Sugi Variant

Sugi Variant/PTPN4

PTPN4 — 154 ClinVar variants

All ClinVar germline PTPN4 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 106 flagged for review →

3 Pathogenic · 10 Likely pathogenic · 1 Conflicting · 3 Benign · 20 Likely benign · 117 Uncertain significance

Full PTPN4 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 106

Variants where the independent computational evidence doesn't line up with the clinical picture — a QC signal for a second look, 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 82

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

Predictors split 23

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

All PTPN4 variants

Pathogenic 3

  • p.Arg249Ter Multiple submitters Inborn genetic diseases
  • p.Gln780Ter Single submitter neurodevelopmental disorder
  • p.Leu64Ter Single submitter Inborn genetic diseases

Likely pathogenic 10

  • c.1355+1G>A Single submitter
  • c.138+2T>C Single submitter
  • c.246+1G>T Single submitter
  • p.Arg22Ter Single submitter Inborn genetic diseases
  • p.Arg6Ter Single submitter Inborn genetic diseases
  • p.Gln180Ter Single submitter PTPN4-related aberrant neurodevelopment and growth
  • p.Gln50fs Single submitter neurodevelopmental disorder
  • p.Gln73fs Single submitter neurodevelopmental disorder
  • p.Thr210fs Single submitter PTPN4-related Neurodevelopmental Disorder
  • p.Asp580Tyr No assertion criteria intellectual disability

Conflicting classifications of pathogenicity 1

Benign 3

Likely benign 20

Uncertain significance 117