • p.Arg410fs Single submitter
  • p.Gln207Ter Single submitter intellectual developmental disorder with behavioral abnormalities and craniofacial dysmorphism with or without seizures
  • p.Gln26Ter Single submitter intellectual developmental disorder with behavioral abnormalities and craniofacial dysmorphism with or without seizures
  • p.Gln676fs Single submitter
  • p.Gln89Ter Single submitter intellectual developmental disorder with behavioral abnormalities and craniofacial dysmorphism with or without seizures
  • p.Gln96Ter Single submitter intellectual developmental disorder with behavioral abnormalities and craniofacial dysmorphism with or without seizures
  • p.Glu382Ter Single submitter
  • p.Leu367fs Single submitter
  • p.Leu520fs Single submitter
  • p.Leu550Ter Single submitter intellectual developmental disorder with behavioral abnormalities and craniofacial dysmorphism with or without seizures
  • p.Leu6fs Single submitter
  • p.Lys411Ter Single submitter Inborn genetic diseases
  • p.Lys525fs Single submitter intellectual developmental disorder with behavioral abnormalities and craniofacial dysmorphism with or without seizures
  • p.Pro222_Pro223insTer Single submitter
  • p.Ser575Ter Single submitter intellectual developmental disorder with behavioral abnormalities and craniofacial dysmorphism with or without seizures
  • p.Thr125fs Single submitter
  • p.Thr201fs Single submitter Inborn genetic diseases
  • p.Thr273fs Single submitter intellectual developmental disorder with behavioral abnormalities and craniofacial dysmorphism with or without seizures
  • p.Thr333fs Single submitter Inborn genetic diseases
  • p.Tyr417Ter Single submitter Inborn genetic diseases
  • p.Val376fs Single submitter
  • p.Glu409fs No assertion criteria intellectual developmental disorder with behavioral abnormalities and craniofacial dysmorphism with or without seizures
  • p.Gly430Ser No assertion criteria intellectual developmental disorder with behavioral abnormalities and craniofacial dysmorphism with or without seizures
  • p.Pro221fs No assertion criteria intellectual developmental disorder with behavioral abnormalities and craniofacial dysmorphism with or without seizures

Pathogenic/Likely pathogenic 6

  • p.Ala654fs Multiple submitters intellectual developmental disorder with behavioral abnormalities and craniofacial dysmorphism with or without seizures
  • p.Arg391Ter Multiple submitters intellectual developmental disorder with behavioral abnormalities and craniofacial dysmorphism with or without seizures
  • p.Arg581Ter Multiple submitters intellectual disability
  • p.Gln88Ter Multiple submitters PHF21A-related disorder
  • p.Pro653fs Multiple submitters intellectual developmental disorder with behavioral abnormalities and craniofacial dysmorphism with or without seizures
  • p.Val285fs Multiple submitters PHF21A-related disorder

Likely pathogenic 13

  • c.1227+1G>T Single submitter
  • c.153+1G>C Single submitter PHF21A-related disorder
  • c.153+1G>T Single submitter intellectual developmental disorder with behavioral abnormalities and craniofacial dysmorphism with or without seizures
  • c.1684+2T>A Single submitter
  • c.361-2A>C Single submitter
  • c.55-2A>G Single submitter
  • c.612+1G>A Single submitter intellectual developmental disorder with behavioral abnormalities and craniofacial dysmorphism with or without seizures
  • c.613-2A>G Single submitter intellectual developmental disorder with behavioral abnormalities and craniofacial dysmorphism with or without seizures
  • p.Gln7fs Single submitter intellectual developmental disorder with behavioral abnormalities and craniofacial dysmorphism with or without seizures
  • p.Gln7Ter Single submitter intellectual developmental disorder with behavioral abnormalities and craniofacial dysmorphism with or without seizures
  • p.Ile282fs Single submitter intellectual developmental disorder with behavioral abnormalities and craniofacial dysmorphism with or without seizures
  • p.Ile487fs Single submitter
  • p.Ser666fs Single submitter Inborn genetic diseases

Conflicting classifications of pathogenicity 16

Benign 38

Benign/Likely benign 6

Likely benign 115

Uncertain significance 176