PTPN3 — 146 ClinVar variants
All ClinVar germline PTPN3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 131 flagged for review →
1 Benign · 6 Likely benign · 139 Uncertain significance
Full PTPN3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 131
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 95
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- PTPN3 p.Asn612Thr Uncertain significance Multiple submitters
- PTPN3 p.Ala146Thr Uncertain significance Single submitter
- PTPN3 p.Ala150Val Uncertain significance Single submitter
- PTPN3 p.Ala153Val Uncertain significance Single submitter
- PTPN3 p.Ala400Glu Uncertain significance Single submitter
- PTPN3 p.Arg16Cys Uncertain significance Single submitter
- PTPN3 p.Arg16His Uncertain significance Single submitter
- PTPN3 p.Arg212Trp Uncertain significance Single submitter
- PTPN3 p.Arg245Gly Uncertain significance Single submitter
- PTPN3 p.Arg265Thr Uncertain significance Single submitter
- PTPN3 p.Arg330Leu Uncertain significance Single submitter
- PTPN3 p.Arg389Gln Uncertain significance Single submitter
- PTPN3 p.Arg392His Uncertain significance Single submitter
- PTPN3 p.Arg392Leu Uncertain significance Single submitter
- PTPN3 p.Arg512His Uncertain significance Single submitter
- PTPN3 p.Arg583Gln Uncertain significance Single submitter
- PTPN3 p.Arg6His Uncertain significance Single submitter
- PTPN3 p.Arg83Gly Uncertain significance Single submitter
- PTPN3 p.Arg848Gln Uncertain significance Single submitter
- PTPN3 p.Arg875Gln Uncertain significance Single submitter
- PTPN3 p.Asn319Ser Uncertain significance Single submitter
- PTPN3 p.Asn378Ser Uncertain significance Single submitter
- PTPN3 p.Asn501Lys Uncertain significance Single submitter
- PTPN3 p.Asn826Ser Uncertain significance Single submitter
- PTPN3 p.Asn826Tyr Uncertain significance Single submitter
- PTPN3 p.Asp173Asn Uncertain significance Single submitter
- PTPN3 p.Asp173Gly Uncertain significance Single submitter
- PTPN3 p.Asp397Gly Uncertain significance Single submitter
- PTPN3 p.Asp479Tyr Uncertain significance Single submitter
- PTPN3 p.Asp502Asn Uncertain significance Single submitter
- PTPN3 p.Asp56His Uncertain significance Single submitter
- PTPN3 p.Asp816Asn Uncertain significance Single submitter
- PTPN3 p.Asp911Gly Uncertain significance Single submitter
- PTPN3 p.Cys301Tyr Uncertain significance Single submitter
- PTPN3 p.Cys842Tyr Uncertain significance Single submitter
- PTPN3 p.Gln200Arg Uncertain significance Single submitter
- PTPN3 p.Gln309Glu Uncertain significance Single submitter
- PTPN3 p.Gln423Glu Uncertain significance Single submitter
- PTPN3 p.Gln52Arg Uncertain significance Single submitter
- PTPN3 p.Gln773Glu Uncertain significance Single submitter
- PTPN3 p.Glu202Lys Uncertain significance Single submitter
- PTPN3 p.Glu278Asp Uncertain significance Single submitter
- PTPN3 p.Glu442Lys Uncertain significance Single submitter
- PTPN3 p.Glu589Gly Uncertain significance Single submitter
- PTPN3 p.Glu642Lys Uncertain significance Single submitter
- PTPN3 p.Gly556Arg Uncertain significance Single submitter
- PTPN3 p.Gly644Arg Uncertain significance Single submitter
- PTPN3 p.Gly850Ser Uncertain significance Single submitter
- PTPN3 p.Gly905Asp Uncertain significance Single submitter
