Sugi Variant

Sugi Variant/TFE3

TFE3 — 147 ClinVar variants

All ClinVar germline TFE3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 87 flagged for review →

9 Pathogenic · 2 Pathogenic/Likely pathogenic · 10 Likely pathogenic · 1 Conflicting · 3 Benign · 28 Likely benign · 94 Uncertain significance

Full TFE3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 87

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 1

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

Predictors lean, ClinVar uncertain 56

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.

Predictors split 28

The independent predictors disagree with each other — read with care.

All TFE3 variants

Pathogenic 9

  • p.Arg113Lys Single submitter ⚠
  • p.Arg117Trp Single submitter
  • p.Leu191Pro Single submitter intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse facies
  • p.Thr187Ala Single submitter intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse facies
  • p.Thr187Lys Single submitter intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse facies
  • c.780+1G>A No assertion criteria intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse facies
  • p.Gln119Pro No assertion criteria intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse facies
  • p.Gln201Pro No assertion criteria intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse facies ⚠
  • p.Thr187Arg No assertion criteria intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse facies

Pathogenic/Likely pathogenic 2

  • p.Arg117Gln Multiple submitters intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse facies ⚠
  • p.Thr187Met Multiple submitters Neurodevelopmental abnormality

Likely pathogenic 10

  • p.123AQ[1] Single submitter intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse facies
  • p.Arg117_Gln119del Single submitter Inborn genetic diseases
  • p.Arg196Pro Single submitter intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse facies ⚠
  • p.Asn185Ser Single submitter ⚠
  • p.His190Arg Single submitter intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse facies ⚠
  • p.Leu203Pro Single submitter intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse facies
  • p.Pro186Leu Single submitter intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse facies
  • p.Pro186Ser Single submitter intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse facies
  • p.Pro186Thr Single submitter intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse facies ⚠
  • p.Tyr189Cys Single submitter intellectual disability ⚠

Conflicting classifications of pathogenicity 1

  • p.Gly531Glu Single submitter intellectual developmental disorder, X-linked, syndromic, with pigmentary mosaicism and coarse facies ⚠

Benign 3

Likely benign 28

Uncertain significance 94