PTPN9 — 65 ClinVar variants
All ClinVar germline PTPN9 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 56 flagged for review →
1 Benign · 3 Likely benign · 61 Uncertain significance
Full PTPN9 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 56
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 47
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- PTPN9 p.Ala244Thr Uncertain significance Single submitter
- PTPN9 p.Ala500Thr Uncertain significance Single submitter
- PTPN9 p.Arg182Cys Uncertain significance Single submitter
- PTPN9 p.Arg211Trp Uncertain significance Single submitter
- PTPN9 p.Arg228Lys Uncertain significance Single submitter
- PTPN9 p.Arg312Cys Uncertain significance Single submitter
- PTPN9 p.Arg349Gln Uncertain significance Single submitter
- PTPN9 p.Arg384Cys Uncertain significance Single submitter
- PTPN9 p.Arg384Gly Uncertain significance Single submitter
- PTPN9 p.Arg384His Uncertain significance Single submitter
- PTPN9 p.Arg458Cys Uncertain significance Single submitter
- PTPN9 p.Arg501Cys Uncertain significance Single submitter
- PTPN9 p.Arg501His Uncertain significance Single submitter
- PTPN9 p.Asn314Ile Uncertain significance Single submitter
- PTPN9 p.Asp421Glu Uncertain significance Single submitter
- PTPN9 p.Asp470Tyr Uncertain significance Single submitter
- PTPN9 p.Gln354Glu Uncertain significance Single submitter
- PTPN9 p.Gln464Arg Uncertain significance Single submitter
- PTPN9 p.Glu229Gln Uncertain significance Single submitter
- PTPN9 p.Glu29Gly Uncertain significance Single submitter
- PTPN9 p.Glu380Gly Uncertain significance Single submitter
- PTPN9 p.Gly256Ser Uncertain significance Single submitter
- PTPN9 p.Gly584Asp Uncertain significance Single submitter
- PTPN9 p.His125Pro Uncertain significance Single submitter
- PTPN9 p.His257Tyr Uncertain significance Single submitter
- PTPN9 p.Ile109Val Uncertain significance Single submitter
- PTPN9 p.Ile241Thr Uncertain significance Single submitter
- PTPN9 p.Ile288Met Uncertain significance Single submitter
- PTPN9 p.Ile424Val Uncertain significance Single submitter
- PTPN9 p.Leu429Pro Uncertain significance Single submitter
- PTPN9 p.Leu538Pro Uncertain significance Single submitter
- PTPN9 p.Leu587Pro Uncertain significance Single submitter
- PTPN9 p.Lys49Arg Uncertain significance Single submitter
- PTPN9 p.Lys55Thr Uncertain significance Single submitter
- PTPN9 p.Met439Val Uncertain significance Single submitter
- PTPN9 p.Pro104Thr Uncertain significance Single submitter
- PTPN9 p.Pro283Thr Uncertain significance Single submitter
- PTPN9 p.Thr446Ala Uncertain significance Single submitter
- PTPN9 p.Thr446Met Uncertain significance Single submitter
- PTPN9 p.Thr452Ile Uncertain significance Single submitter
- PTPN9 p.Thr71Ala Uncertain significance Single submitter
- PTPN9 p.Trp275Arg Uncertain significance Single submitter
- PTPN9 p.Tyr442Phe Uncertain significance Single submitter
- PTPN9 p.Val239Ile Uncertain significance Single submitter
- PTPN9 p.Val239Leu Uncertain significance Single submitter
- PTPN9 p.Val316Ala Uncertain significance Single submitter
- PTPN9 p.Val436Met Uncertain significance Single submitter
Predictors split 9
The independent predictors disagree with each other — read with care.
- PTPN9 p.Ala61Ser Uncertain significance Single submitter
- PTPN9 p.Glu562Gln Uncertain significance Single submitter
- PTPN9 p.Ile30Thr Uncertain significance Single submitter
- PTPN9 p.Ile91Met Uncertain significance Single submitter
- PTPN9 p.Leu183Val Uncertain significance Single submitter
- PTPN9 p.Phe65Tyr Uncertain significance Single submitter
- PTPN9 p.Ser220Phe Uncertain significance Single submitter
- PTPN9 p.Ser422Phe Uncertain significance Single submitter
- PTPN9 p.Thr34Ile Uncertain significance Single submitter
All PTPN9 variants
Benign 1
- p.Gln129= Single submitter
Likely benign 3
- c.1567+5C>T Single submitter
- p.Arg403= Single submitter
- p.Leu206= Single submitter
Uncertain significance 61
- p.Ala244Thr Single submitter ⚠
- p.Ala500Thr Single submitter ⚠
- p.Ala61Ser Single submitter ⚠
- p.Arg182Cys Single submitter ⚠
- p.Arg211Trp Single submitter ⚠
- p.Arg228Lys Single submitter ⚠
- p.Arg312Cys Single submitter ⚠
- p.Arg349Gln Single submitter ⚠
- p.Arg384Cys Single submitter ⚠
- p.Arg384Gly Single submitter ⚠
- p.Arg384His Single submitter ⚠
- p.Arg458Cys Single submitter ⚠
- p.Arg501Cys Single submitter ⚠
- p.Arg501His Single submitter ⚠
- p.Arg88His Single submitter
- p.Asn255Lys Single submitter
- p.Asn314Ile Single submitter ⚠
- p.Asp421Glu Single submitter ⚠
- p.Asp470Tyr Single submitter ⚠
- p.Gln354Glu Single submitter ⚠
- p.Gln464Arg Single submitter ⚠
- p.Glu229Gln Single submitter ⚠
- p.Glu29Gly Single submitter ⚠
- p.Glu380Gly Single submitter ⚠
- p.Glu562Gln Single submitter ⚠
- p.Gly256Ser Single submitter ⚠
- p.Gly584Asp Single submitter ⚠
- p.His125Pro Single submitter ⚠
- p.His257Tyr Single submitter ⚠
- p.Ile109Val Single submitter ⚠
- p.Ile241Thr Single submitter ⚠
- p.Ile288Met Single submitter ⚠
- p.Ile303Met Single submitter
- p.Ile30Thr Single submitter ⚠
- p.Ile424Val Single submitter ⚠
- p.Ile91Met Single submitter ⚠
- p.Leu183Val Single submitter ⚠
- p.Leu429Pro Single submitter ⚠
- p.Leu538Pro Single submitter ⚠
- p.Leu587Pro Single submitter ⚠
- p.Lys49Arg Single submitter ⚠
- p.Lys55Thr Single submitter ⚠
- p.Met439Val Single submitter ⚠
- p.Phe65Tyr Single submitter ⚠
- p.Pro104Gln Single submitter
- p.Pro104Thr Single submitter ⚠
- p.Pro283Thr Single submitter ⚠
- p.Ser220Phe Single submitter ⚠
- p.Ser422Phe Single submitter ⚠
- p.Thr34Ile Single submitter ⚠
- p.Thr446Ala Single submitter ⚠
- p.Thr446Met Single submitter ⚠
- p.Thr452Ile Single submitter ⚠
- p.Thr540Ile Single submitter
- p.Thr71Ala Single submitter ⚠
- p.Trp275Arg Single submitter ⚠
- p.Tyr442Phe Single submitter ⚠
- p.Val239Ile Single submitter ⚠
- p.Val239Leu Single submitter ⚠
- p.Val316Ala Single submitter ⚠
- p.Val436Met Single submitter ⚠