PTPRT — 227 ClinVar variants
All ClinVar germline PTPRT variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 153 flagged for review →
2 Likely pathogenic · 33 Benign · 1 Benign/Likely benign · 24 Likely benign · 167 Uncertain significance
Full PTPRT gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 153
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.
-
PTPRT p.Val69Ala
Likely pathogenic
Single submitter
Abnormal brain morphology
Predictors lean, ClinVar uncertain 116
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- PTPRT p.Ala1342Val Uncertain significance Single submitter
- PTPRT p.Ala28Thr Uncertain significance Single submitter
- PTPRT p.Ala2Glu Uncertain significance Single submitter
- PTPRT p.Ala335Ser Uncertain significance Single submitter
- PTPRT p.Ala571Thr Uncertain significance Single submitter
- PTPRT p.Ala68Thr Uncertain significance Single submitter
- PTPRT p.Ala727Thr Uncertain significance Single submitter
- PTPRT p.Ala868Thr Uncertain significance Single submitter
- PTPRT p.Ala981Thr Uncertain significance Single submitter
- PTPRT p.Arg1043His Uncertain significance Single submitter
- PTPRT p.Arg1117His Uncertain significance Single submitter
- PTPRT p.Arg112Gly Uncertain significance Single submitter
- PTPRT p.Arg1188His Uncertain significance Single submitter
- PTPRT p.Arg1207Gln Uncertain significance Single submitter
- PTPRT p.Arg1216Leu Uncertain significance Single submitter
- PTPRT p.Arg1318Cys Uncertain significance Single submitter
- PTPRT p.Arg1318His Uncertain significance Single submitter
- PTPRT p.Arg1358Gln Uncertain significance Single submitter
-
PTPRT p.Arg1358Pro
Uncertain significance
Single submitter
PTPRT-associated neurodevelopmentaldisorder
- PTPRT p.Arg1373His Uncertain significance Single submitter
- PTPRT p.Arg1414Cys Uncertain significance Single submitter
- PTPRT p.Arg1414Gly Uncertain significance Single submitter
- PTPRT p.Arg1414His Uncertain significance Single submitter
- PTPRT p.Arg1414Ser Uncertain significance Single submitter
- PTPRT p.Arg24Gln Uncertain significance Single submitter
- PTPRT p.Arg260Gln Uncertain significance Single submitter
- PTPRT p.Arg539Lys Uncertain significance Single submitter
- PTPRT p.Arg617Trp Uncertain significance Single submitter
- PTPRT p.Arg653Trp Uncertain significance Single submitter
- PTPRT p.Arg815Leu Uncertain significance Single submitter
- PTPRT p.Arg835Cys Uncertain significance Single submitter
- PTPRT p.Arg862Gln Uncertain significance Single submitter
- PTPRT p.Asn1268Ser Uncertain significance Single submitter
- PTPRT p.Asn200Ser Uncertain significance Single submitter
- PTPRT p.Asn208His Uncertain significance Single submitter
- PTPRT p.Asn392Lys Uncertain significance Single submitter
- PTPRT p.Asn50Ser Uncertain significance Single submitter
- PTPRT p.Asn743His Uncertain significance Single submitter
- PTPRT p.Asn816Asp Uncertain significance Single submitter
- PTPRT p.Asn828Lys Uncertain significance Single submitter
- PTPRT p.Asn979Ile Uncertain significance Single submitter
- PTPRT p.Asp113Asn Uncertain significance Single submitter
- PTPRT p.Asp1266Asn Uncertain significance Single submitter
- PTPRT p.Asp272His Uncertain significance Single submitter
- PTPRT p.Asp659Asn Uncertain significance Single submitter
- PTPRT p.Asp659Gly Uncertain significance Single submitter
- PTPRT p.Asp805Glu Uncertain significance Single submitter
- PTPRT p.Asp817Glu Uncertain significance Single submitter
- PTPRT p.Asp826Gly Uncertain significance Single submitter
- PTPRT p.Asp949Gly Uncertain significance Single submitter
- PTPRT p.Cys1395Arg Uncertain significance Single submitter
- PTPRT p.Gln677Arg Uncertain significance Single submitter
- PTPRT p.Gln791His Uncertain significance Single submitter
- PTPRT p.Glu326Lys Uncertain significance Single submitter
- PTPRT p.Glu367Asp Uncertain significance Single submitter