- PTPN3 p.Gly98Cys Uncertain significance Single submitter
- PTPN3 p.His436Tyr Uncertain significance Single submitter
- PTPN3 p.Ile177Val Uncertain significance Single submitter
- PTPN3 p.Ile258Val Uncertain significance Single submitter
- PTPN3 p.Ile388Val Uncertain significance Single submitter
- PTPN3 p.Leu149Pro Uncertain significance Single submitter
- PTPN3 p.Leu630Ser Uncertain significance Single submitter
- PTPN3 p.Leu871Arg Uncertain significance Single submitter
- PTPN3 p.Lys199Arg Uncertain significance Single submitter
- PTPN3 p.Lys532Gln Uncertain significance Single submitter
- PTPN3 p.Met327Val Uncertain significance Single submitter
- PTPN3 p.Met354Thr Uncertain significance Single submitter
- PTPN3 p.Met765Val Uncertain significance Single submitter
- PTPN3 p.Met859Thr Uncertain significance Single submitter
- PTPN3 p.Phe605Leu Uncertain significance Single submitter
- PTPN3 p.Phe728Ile Uncertain significance Single submitter
- PTPN3 p.Pro315Leu Uncertain significance Single submitter
- PTPN3 p.Pro435Thr Uncertain significance Single submitter
- PTPN3 p.Pro624Leu Uncertain significance Single submitter
- PTPN3 p.Ser18Leu Uncertain significance Single submitter
- PTPN3 p.Ser456Ile Uncertain significance Single submitter
- PTPN3 p.Ser538Thr Uncertain significance Single submitter
- PTPN3 p.Ser81Phe Uncertain significance Single submitter
- PTPN3 p.Ser81Pro Uncertain significance Single submitter
- PTPN3 p.Thr326Pro Uncertain significance Single submitter
- PTPN3 p.Thr415Met Uncertain significance Single submitter
- PTPN3 p.Thr645Met Uncertain significance Single submitter
- PTPN3 p.Trp758Arg Uncertain significance Single submitter
- PTPN3 p.Tyr126Cys Uncertain significance Single submitter
- PTPN3 p.Tyr152Cys Uncertain significance Single submitter
- PTPN3 p.Tyr247His Uncertain significance Single submitter
- PTPN3 p.Tyr416Phe Uncertain significance Single submitter
- PTPN3 p.Tyr783Cys Uncertain significance Single submitter
- PTPN3 p.Val29Asp Uncertain significance Single submitter
- PTPN3 p.Val320Ile Uncertain significance Single submitter
- PTPN3 p.Val39Met Uncertain significance Single submitter
- PTPN3 p.Val473Ile Uncertain significance Single submitter
- PTPN3 p.Val536Met Uncertain significance Single submitter
- PTPN3 p.Val53Ile Uncertain significance Single submitter
- PTPN3 p.Val53Phe Uncertain significance Single submitter
- PTPN3 p.Val575Glu Uncertain significance Single submitter
- PTPN3 p.Val679Met Uncertain significance Single submitter
- PTPN3 p.Val731Ile Uncertain significance Single submitter
- PTPN3 p.Val79Met Uncertain significance Single submitter
- PTPN3 p.Val807Ile Uncertain significance Single submitter
- PTPN3 p.Val885Met Uncertain significance Single submitter
Predictors split 36
The independent predictors disagree with each other — read with care.
- PTPN3 p.Arg292Gln Uncertain significance Single submitter
- PTPN3 p.Arg330Trp Uncertain significance Single submitter
- PTPN3 p.Arg371Leu Uncertain significance Single submitter
- PTPN3 p.Arg380Gly Uncertain significance Single submitter
- PTPN3 p.Arg385Pro Uncertain significance Single submitter
- PTPN3 p.Arg588Leu Uncertain significance Single submitter
- PTPN3 p.Arg588Trp Uncertain significance Single submitter
