PTPN2 — 55 ClinVar variants

All ClinVar germline PTPN2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 34 flagged for review →

1 Likely pathogenic · 1 Conflicting · 4 Benign · 6 Likely benign · 43 Uncertain significance

Full PTPN2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 34

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 1

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

PTPN2 p.Ile244Val Conflicting Single submitter

Predictors lean, ClinVar uncertain 27

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

Predictors split 6

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

All PTPN2 variants

Likely pathogenic 1

p.Arg45Ter Single submitter

Conflicting classifications of pathogenicity 1

p.Ile244Val Single submitter ⚠

Benign 4

p.Thr171Lys Multiple submitters
p.Val234Ile Multiple submitters
c.1041-3210T>C Single submitter
c.1041-4A>G Single submitter

Likely benign 6

p.Asn344= Single submitter
p.Glu8= Single submitter
p.Gly401= Single submitter
p.Ser166= Single submitter
p.Thr14Ala Single submitter
p.Thr93= Single submitter

Uncertain significance 43

c.161-3856C>T Single submitter
c.360+1G>C Single submitter
p.Ala212Val Single submitter ⚠
p.Ala276Thr Single submitter ⚠
p.Arg16Leu Single submitter ⚠
p.Arg255Ter Single submitter
p.Arg288Gln Single submitter ⚠
p.Arg329Leu Single submitter ⚠
p.Arg350Gln Single submitter ⚠
p.Arg350Trp Single submitter ⚠
p.Arg354Gln Single submitter ⚠
p.Asn27Ser Single submitter ⚠
p.Asp241Gly Single submitter ⚠
p.Cys330Ser Single submitter ⚠
p.Gln132His Single submitter ⚠
p.Gln338Lys Single submitter ⚠
p.Glu8Lys Single submitter ⚠
p.Glu8Ter Single submitter
p.His209Arg Single submitter ⚠
p.Ile220fs Single submitter
p.Ile273Met Single submitter ⚠
p.Ile388Val Single submitter ⚠
p.Leu135Met Single submitter ⚠
p.Leu158Val Single submitter ⚠
p.Leu233Ile Single submitter ⚠
p.Lys118Glu Single submitter ⚠
p.Lys198Glu Single submitter
p.Lys238Glu Single submitter ⚠
p.Lys280Asn Single submitter ⚠
p.Lys290Glu Single submitter ⚠
p.Lys358Asn Single submitter ⚠
p.Phe409Val Single submitter ⚠
p.Pro20Leu Single submitter ⚠
p.Pro262Ser Single submitter
p.Ser152Ala Single submitter ⚠
p.Thr106Ser Single submitter ⚠
p.Thr178Ala Single submitter ⚠
p.Thr179Ser Single submitter
p.Tyr22Ter Single submitter
p.Tyr68fs Single submitter
p.Val150Leu Single submitter ⚠
p.Val365Met Single submitter ⚠
p.Val404Phe Single submitter ⚠