PTPN1 — 38 ClinVar variants
All ClinVar germline PTPN1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 26 flagged for review →
2 Pathogenic · 1 Likely pathogenic · 2 Benign · 5 Likely benign · 28 Uncertain significance
Full PTPN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 26
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 23
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- PTPN1 p.Ala416Thr Uncertain significance Single submitter
- PTPN1 p.Arg238Lys Uncertain significance Single submitter
- PTPN1 p.Arg380Gly Uncertain significance Single submitter
- PTPN1 p.Asp265His Uncertain significance Single submitter
- PTPN1 p.Gln166Lys Uncertain significance Single submitter
- PTPN1 p.Gln290His Uncertain significance Single submitter
- PTPN1 p.Glu349Gly Uncertain significance Single submitter
- PTPN1 p.Glu399Lys Uncertain significance Single submitter
- PTPN1 p.Ile10Leu Uncertain significance Single submitter
- PTPN1 p.Ile361Thr Uncertain significance Single submitter
- PTPN1 p.Leu172Ser Uncertain significance Single submitter
- PTPN1 p.Pro313Leu Uncertain significance Single submitter
- PTPN1 p.Pro353Arg Uncertain significance Single submitter
- PTPN1 p.Ser15Arg Uncertain significance Single submitter
- PTPN1 p.Ser352Asn Uncertain significance Single submitter
- PTPN1 p.Ser365Cys Uncertain significance Single submitter
- PTPN1 p.Ser378Asn Uncertain significance Single submitter
- PTPN1 p.Thr165Ile Uncertain significance Single submitter
- PTPN1 p.Thr230Ser Uncertain significance Single submitter
- PTPN1 p.Val108Ile Uncertain significance Single submitter
- PTPN1 p.Val184Asp Uncertain significance Single submitter
- PTPN1 p.Val287Leu Uncertain significance Single submitter
- PTPN1 p.Val287Met Uncertain significance Single submitter
Predictors split 3
The independent predictors disagree with each other — read with care.
All PTPN1 variants
Pathogenic 2
- p.Gly209Arg Single submitter Autoinflammatory encephalopathy due to PTPN1 haploinsufficiency
- p.Tyr153fs Single submitter
Likely pathogenic 1
- p.Asp137fs Single submitter type 1 interferonopathy of childhood
Likely benign 5
- p.Asn68= Single submitter
- p.Glu396Lys Single submitter
- p.Pro302Leu Single submitter
- p.Pro387Leu Single submitter
- p.Val211Ile Single submitter
Uncertain significance 28
- p.Ala189Gly Single submitter ⚠
- p.Ala416Thr Single submitter ⚠
- p.Arg238Lys Single submitter ⚠
- p.Arg380Gly Single submitter ⚠
- p.Asp265His Single submitter ⚠
- p.Gln123fs Single submitter type 2 diabetes mellitus
- p.Gln166Lys Single submitter ⚠
- p.Gln290His Single submitter ⚠
- p.Gln78Arg Single submitter ⚠
- p.Glu349Gly Single submitter ⚠
- p.Glu399Lys Single submitter ⚠
- p.Ile10Leu Single submitter ⚠
- p.Ile361Thr Single submitter ⚠
- p.Leu172Ser Single submitter ⚠
- p.Pro302Arg Single submitter ⚠
- p.Pro313Leu Single submitter ⚠
- p.Pro353Arg Single submitter ⚠
- p.Pro89Ser Single submitter
- p.Ser15Arg Single submitter ⚠
- p.Ser352Asn Single submitter ⚠
- p.Ser365Cys Single submitter ⚠
- p.Ser378Asn Single submitter ⚠
- p.Thr165Ile Single submitter ⚠
- p.Thr230Ser Single submitter ⚠
- p.Val108Ile Single submitter ⚠
- p.Val184Asp Single submitter ⚠
- p.Val287Leu Single submitter ⚠
- p.Val287Met Single submitter ⚠