Sugi Variant

Sugi Variant/MTOR

MTOR — 2991 ClinVar variants

All ClinVar germline MTOR variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 979 flagged for review →

23 Pathogenic · 2 Pathogenic/Likely pathogenic · 31 Likely pathogenic · 113 Conflicting · 361 Benign · 96 Benign/Likely benign · 1291 Likely benign · 1074 Uncertain significance

Full MTOR gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 979

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 2

ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.

Predictors agree, ClinVar conflicts 71

ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.

Predicted LoF vs a conflicting call 1

ClinVar submitters conflict, and it's a predicted loss-of-function change in a gene where LoF causes disease — flagged for review, not resolved (verify NMD-escape for C-terminal truncations). Non-missense.

Predictors lean, ClinVar uncertain 568

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification. · showing the 150 best-reviewed of 568

Predictors split 337

The independent predictors disagree with each other — read with care. · showing the 150 best-reviewed of 337

All MTOR variants

Pathogenic 23

  • p.Cys1483Arg Expert panel overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes
  • p.Cys1483Tyr Expert panel overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes
  • p.Leu1460Pro Expert panel overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes
  • p.Leu2427Pro Expert panel overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes
  • p.Ser2215Phe Expert panel overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes
  • p.Ser2215Tyr Expert panel overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes
  • p.Thr1977Arg Expert panel overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes
  • p.Thr1977Lys Expert panel overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes
  • p.Ala1459Asp Multiple submitters isolated focal cortical dysplasia type II
  • p.Glu1799Lys Multiple submitters MTOR-related disorder ⚠
  • p.Glu2419Lys Multiple submitters CEBALID syndrome
  • p.Met2327Ile Multiple submitters macrocephaly-intellectual disability-neurodevelopmental disorder-small thorax syndrome
  • p.Ser2413Ile Multiple submitters macrocephaly-intellectual disability-neurodevelopmental disorder-small thorax syndrome
  • p.Thr1977Ile Multiple submitters isolated focal cortical dysplasia type II
  • p.Cys1483Phe Single submitter macrocephaly-intellectual disability-neurodevelopmental disorder-small thorax syndrome
  • p.Ile2501Phe Single submitter CEBALID syndrome
  • p.Leu2427Arg Single submitter isolated focal cortical dysplasia type II
  • p.Lys1395Arg Single submitter ⚠
  • p.Met1595Ile Single submitter macrocephaly-intellectual disability-neurodevelopmental disorder-small thorax syndrome ⚠
  • p.Tyr1450Asp Single submitter isolated focal cortical dysplasia type II
  • p.Gly86fs No assertion criteria macrocephaly-intellectual disability-neurodevelopmental disorder-small thorax syndrome
  • p.Leu2427Gln No assertion criteria isolated focal cortical dysplasia type II
  • p.Trp1456Gly No assertion criteria isolated focal cortical dysplasia type II

Pathogenic/Likely pathogenic 2

  • p.Phe1888Cys Multiple submitters macrocephaly-intellectual disability-neurodevelopmental disorder-small thorax syndrome
  • p.Val2406Met Multiple submitters macrocephaly-intellectual disability-neurodevelopmental disorder-small thorax syndrome ⚠

Likely pathogenic 31

  • p.Ala1669Ser Expert panel overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes ⚠
  • p.Trp1490Arg Expert panel overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes
  • c.3945-26_4016dup Single submitter macrocephaly-intellectual disability-neurodevelopmental disorder-small thorax syndrome
  • p.Ala1459Pro Single submitter isolated focal cortical dysplasia type II
  • p.Ala1517Val Single submitter ⚠
  • p.Ala1794Thr Single submitter
  • p.Ala1971Val Single submitter macrocephaly-intellectual disability-neurodevelopmental disorder-small thorax syndrome
  • p.Arg1568Gly Single submitter macrocephaly-intellectual disability-neurodevelopmental disorder-small thorax syndrome ⚠
  • p.Asp2102Glu Single submitter MTOR-related disorder ⚠
  • p.Asp2512Gly Single submitter macrocephaly-intellectual disability-neurodevelopmental disorder-small thorax syndrome
  • p.Gly1887Val Single submitter
  • p.Gly1954Arg Single submitter macrocephaly-intellectual disability-neurodevelopmental disorder-small thorax syndrome ⚠
  • p.Gly2359Glu Single submitter
  • p.His1803Pro Single submitter macrocephaly-intellectual disability-neurodevelopmental disorder-small thorax syndrome ⚠
  • p.Ile1417Thr Single submitter Inborn genetic diseases
  • p.Ile1973Phe Single submitter isolated focal cortical dysplasia type II
  • p.Ile2500Met Single submitter macrocephaly-intellectual disability-neurodevelopmental disorder-small thorax syndrome ⚠
  • p.Leu1433Ser Single submitter isolated focal cortical dysplasia type II
  • p.Leu1484Pro Single submitter
  • p.Leu1654Pro Single submitter macrocephaly-intellectual disability-neurodevelopmental disorder-small thorax syndrome
  • p.Leu2220Pro Single submitter
  • p.Leu2431Pro Single submitter macrocephaly-intellectual disability-neurodevelopmental disorder-small thorax syndrome
  • p.Lys1452_Glu1455del Single submitter isolated focal cortical dysplasia type II
  • p.Phe1888Leu Single submitter ⚠
  • p.Ser2215Pro Single submitter
  • p.Val2006Leu Single submitter MTOR-related disorder ⚠
  • p.Ala1519Val No assertion criteria CEBALID syndrome
  • p.Arg2076Gln No assertion criteria macrocephaly-intellectual disability-neurodevelopmental disorder-small thorax syndrome ⚠
  • p.Ile2017Thr No assertion criteria CEBALID syndrome ⚠
  • p.Ile2153Val No assertion criteria macrocephaly-intellectual disability-neurodevelopmental disorder-small thorax syndrome ⚠
  • p.Lys1452Asn No assertion criteria CEBALID syndrome ⚠

Conflicting classifications of pathogenicity 113

Benign 361

Showing the top 300 by review status; the full set is in the sitemap.

Benign/Likely benign 96

Likely benign 1291

Showing the top 300 by review status; the full set is in the sitemap.

Uncertain significance 1074

Showing the top 300 by review status; the full set is in the sitemap.