- PTPRT p.Glu436Lys Uncertain significance Single submitter
- PTPRT p.Gly1294Arg Uncertain significance Single submitter
- PTPRT p.Gly140Arg Uncertain significance Single submitter
-
PTPRT p.Gly274Val
Uncertain significance
Single submitter
PTPRT-associated neurodevelopmental disorder
- PTPRT p.Gly496Glu Uncertain significance Single submitter
- PTPRT p.Gly527Ser Uncertain significance Single submitter
- PTPRT p.Gly829Arg Uncertain significance Single submitter
- PTPRT p.His1037Gln Uncertain significance Single submitter
- PTPRT p.His446Leu Uncertain significance Single submitter
- PTPRT p.His926Tyr Uncertain significance Single submitter
- PTPRT p.Ile103Leu Uncertain significance Single submitter
- PTPRT p.Ile1184Thr Uncertain significance Single submitter
- PTPRT p.Ile1398Val Uncertain significance Single submitter
- PTPRT p.Ile1404Met Uncertain significance Single submitter
- PTPRT p.Ile586Thr Uncertain significance Single submitter
- PTPRT p.Ile642Phe Uncertain significance Single submitter
- PTPRT p.Ile717Val Uncertain significance Single submitter
- PTPRT p.Ile751Val Uncertain significance Single submitter
- PTPRT p.Ile768Val Uncertain significance Single submitter
- PTPRT p.Ile958Thr Uncertain significance Single submitter
- PTPRT p.Leu322Met Uncertain significance Single submitter
- PTPRT p.Leu708Ile Uncertain significance Single submitter
- PTPRT p.Lys1355Arg Uncertain significance Single submitter
- PTPRT p.Lys264Gln Uncertain significance Single submitter
- PTPRT p.Lys264Thr Uncertain significance Single submitter
- PTPRT p.Lys544Glu Uncertain significance Single submitter
- PTPRT p.Phe105Leu Uncertain significance Single submitter
- PTPRT p.Phe553Ser Uncertain significance Single submitter
- PTPRT p.Pro1075Leu Uncertain significance Single submitter
- PTPRT p.Pro1168Ala Uncertain significance Single submitter
- PTPRT p.Pro1348Ala Uncertain significance Single submitter
- PTPRT p.Pro508Thr Uncertain significance Single submitter
- PTPRT p.Pro620Ser Uncertain significance Single submitter
- PTPRT p.Pro938Leu Uncertain significance Single submitter
- PTPRT p.Ser3Ile Uncertain significance Single submitter
- PTPRT p.Ser44Asn Uncertain significance Single submitter
- PTPRT p.Ser532Thr Uncertain significance Single submitter
- PTPRT p.Ser79Cys Uncertain significance Single submitter
- PTPRT p.Ser823Arg Uncertain significance Single submitter
- PTPRT p.Thr1005Lys Uncertain significance Single submitter
- PTPRT p.Thr1099Ala Uncertain significance Single submitter
- PTPRT p.Thr1170Ile Uncertain significance Single submitter
- PTPRT p.Thr290Met Uncertain significance Single submitter
- PTPRT p.Thr808Ile Uncertain significance Single submitter
- PTPRT p.Thr844Met Uncertain significance Single submitter
- PTPRT p.Val122Ile Uncertain significance Single submitter
- PTPRT p.Val1247Leu Uncertain significance Single submitter
- PTPRT p.Val1264Met Uncertain significance Single submitter
- PTPRT p.Val1304Ile Uncertain significance Single submitter
- PTPRT p.Val142Ile Uncertain significance Single submitter
- PTPRT p.Val1430Leu Uncertain significance Single submitter
- PTPRT p.Val201Met Uncertain significance Single submitter
- PTPRT p.Val239Ile Uncertain significance Single submitter
- PTPRT p.Val277Gly Uncertain significance Single submitter
- PTPRT p.Val515Ile Uncertain significance Single submitter
- PTPRT p.Val720Ile Uncertain significance Single submitter
-
PTPRT p.Val735Met
Uncertain significance
Single submitter
PTPRT-related disorder
- PTPRT p.Val745Met Uncertain significance Single submitter
- PTPRT p.Val764Met Uncertain significance Single submitter
- PTPRT p.Val827Ile Uncertain significance Single submitter
-
PTPRT p.Gln1366Leu
Uncertain significance
No assertion criteria
PTPRT-related disorder
Predictors split 36
The independent predictors disagree with each other — read with care.