- PTPN3 p.Arg864Gly Uncertain significance Single submitter
- PTPN3 p.Arg864Thr Uncertain significance Single submitter
- PTPN3 p.Asp226Asn Uncertain significance Single submitter
- PTPN3 p.Asp778Gly Uncertain significance Single submitter
- PTPN3 p.Cys301Ser Uncertain significance Single submitter
- PTPN3 p.Cys774Ser Uncertain significance Single submitter
- PTPN3 p.Gln118Pro Uncertain significance Single submitter
- PTPN3 p.Gln730His Uncertain significance Single submitter
- PTPN3 p.Gln735Arg Uncertain significance Single submitter
- PTPN3 p.Gly218Ala Uncertain significance Single submitter
- PTPN3 p.Gly224Val Uncertain significance Single submitter
- PTPN3 p.Gly347Arg Uncertain significance Single submitter
- PTPN3 p.Gly659Asp Uncertain significance Single submitter
- PTPN3 p.His586Arg Uncertain significance Single submitter
- PTPN3 p.His723Arg Uncertain significance Single submitter
- PTPN3 p.His812Gln Uncertain significance Single submitter
- PTPN3 p.Ile579Val Uncertain significance Single submitter
- PTPN3 p.Ile846Leu Uncertain significance Single submitter
- PTPN3 p.Lys532Thr Uncertain significance Single submitter
- PTPN3 p.Lys892Asn Uncertain significance Single submitter
- PTPN3 p.Pro837Thr Uncertain significance Single submitter
- PTPN3 p.Ser251Arg Uncertain significance Single submitter
- PTPN3 p.Ser843Arg Uncertain significance Single submitter
- PTPN3 p.Thr571Arg Uncertain significance Single submitter
- PTPN3 p.Thr571Lys Uncertain significance Single submitter
- PTPN3 p.Thr745Pro Uncertain significance Single submitter
- PTPN3 p.Trp379Cys Uncertain significance Single submitter
- PTPN3 p.Val894Ala Uncertain significance Single submitter
-
PTPN3 p.Ala211Val
Uncertain significance
No assertion criteria
prostate cancer
All PTPN3 variants
Benign 1
- p.Ile715= Multiple submitters
Likely benign 6
- p.Gln794Glu Single submitter
- p.Gly769Ser Single submitter
- p.Leu477Phe Single submitter
- p.Pro178= Single submitter
- p.Pro616= Single submitter
- p.Pro837= Single submitter
Uncertain significance 139
- p.Asn612Thr Multiple submitters ⚠
- p.Ala146Thr Single submitter ⚠
- p.Ala150Val Single submitter ⚠
- p.Ala153Val Single submitter ⚠
- p.Ala310Pro Single submitter
- p.Ala400Glu Single submitter ⚠
- p.Arg16Cys Single submitter ⚠
- p.Arg16His Single submitter ⚠
- p.Arg212Trp Single submitter ⚠
- p.Arg245Gly Single submitter ⚠
- p.Arg265Thr Single submitter ⚠
- p.Arg292Gln Single submitter ⚠
- p.Arg330Leu Single submitter ⚠
- p.Arg330Trp Single submitter ⚠
- p.Arg371Leu Single submitter ⚠
- p.Arg380Gly Single submitter ⚠
- p.Arg385Pro Single submitter ⚠
- p.Arg389Gln Single submitter ⚠
- p.Arg392His Single submitter ⚠
- p.Arg392Leu Single submitter ⚠
- p.Arg512His Single submitter ⚠
- p.Arg583Gln Single submitter ⚠
- p.Arg588Leu Single submitter ⚠
- p.Arg588Trp Single submitter ⚠
- p.Arg6His Single submitter ⚠
- p.Arg83Gly Single submitter ⚠
- p.Arg848Gln Single submitter ⚠
- p.Arg864Gly Single submitter ⚠
- p.Arg864Thr Single submitter ⚠
- p.Arg875Gln Single submitter ⚠
- p.Asn319Ser Single submitter ⚠
- p.Asn378Ser Single submitter ⚠
- p.Asn501Lys Single submitter ⚠
- p.Asn826Ser Single submitter ⚠
- p.Asn826Tyr Single submitter ⚠
- p.Asp173Asn Single submitter ⚠
- p.Asp173Gly Single submitter ⚠
- p.Asp226Asn Single submitter ⚠
- p.Asp397Gly Single submitter ⚠
