PTPN12 — 92 ClinVar variants
All ClinVar germline PTPN12 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 74 flagged for review →
1 Pathogenic · 5 Benign · 10 Likely benign · 76 Uncertain significance
Full PTPN12 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 74
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 lean, ClinVar uncertain 64
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- PTPN12 p.Arg339Gly Uncertain significance Single submitter
- PTPN12 p.Arg652Thr Uncertain significance Single submitter
- PTPN12 p.Arg74Leu Uncertain significance Single submitter
- PTPN12 p.Asn457His Uncertain significance Single submitter
- PTPN12 p.Asn554Ser Uncertain significance Single submitter
- PTPN12 p.Asn559Ser Uncertain significance Single submitter
- PTPN12 p.Asp404Glu Uncertain significance Single submitter
- PTPN12 p.Asp427Val Uncertain significance Single submitter
- PTPN12 p.Asp518Glu Uncertain significance Single submitter
- PTPN12 p.Asp557Gly Uncertain significance Single submitter
- PTPN12 p.Asp607Val Uncertain significance Single submitter
- PTPN12 p.Cys495Ser Uncertain significance Single submitter
- PTPN12 p.Gln425Glu Uncertain significance Single submitter
- PTPN12 p.Gln502Lys Uncertain significance Single submitter
- PTPN12 p.Glu610Lys Uncertain significance Single submitter
- PTPN12 p.Glu664Asp Uncertain significance Single submitter
- PTPN12 p.Glu690Lys Uncertain significance Single submitter
- PTPN12 p.Glu701Ala Uncertain significance Single submitter
- PTPN12 p.Glu734Gly Uncertain significance Single submitter
- PTPN12 p.Glu778Val Uncertain significance Single submitter
- PTPN12 p.Gly312Glu Uncertain significance Single submitter
- PTPN12 p.Gly657Glu Uncertain significance Single submitter
- PTPN12 p.Gly662Ser Uncertain significance Single submitter
- PTPN12 p.Gly715Cys Uncertain significance Single submitter
-
PTPN12 p.His287Arg
Uncertain significance
Single submitter
colorectal cancer
- PTPN12 p.His304Arg Uncertain significance Single submitter
- PTPN12 p.His584Tyr Uncertain significance Single submitter
- PTPN12 p.His653Tyr Uncertain significance Single submitter
- PTPN12 p.Ile309Thr Uncertain significance Single submitter
- PTPN12 p.Ile325Thr Uncertain significance Single submitter
- PTPN12 p.Ile462Asn Uncertain significance Single submitter
- PTPN12 p.Ile471Arg Uncertain significance Single submitter
- PTPN12 p.Ile47Met Uncertain significance Single submitter
- PTPN12 p.Ile558Thr Uncertain significance Single submitter
- PTPN12 p.Ile650Val Uncertain significance Single submitter
- PTPN12 p.Ile655Val Uncertain significance Single submitter
- PTPN12 p.Ile760Thr Uncertain significance Single submitter
- PTPN12 p.Leu415Phe Uncertain significance Single submitter
- PTPN12 p.Leu485Ile Uncertain significance Single submitter
- PTPN12 p.Leu485Pro Uncertain significance Single submitter
- PTPN12 p.Lys429Thr Uncertain significance Single submitter
- PTPN12 p.Met395Val Uncertain significance Single submitter
- PTPN12 p.Met648Val Uncertain significance Single submitter
- PTPN12 p.Pro510Ser Uncertain significance Single submitter
- PTPN12 p.Pro546Leu Uncertain significance Single submitter
- PTPN12 p.Pro548Ala Uncertain significance Single submitter
- PTPN12 p.Pro682Ala Uncertain significance Single submitter
- PTPN12 p.Pro694Ser Uncertain significance Single submitter
- PTPN12 p.Pro740Gln Uncertain significance Single submitter
- PTPN12 p.Ser514Phe Uncertain significance Single submitter
- PTPN12 p.Ser517Thr Uncertain significance Single submitter
- PTPN12 p.Ser551Pro Uncertain significance Single submitter
- PTPN12 p.Ser556Leu Uncertain significance Single submitter
- PTPN12 p.Ser571Gly Uncertain significance Single submitter
- PTPN12 p.Ser613Cys Uncertain significance Single submitter
- PTPN12 p.Ser628Asn Uncertain significance Single submitter
- PTPN12 p.Ser751Pro Uncertain significance Single submitter
- PTPN12 p.Thr378Ser Uncertain significance Single submitter
- PTPN12 p.Thr490Asn Uncertain significance Single submitter
- PTPN12 p.Thr535Met Uncertain significance Single submitter
- PTPN12 p.Thr626Ala Uncertain significance Single submitter
- PTPN12 p.Tyr246His Uncertain significance Single submitter
- PTPN12 p.Val669Ile Uncertain significance Single submitter
- PTPN12 p.Val97Ile Uncertain significance Single submitter
Predictors split 10
The independent predictors disagree with each other — read with care.
