PTPN6 — 72 ClinVar variants
All ClinVar germline PTPN6 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 44 flagged for review →
1 Conflicting · 9 Benign · 7 Likely benign · 55 Uncertain significance
Full PTPN6 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 44
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 36
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- PTPN6 p.Ala205Thr Uncertain significance Single submitter
- PTPN6 p.Ala240Val Uncertain significance Single submitter
- PTPN6 p.Ala446Ser Uncertain significance Single submitter
- PTPN6 p.Ala493Thr Uncertain significance Single submitter
- PTPN6 p.Arg163Lys Uncertain significance Single submitter
- PTPN6 p.Arg210Gln Uncertain significance Single submitter
- PTPN6 p.Arg345Cys Uncertain significance Single submitter
- PTPN6 p.Arg372His Uncertain significance Single submitter
- PTPN6 p.Arg554His Uncertain significance Single submitter
- PTPN6 p.Arg89Cys Uncertain significance Single submitter
- PTPN6 p.Asp189Glu Uncertain significance Single submitter
- PTPN6 p.Asp238Tyr Uncertain significance Single submitter
- PTPN6 p.Asp404Glu Uncertain significance Single submitter
- PTPN6 p.Gln83His Uncertain significance Single submitter
- PTPN6 p.Glu367Lys Uncertain significance Single submitter
- PTPN6 p.Glu389Ala Uncertain significance Single submitter
- PTPN6 p.Glu67Ala Uncertain significance Single submitter
- PTPN6 p.Gly20Cys Uncertain significance Single submitter
- PTPN6 p.His385Arg Uncertain significance Single submitter
- PTPN6 p.His549Arg Uncertain significance Single submitter
- PTPN6 p.His559Arg Uncertain significance Single submitter
- PTPN6 p.Ile322Leu Uncertain significance Single submitter
- PTPN6 p.Leu12Arg Uncertain significance Single submitter
- PTPN6 p.Lys319Asn Uncertain significance Single submitter
- PTPN6 p.Phe145Val Uncertain significance Single submitter
- PTPN6 p.Pro212Leu Uncertain significance Single submitter
- PTPN6 p.Pro99Ser Uncertain significance Single submitter
- PTPN6 p.Ser294Gly Uncertain significance Single submitter
- PTPN6 p.Ser528Leu Uncertain significance Single submitter
- PTPN6 p.Ser534Leu Uncertain significance Single submitter
- PTPN6 p.Ser553Phe Uncertain significance Single submitter
- PTPN6 p.Ser553Tyr Uncertain significance Single submitter
- PTPN6 p.Thr16Ile Uncertain significance Single submitter
- PTPN6 p.Thr183Ser Uncertain significance Single submitter
- PTPN6 p.Thr518Ser Uncertain significance Single submitter
- PTPN6 p.Val510Met Uncertain significance Single submitter
Predictors split 8
The independent predictors disagree with each other — read with care.
- PTPN6 p.Arg163Gly Uncertain significance Single submitter
- PTPN6 p.Arg175Cys Uncertain significance Single submitter
- PTPN6 p.Glu249Lys Uncertain significance Single submitter
- PTPN6 p.Gly157Asp Uncertain significance Single submitter
- PTPN6 p.Met470Thr Uncertain significance Single submitter
- PTPN6 p.Ser528Trp Uncertain significance Single submitter
- PTPN6 p.Ser557Cys Uncertain significance Single submitter
- PTPN6 p.Val43Ile Uncertain significance Single submitter
All PTPN6 variants
Conflicting classifications of pathogenicity 1
- c.9-6G>A Single submitter
Benign 9
- p.Cys361= Multiple submitters
- p.Pro399= Multiple submitters
- p.Ser42= Multiple submitters
- c.1074+15dup Single submitter
- c.1207-8C>T Single submitter
- c.1582-10C>G Single submitter
- p.Gly326= Single submitter
- p.Ile466= Single submitter
- p.Phe507= Single submitter
Likely benign 7
- c.8+8C>A Single submitter
- p.Ala318Thr Single submitter
- p.Ala339Val Single submitter
- p.Gly383Arg Single submitter
- p.His568Tyr Single submitter
- p.Ser454= Single submitter
- p.Thr569Ala Single submitter
Uncertain significance 55
- c.9-7C>T Multiple submitters
- c.1206+2T>G Single submitter autism spectrum disorder
- c.1674-22G>C Single submitter
- c.1674-34C>G Single submitter
- c.1674-42T>C Single submitter
- c.1674-51C>G Single submitter
- c.1674-82G>A Single submitter
- c.1674-83G>C Single submitter
- c.1674-9C>T Single submitter
- p.Ala205Thr Single submitter ⚠
- p.Ala240Val Single submitter ⚠
- p.Ala446Ser Single submitter ⚠
- p.Ala493Thr Single submitter ⚠
- p.Arg163Gly Single submitter ⚠
- p.Arg163Lys Single submitter ⚠
- p.Arg175Cys Single submitter ⚠
- p.Arg210Gln Single submitter ⚠
- p.Arg345Cys Single submitter ⚠
- p.Arg352Gln Single submitter
- p.Arg372His Single submitter ⚠
- p.Arg554His Single submitter ⚠
- p.Arg89Cys Single submitter ⚠
- p.Asp189Glu Single submitter ⚠
- p.Asp238Tyr Single submitter ⚠
- p.Asp404Glu Single submitter ⚠
- p.Gln83His Single submitter ⚠
- p.Glu249Lys Single submitter ⚠
- p.Glu367Lys Single submitter ⚠
- p.Glu389Ala Single submitter ⚠
- p.Glu67Ala Single submitter ⚠
- p.Gly157Asp Single submitter ⚠
- p.Gly20Cys Single submitter ⚠
- p.His385Arg Single submitter ⚠
- p.His549Arg Single submitter ⚠
- p.His559Arg Single submitter ⚠
- p.Ile322Leu Single submitter ⚠
- p.Leu12Arg Single submitter ⚠
- p.Lys319Asn Single submitter ⚠
- p.Met470Thr Single submitter ⚠
- p.Phe145Val Single submitter ⚠
- p.Pro212Leu Single submitter ⚠
- p.Pro99Ser Single submitter ⚠
- p.Ser294Gly Single submitter ⚠
- p.Ser528Leu Single submitter ⚠
- p.Ser528Trp Single submitter ⚠
- p.Ser534Leu Single submitter ⚠
- p.Ser553Phe Single submitter ⚠
- p.Ser553Tyr Single submitter ⚠
- p.Ser557Cys Single submitter ⚠
- p.Thr16Ile Single submitter ⚠
- p.Thr183Ser Single submitter ⚠
- p.Thr518Ser Single submitter ⚠
- p.Val43Ile Single submitter ⚠
- p.Val510Met Single submitter ⚠
- c.845_854delTTGACCACAG No assertion criteria Neurodevelopmental abnormality