- p.Asp479Tyr Single submitter ⚠
- p.Asp502Asn Single submitter ⚠
- p.Asp56His Single submitter ⚠
- p.Asp778Gly Single submitter ⚠
- p.Asp816Asn Single submitter ⚠
- p.Asp820Asn Single submitter
- p.Asp911Gly Single submitter ⚠
- p.Cys301Ser Single submitter ⚠
- p.Cys301Tyr Single submitter ⚠
- p.Cys774Ser Single submitter ⚠
- p.Cys842Tyr Single submitter ⚠
- p.Gln118Pro Single submitter ⚠
- p.Gln200Arg Single submitter ⚠
- p.Gln309Glu Single submitter ⚠
- p.Gln423Glu Single submitter ⚠
- p.Gln52Arg Single submitter ⚠
- p.Gln730His Single submitter ⚠
- p.Gln735Arg Single submitter ⚠
- p.Gln73His Single submitter
- p.Gln773Glu Single submitter ⚠
- p.Glu202Lys Single submitter ⚠
- p.Glu278Asp Single submitter ⚠
- p.Glu442Lys Single submitter ⚠
- p.Glu589Gly Single submitter ⚠
- p.Glu642Lys Single submitter ⚠
- p.Gly218Ala Single submitter ⚠
- p.Gly224Val Single submitter ⚠
- p.Gly347Arg Single submitter ⚠
- p.Gly556Arg Single submitter ⚠
- p.Gly644Arg Single submitter ⚠
- p.Gly659Asp Single submitter ⚠
- p.Gly850Ser Single submitter ⚠
- p.Gly905Asp Single submitter ⚠
- p.Gly98Cys Single submitter ⚠
- p.His436Tyr Single submitter ⚠
- p.His586Arg Single submitter ⚠
- p.His723Arg Single submitter ⚠
- p.His812Gln Single submitter ⚠
- p.Ile177Val Single submitter ⚠
- p.Ile258Val Single submitter ⚠
- p.Ile388Val Single submitter ⚠
- p.Ile579Val Single submitter ⚠
- p.Ile846Leu Single submitter ⚠
- p.Ile846Val Single submitter
- p.Leu149Pro Single submitter ⚠
- p.Leu630Ser Single submitter ⚠
- p.Leu871Arg Single submitter ⚠
- p.Lys199Arg Single submitter ⚠
- p.Lys532Gln Single submitter ⚠
- p.Lys532Thr Single submitter ⚠
- p.Lys892Asn Single submitter ⚠
- p.Met327Val Single submitter ⚠
- p.Met354Thr Single submitter ⚠
- p.Met765Val Single submitter ⚠
- p.Met859Thr Single submitter ⚠
- p.Phe605Leu Single submitter ⚠
- p.Phe728Ile Single submitter ⚠
- p.Pro315Leu Single submitter ⚠
- p.Pro435Thr Single submitter ⚠
- p.Pro624Leu Single submitter ⚠
- p.Pro837Thr Single submitter ⚠
- p.Ser18Leu Single submitter ⚠
- p.Ser251Arg Single submitter ⚠
- p.Ser456Ile Single submitter ⚠
- p.Ser538Thr Single submitter ⚠
- p.Ser81Phe Single submitter ⚠
- p.Ser81Pro Single submitter ⚠
- p.Ser843Arg Single submitter ⚠
- p.Thr250Ile Single submitter
- p.Thr326Pro Single submitter ⚠
- p.Thr415Met Single submitter ⚠
- p.Thr571Arg Single submitter ⚠
- p.Thr571Lys Single submitter ⚠
- p.Thr645Met Single submitter ⚠
- p.Thr745Pro Single submitter ⚠
- p.Trp379Cys Single submitter ⚠
- p.Trp758Arg Single submitter ⚠
- p.Tyr126Cys Single submitter ⚠
- p.Tyr152Cys Single submitter ⚠
- p.Tyr247His Single submitter ⚠
- p.Tyr416Phe Single submitter ⚠
- p.Tyr783Cys Single submitter ⚠
- p.Tyr783Ser Single submitter
- p.Val29Asp Single submitter ⚠
- p.Val320Ile Single submitter ⚠
- p.Val39Met Single submitter ⚠
- p.Val473Ile Single submitter ⚠
- p.Val536Met Single submitter ⚠
- p.Val53Ile Single submitter ⚠
- p.Val53Phe Single submitter ⚠
- p.Val575Glu Single submitter ⚠
- p.Val64Ala Single submitter
- p.Val679Met Single submitter ⚠
- p.Val731Ile Single submitter ⚠
- p.Val79Met Single submitter ⚠
- p.Val807Ile Single submitter ⚠
- p.Val825Ala Single submitter
- p.Val885Met Single submitter ⚠
- p.Val894Ala Single submitter ⚠
- p.Ala211Val No assertion criteria prostate cancer ⚠