- PTPN12 p.Arg134Gln Uncertain significance Single submitter
- PTPN12 p.Arg187His Uncertain significance Single submitter
- PTPN12 p.Asp85His Uncertain significance Single submitter
- PTPN12 p.Leu601Phe Uncertain significance Single submitter
- PTPN12 p.Pro769Ser Uncertain significance Single submitter
- PTPN12 p.Ser163Tyr Uncertain significance Single submitter
- PTPN12 p.Ser214Arg Uncertain significance Single submitter
- PTPN12 p.Tyr98Cys Uncertain significance Single submitter
- PTPN12 p.Val362Met Uncertain significance Single submitter
-
PTPN12 p.Lys61Arg
Pathogenic
No assertion criteria
colon carcinoma
All PTPN12 variants
Pathogenic 1
- p.Lys61Arg No assertion criteria colon carcinoma ⚠
Benign 5
- p.Thr573Ala Multiple submitters
- c.100-3A>T No assertion criteria PTPN12-related disorder
- p.Glu706Lys No assertion criteria PTPN12-related disorder
- p.Gly657= No assertion criteria PTPN12-related disorder
- p.Val322Ile No assertion criteria PTPN12-related disorder
Likely benign 10
- c.553-4G>A Single submitter
- p.Ala728Val Single submitter
- p.Arg525Cys Single submitter
- p.Lys218= Single submitter
- p.Ser603= Single submitter
- p.Ser704= Single submitter
- c.420+7A>G No assertion criteria PTPN12-related disorder
- p.Gly96= No assertion criteria PTPN12-related disorder
- p.Leu110= No assertion criteria PTPN12-related disorder
- p.Pro357= No assertion criteria PTPN12-related disorder
Uncertain significance 76
- p.Arg134Gln Single submitter ⚠
- p.Arg187His Single submitter ⚠
- p.Arg339Gly Single submitter ⚠
- p.Arg652Thr Single submitter ⚠
- p.Arg707Ter Single submitter
- p.Arg74Leu Single submitter ⚠
- p.Asn457His Single submitter ⚠
- p.Asn554Ser Single submitter ⚠
- p.Asn559Ser Single submitter ⚠
- p.Asp404Glu Single submitter ⚠
- p.Asp427Val Single submitter ⚠
- p.Asp518Glu Single submitter ⚠
- p.Asp557Gly Single submitter ⚠
- p.Asp607Val Single submitter ⚠
- p.Asp85His Single submitter ⚠
- p.Cys495Ser Single submitter ⚠
- p.Gln425Glu Single submitter ⚠
- p.Gln502Lys Single submitter ⚠
- p.Glu610Lys Single submitter ⚠
- p.Glu664Asp Single submitter ⚠
- p.Glu690Lys Single submitter ⚠
- p.Glu701Ala Single submitter ⚠
- p.Glu734Gly Single submitter ⚠
- p.Glu778Val Single submitter ⚠
- p.Gly312Glu Single submitter ⚠
- p.Gly657Glu Single submitter ⚠
- p.Gly662Ser Single submitter ⚠
- p.Gly715Cys Single submitter ⚠
- p.His287Arg Single submitter colorectal cancer ⚠
- p.His304Arg Single submitter ⚠
- p.His394Arg Single submitter
- p.His584Tyr Single submitter ⚠
- p.His653Tyr Single submitter ⚠
- p.Ile309Thr Single submitter ⚠
- p.Ile325Thr Single submitter ⚠
- p.Ile462Asn Single submitter ⚠
- p.Ile471Arg Single submitter ⚠
- p.Ile47Met Single submitter ⚠
- p.Ile558Thr Single submitter ⚠
- p.Ile650Val Single submitter ⚠
- p.Ile655Val Single submitter ⚠
- p.Ile760Thr Single submitter ⚠
- p.Leu415Phe Single submitter ⚠
- p.Leu485Ile Single submitter ⚠
- p.Leu485Pro Single submitter ⚠
- p.Leu601Phe Single submitter ⚠
- p.Lys429Thr Single submitter ⚠
- p.Met395Val Single submitter ⚠
- p.Met648Val Single submitter ⚠
- p.Pro510Ser Single submitter ⚠
- p.Pro546Leu Single submitter ⚠
- p.Pro548Ala Single submitter ⚠
- p.Pro682Ala Single submitter ⚠
- p.Pro694Ser Single submitter ⚠
- p.Pro740Gln Single submitter ⚠
- p.Pro769Ser Single submitter ⚠
- p.Ser163Tyr Single submitter ⚠
- p.Ser214Arg Single submitter ⚠
- p.Ser514Phe Single submitter ⚠
- p.Ser517Thr Single submitter ⚠
- p.Ser551Pro Single submitter ⚠
- p.Ser556Leu Single submitter ⚠
- p.Ser571Gly Single submitter ⚠
- p.Ser613Cys Single submitter ⚠
- p.Ser628Asn Single submitter ⚠
- p.Ser751Pro Single submitter ⚠
- p.Thr378Ser Single submitter ⚠
- p.Thr490Asn Single submitter ⚠
- p.Thr535Met Single submitter ⚠
- p.Thr626Ala Single submitter ⚠
- p.Tyr246His Single submitter ⚠
- p.Tyr98Cys Single submitter ⚠
- p.Val362Met Single submitter ⚠
- p.Val380fs Single submitter
- p.Val669Ile Single submitter ⚠
- p.Val97Ile Single submitter ⚠