- PTPRT p.Thr1249Ala Likely benign Multiple submitters
- PTPRT p.Val998Ala Benign Multiple submitters
- PTPRT p.Ala1245Thr Uncertain significance Single submitter
- PTPRT p.Ala1390Thr Uncertain significance Single submitter
- PTPRT p.Ala525Thr Uncertain significance Single submitter
- PTPRT p.Ala774Asp Uncertain significance Single submitter
- PTPRT p.Arg1043Cys Uncertain significance Single submitter
- PTPRT p.Arg1201Pro Uncertain significance Single submitter
- PTPRT p.Arg1324Gln Uncertain significance Single submitter
- PTPRT p.Arg190Ile Uncertain significance Single submitter
- PTPRT p.Arg247His Uncertain significance Single submitter
- PTPRT p.Arg416His Uncertain significance Single submitter
- PTPRT p.Arg870Gln Uncertain significance Single submitter
- PTPRT p.Asn1073Ser Uncertain significance Single submitter
- PTPRT p.Asn344Lys Uncertain significance Single submitter
- PTPRT p.Asp1327Gly Uncertain significance Single submitter
- PTPRT p.Asp385His Uncertain significance Single submitter
- PTPRT p.Glu1105Lys Uncertain significance Single submitter
- PTPRT p.Glu336Asp Uncertain significance Single submitter
-
PTPRT p.Gly232Ser
Uncertain significance
Single submitter
PTPRT-related disorder
- PTPRT p.Gly888Arg Uncertain significance Single submitter
- PTPRT p.His159Arg Uncertain significance Single submitter
- PTPRT p.His245Tyr Uncertain significance Single submitter
- PTPRT p.Ile760Thr Uncertain significance Single submitter
- PTPRT p.Met591Thr Uncertain significance Single submitter
- PTPRT p.Phe1265Leu Uncertain significance Single submitter
- PTPRT p.Phe1265Ser Uncertain significance Single submitter
- PTPRT p.Pro592Ser Uncertain significance Single submitter
-
PTPRT p.Thr1346Met
Uncertain significance
Single submitter
intellectual disability
- PTPRT p.Thr59Ala Uncertain significance Single submitter
- PTPRT p.Tyr345His Uncertain significance Single submitter
- PTPRT p.Tyr428His Uncertain significance Single submitter
- PTPRT p.Val1211Ala Uncertain significance Single submitter
- PTPRT p.Val1257Met Uncertain significance Single submitter
- PTPRT p.Val488Leu Uncertain significance Single submitter
-
PTPRT p.Ser1208Gly
Likely benign
No assertion criteria
PTPRT-related disorder
All PTPRT variants
Likely pathogenic 2
- c.1561-3C>T Single submitter Abnormal brain morphology
- p.Val69Ala Single submitter Abnormal brain morphology ⚠
Benign 33
- c.*1640G>A Multiple submitters
- p.Ala152= Multiple submitters
- p.Ala250= Multiple submitters
- p.Ala571= Multiple submitters
- p.Ala813Thr Multiple submitters
- p.Arg399= Multiple submitters
- p.Asn40= Multiple submitters
- p.Asp353= Multiple submitters
- p.His1053= Multiple submitters
- p.Leu838= Multiple submitters
- p.Tyr435= Multiple submitters
- p.Val242= Multiple submitters
- p.Val387= Multiple submitters
- p.Val396Ile Multiple submitters
- p.Val478= Multiple submitters
- p.Val933Leu Multiple submitters
- p.Val998Ala Multiple submitters ⚠
- c.1153+7dup Single submitter
- c.2176+12068A>C Single submitter
- p.Asn392= Single submitter
- p.Cys1115= Single submitter
- p.Ser980= Single submitter
- p.Tyr38= Single submitter
- p.Tyr447= Single submitter
- p.Val135= Single submitter
- c.1154-10T>C No assertion criteria PTPRT-related disorder
- c.2683-9G>T No assertion criteria PTPRT-related disorder
- c.3099+10T>C No assertion criteria PTPRT-related disorder
- c.4136+8C>T No assertion criteria PTPRT-related disorder
- p.Ala29Pro No assertion criteria PTPRT-related disorder
