PTPMT1 — 37 ClinVar variants
All ClinVar germline PTPMT1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 26 flagged for review →
1 Pathogenic · 1 Benign · 8 Likely benign · 27 Uncertain significance
Full PTPMT1 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 vs ClinVar 1
ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.
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PTPMT1 p.Gln85His
Pathogenic
No assertion criteria
neurodevelopmental disorder with ataxia and brain abnormalities
Predictors lean, ClinVar uncertain 21
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- PTPMT1 p.Ala118Val Uncertain significance Single submitter
- PTPMT1 p.Ala145Thr Uncertain significance Single submitter
- PTPMT1 p.Ala188Thr Uncertain significance Single submitter
- PTPMT1 p.Arg189Trp Uncertain significance Single submitter
- PTPMT1 p.Arg78Lys Uncertain significance Single submitter
- PTPMT1 p.Gln175Pro Uncertain significance Single submitter
- PTPMT1 p.Gln61His Uncertain significance Single submitter
- PTPMT1 p.Glu73Lys Uncertain significance Single submitter
- PTPMT1 p.Glu74Asp Uncertain significance Single submitter
- PTPMT1 p.Glu8Gln Uncertain significance Single submitter
- PTPMT1 p.Gly104Val Uncertain significance Single submitter
- PTPMT1 p.Leu119Val Uncertain significance Single submitter
- PTPMT1 p.Leu176Val Uncertain significance Single submitter
- PTPMT1 p.Lys113Glu Uncertain significance Single submitter
- PTPMT1 p.Lys192Arg Uncertain significance Single submitter
- PTPMT1 p.Met142Thr Uncertain significance Single submitter
- PTPMT1 p.Phe196Ser Uncertain significance Single submitter
- PTPMT1 p.Ser139Asn Uncertain significance Single submitter
- PTPMT1 p.Thr103Ser Uncertain significance Single submitter
- PTPMT1 p.Thr77Met Uncertain significance Single submitter
- PTPMT1 p.Trp87Cys Uncertain significance Single submitter
Predictors split 4
The independent predictors disagree with each other — read with care.
All PTPMT1 variants
Pathogenic 1
- p.Gln85His No assertion criteria neurodevelopmental disorder with ataxia and brain abnormalities ⚠
Benign 1
- p.Ter202Ser Multiple submitters
Likely benign 8
- c.174+42C>T Single submitter
- p.Ala163Thr Single submitter
- p.Gln175= Single submitter
- p.His151= Single submitter
- p.Ile165= Single submitter
- p.Ile171= Single submitter
- p.Leu90Val Single submitter
- p.Val68= Single submitter
Uncertain significance 27
- p.Ala118Val Single submitter ⚠
- p.Ala145Thr Single submitter ⚠
- p.Ala188Thr Single submitter ⚠
- p.Arg136His Single submitter ⚠
- p.Arg172Ser Single submitter
- p.Arg189Trp Single submitter ⚠
- p.Arg78Lys Single submitter ⚠
- p.Arg96Trp Single submitter ⚠
- p.Gln175Pro Single submitter ⚠
- p.Gln61His Single submitter ⚠
- p.Glu73Lys Single submitter ⚠
- p.Glu74Asp Single submitter ⚠
- p.Glu8Gln Single submitter ⚠
- p.Glu93Lys Single submitter ⚠
- p.Gly104Val Single submitter ⚠
- p.Leu119Val Single submitter ⚠
- p.Leu176Val Single submitter ⚠
- p.Lys113Glu Single submitter ⚠
- p.Lys192Arg Single submitter ⚠
- p.Met142Thr Single submitter ⚠
- p.Phe196Ser Single submitter ⚠
- p.Pro155Thr Single submitter ⚠
- p.Ser139Asn Single submitter ⚠
- p.Thr103Ser Single submitter ⚠
- p.Thr77Met Single submitter ⚠
- p.Trp87Cys Single submitter ⚠
- p.Val60Ala Single submitter