- p.Leu47= No assertion criteria PTPRT-related disorder
- p.Phe34= No assertion criteria PTPRT-related disorder
- p.Tyr1287= No assertion criteria PTPRT-related disorder
Benign/Likely benign 1
- p.Ala215= Multiple submitters
Likely benign 24
- p.Ala1235Thr Multiple submitters
- p.Thr1249Ala Multiple submitters ⚠
- c.2313-4A>G Single submitter
- p.Arg1384His Single submitter
- p.Asp1210= Single submitter
- p.Gly374= Single submitter
- p.Gly496= Single submitter
- p.Gly555= Single submitter
- p.Leu761Val Single submitter
- p.Phe1246= Single submitter
- p.Pro963= Single submitter
- p.Thr844= Single submitter
- p.Tyr594= Single submitter
- p.Arg930= No assertion criteria PTPRT-related disorder
- p.Asp683= No assertion criteria PTPRT-related disorder
- p.Cys1295Ser No assertion criteria PTPRT-related disorder
- p.Ile717= No assertion criteria PTPRT-related disorder
- p.Leu658= No assertion criteria PTPRT-related disorder
- p.Pro352= No assertion criteria PTPRT-related disorder
- p.Pro467= No assertion criteria PTPRT-related disorder
- p.Ser1208Gly No assertion criteria PTPRT-related disorder ⚠
- p.Ser528= No assertion criteria PTPRT-related disorder
- p.Thr1346= No assertion criteria PTPRT-related disorder
- p.Val1430= No assertion criteria PTPRT-related disorder
Uncertain significance 167
- c.2176+12038C>T Single submitter
- c.2176+12041A>G Single submitter
- c.2176+12062C>T Single submitter
- c.2176+12063C>T Single submitter
- c.89-1G>A Single submitter
- p.Ala1245Thr Single submitter ⚠
- p.Ala1342Val Single submitter ⚠
- p.Ala1390Thr Single submitter ⚠
- p.Ala192fs Single submitter
- p.Ala28Thr Single submitter ⚠
- p.Ala2Glu Single submitter ⚠
- p.Ala335Ser Single submitter ⚠
- p.Ala525Thr Single submitter ⚠
- p.Ala571Thr Single submitter ⚠
- p.Ala68Thr Single submitter ⚠
- p.Ala727Thr Single submitter ⚠
- p.Ala774Asp Single submitter ⚠
- p.Ala868Thr Single submitter ⚠
- p.Ala981Thr Single submitter ⚠
- p.Arg1043Cys Single submitter ⚠
- p.Arg1043His Single submitter ⚠
- p.Arg1117Cys Single submitter
- p.Arg1117His Single submitter ⚠
- p.Arg112Gly Single submitter ⚠
- p.Arg1157Cys Single submitter
- p.Arg1188His Single submitter ⚠
- p.Arg1201Pro Single submitter ⚠
- p.Arg1207Gln Single submitter ⚠
- p.Arg1216His Single submitter
- p.Arg1216Leu Single submitter ⚠
- p.Arg1318Cys Single submitter ⚠
- p.Arg1318His Single submitter ⚠
- p.Arg1324Gln Single submitter ⚠
- p.Arg1358Gln Single submitter ⚠
- p.Arg1358Pro Single submitter PTPRT-associated neurodevelopmentaldisorder ⚠
- p.Arg1373His Single submitter ⚠
- p.Arg1414Cys Single submitter ⚠
- p.Arg1414Gly Single submitter ⚠
- p.Arg1414His Single submitter ⚠
- p.Arg1414Ser Single submitter ⚠
- p.Arg190Ile Single submitter ⚠
- p.Arg197Ter Single submitter
- p.Arg247His Single submitter ⚠
- p.Arg24Gln Single submitter ⚠
- p.Arg260Gln Single submitter ⚠
- p.Arg416His Single submitter ⚠
- p.Arg539Lys Single submitter ⚠
- p.Arg617Trp Single submitter ⚠
- p.Arg653Trp Single submitter ⚠
- p.Arg815Leu Single submitter ⚠
- p.Arg835Cys Single submitter ⚠
- p.Arg862fs Single submitter
- p.Arg862Gln Single submitter ⚠
- p.Arg870Gln Single submitter ⚠
- p.Asn1073Ser Single submitter ⚠
- p.Asn1268Ser Single submitter ⚠
- p.Asn200Ser Single submitter ⚠
- p.Asn208His Single submitter ⚠
- p.Asn344Lys Single submitter ⚠
- p.Asn392Lys Single submitter ⚠
- p.Asn50Ser Single submitter ⚠
- p.Asn743His Single submitter ⚠
- p.Asn816Asp Single submitter ⚠
- p.Asn828Lys Single submitter ⚠
- p.Asn979Ile Single submitter ⚠
- p.Asp113Asn Single submitter ⚠
- p.Asp1266Asn Single submitter ⚠
- p.Asp1327Gly Single submitter ⚠
- p.Asp272His Single submitter ⚠
- p.Asp385His Single submitter ⚠
- p.Asp659Asn Single submitter ⚠
- p.Asp659Gly Single submitter ⚠
- p.Asp805Glu Single submitter ⚠
- p.Asp817Glu Single submitter ⚠
- p.Asp826Gly Single submitter ⚠
- p.Asp949Gly Single submitter ⚠
- p.Asp970fs Single submitter
- p.Cys1395Arg Single submitter ⚠
- p.Gln677Arg Single submitter ⚠
- p.Gln791His Single submitter ⚠
- p.Glu1105Lys Single submitter ⚠
- p.Glu326Lys Single submitter ⚠
- p.Glu336Asp Single submitter ⚠
- p.Glu367Asp Single submitter ⚠
- p.Glu436Lys Single submitter ⚠
- p.Gly1294Arg Single submitter ⚠
- p.Gly1369Arg Single submitter
- p.Gly140Arg Single submitter ⚠
- p.Gly232Ser Single submitter PTPRT-related disorder ⚠
- p.Gly274Val Single submitter PTPRT-associated neurodevelopmental disorder ⚠
- p.Gly496Glu Single submitter ⚠
- p.Gly527Ser Single submitter ⚠
- p.Gly829Arg Single submitter ⚠
- p.Gly888Arg Single submitter ⚠
- p.His1037Gln Single submitter ⚠
- p.His159Arg Single submitter ⚠
- p.His245Tyr Single submitter ⚠
- p.His446Leu Single submitter ⚠
- p.His926Tyr Single submitter ⚠
- p.Ile103Leu Single submitter ⚠
- p.Ile1095fs Single submitter
- p.Ile1184Thr Single submitter ⚠
- p.Ile1222Met Single submitter
- p.Ile1398Val Single submitter ⚠
- p.Ile1404Met Single submitter ⚠
- p.Ile586Thr Single submitter ⚠
- p.Ile642Phe Single submitter ⚠
- p.Ile717Val Single submitter ⚠
- p.Ile751Val Single submitter ⚠
- p.Ile760Thr Single submitter ⚠
- p.Ile768Val Single submitter ⚠
- p.Ile958Thr Single submitter ⚠
- p.Leu322Met Single submitter ⚠
- p.Leu708Ile Single submitter ⚠
- p.Lys1355Arg Single submitter ⚠
- p.Lys264Gln Single submitter ⚠
- p.Lys264Thr Single submitter ⚠
- p.Lys544Glu Single submitter ⚠
- p.Met1237Thr Single submitter
- p.Met591Thr Single submitter ⚠
- p.Phe105Leu Single submitter ⚠
- p.Phe1265Leu Single submitter ⚠
- p.Phe1265Ser Single submitter ⚠
- p.Phe553Ser Single submitter ⚠
- p.Pro1075Leu Single submitter ⚠
- p.Pro1152Leu Single submitter
- p.Pro1168Ala Single submitter ⚠
- p.Pro1348Ala Single submitter ⚠
- p.Pro508Thr Single submitter ⚠
- p.Pro592Ser Single submitter ⚠
- p.Pro620Ser Single submitter ⚠
- p.Pro938Leu Single submitter ⚠
- p.Ser3Ile Single submitter ⚠
- p.Ser44Asn Single submitter ⚠
- p.Ser532Thr Single submitter ⚠
- p.Ser536Trp Single submitter
- p.Ser79Cys Single submitter ⚠
- p.Ser823Arg Single submitter ⚠
- p.Thr1005Lys Single submitter ⚠
- p.Thr1099Ala Single submitter ⚠
- p.Thr1170Ile Single submitter ⚠
- p.Thr1346Met Single submitter intellectual disability ⚠
- p.Thr290Met Single submitter ⚠
- p.Thr59Ala Single submitter ⚠
- p.Thr808Ile Single submitter ⚠
- p.Thr844Met Single submitter ⚠
- p.Tyr345His Single submitter ⚠
- p.Tyr428His Single submitter ⚠
- p.Val1211Ala Single submitter ⚠
- p.Val122Ile Single submitter ⚠
- p.Val1247Leu Single submitter ⚠
- p.Val1257Met Single submitter ⚠
- p.Val1264Met Single submitter ⚠
- p.Val1304Ile Single submitter ⚠
- p.Val142Ile Single submitter ⚠
- p.Val1430Leu Single submitter ⚠
- p.Val201Met Single submitter ⚠
- p.Val239Ile Single submitter ⚠
- p.Val277Gly Single submitter ⚠
- p.Val488Leu Single submitter ⚠
- p.Val515Ile Single submitter ⚠
- p.Val720Ile Single submitter ⚠
- p.Val735Met Single submitter PTPRT-related disorder ⚠
- p.Val745Met Single submitter ⚠
- p.Val764Met Single submitter ⚠
- p.Val827Ile Single submitter ⚠
- p.Gln1366Leu No assertion criteria PTPRT-related disorder ⚠