GTF3C3 — 101 ClinVar variants
All ClinVar germline GTF3C3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 76 flagged for review →
8 Pathogenic · 3 Likely pathogenic · 3 Benign · 12 Likely benign · 75 Uncertain significance
Full GTF3C3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 76
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 56
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- GTF3C3 p.Ala118Val Uncertain significance Single submitter
- GTF3C3 p.Ala210Val Uncertain significance Single submitter
- GTF3C3 p.Ala243Gly Uncertain significance Single submitter
- GTF3C3 p.Ala293Val Uncertain significance Single submitter
- GTF3C3 p.Ala332Ser Uncertain significance Single submitter
- GTF3C3 p.Ala446Val Uncertain significance Single submitter
- GTF3C3 p.Arg162Gln Uncertain significance Single submitter
- GTF3C3 p.Arg276His Uncertain significance Single submitter
- GTF3C3 p.Arg641Pro Uncertain significance Single submitter
- GTF3C3 p.Arg761Cys Uncertain significance Single submitter
- GTF3C3 p.Arg761His Uncertain significance Single submitter
- GTF3C3 p.Arg79Thr Uncertain significance Single submitter
- GTF3C3 p.Arg819Cys Uncertain significance Single submitter
- GTF3C3 p.Asn232Ser Uncertain significance Single submitter
- GTF3C3 p.Asn400Lys Uncertain significance Single submitter
- GTF3C3 p.Asn698Ser Uncertain significance Single submitter
- GTF3C3 p.Asp120Asn Uncertain significance Single submitter
- GTF3C3 p.Asp419Val Uncertain significance Single submitter
- GTF3C3 p.Cys637Gly Uncertain significance Single submitter
- GTF3C3 p.Cys772Ser Uncertain significance Single submitter
- GTF3C3 p.Gln196Arg Uncertain significance Single submitter
- GTF3C3 p.Gln758His Uncertain significance Single submitter
- GTF3C3 p.Gln877Leu Uncertain significance Single submitter
- GTF3C3 p.Glu105Asp Uncertain significance Single submitter
- GTF3C3 p.Glu364Asp Uncertain significance Single submitter
- GTF3C3 p.Gly40Asp Uncertain significance Single submitter
- GTF3C3 p.His267Arg Uncertain significance Single submitter
- GTF3C3 p.His712Leu Uncertain significance Single submitter
- GTF3C3 p.His832Arg Uncertain significance Single submitter
- GTF3C3 p.Ile175Val Uncertain significance Single submitter
- GTF3C3 p.Leu647Met Uncertain significance Single submitter
- GTF3C3 p.Leu826Met Uncertain significance Single submitter
- GTF3C3 p.Met326Val Uncertain significance Single submitter
- GTF3C3 p.Phe797Ser Uncertain significance Single submitter
- GTF3C3 p.Pro407Leu Uncertain significance Single submitter
- GTF3C3 p.Pro417Leu Uncertain significance Single submitter
- GTF3C3 p.Pro506Ser Uncertain significance Single submitter
- GTF3C3 p.Pro6Leu Uncertain significance Single submitter
- GTF3C3 p.Pro700Ser Uncertain significance Single submitter
- GTF3C3 p.Ser325Cys Uncertain significance Single submitter
- GTF3C3 p.Ser43Pro Uncertain significance Single submitter
- GTF3C3 p.Ser450Pro Uncertain significance Single submitter
- GTF3C3 p.Ser604Leu Uncertain significance Single submitter
- GTF3C3 p.Ser674Cys Uncertain significance Single submitter
- GTF3C3 p.Thr117Ser Uncertain significance Single submitter
- GTF3C3 p.Thr62Ile Uncertain significance Single submitter
- GTF3C3 p.Thr878Met Uncertain significance Single submitter
- GTF3C3 p.Thr882Ala Uncertain significance Single submitter
- GTF3C3 p.Thr882Asn Uncertain significance Single submitter
-
GTF3C3 p.Tyr833Cys
Uncertain significance
Single submitter
neurodevelopmental disorder with dysmorphic facies, brain anomalies, and seizures
- GTF3C3 p.Tyr861Cys Uncertain significance Single submitter
- GTF3C3 p.Val384Met Uncertain significance Single submitter
- GTF3C3 p.Val483Ala Uncertain significance Single submitter
- GTF3C3 p.Val483Ile Uncertain significance Single submitter
- GTF3C3 p.Val615Met Uncertain significance Single submitter
- GTF3C3 p.Val619Ile Uncertain significance Single submitter
Predictors split 20
The independent predictors disagree with each other — read with care.
- GTF3C3 p.Ala752Gly Uncertain significance Single submitter
- GTF3C3 p.Arg717Gly Uncertain significance Single submitter
- GTF3C3 p.Asp525Asn Uncertain significance Single submitter
-
GTF3C3 p.Gln823His
Uncertain significance
Single submitter
chromosome 2q32-q33 deletion syndrome
- GTF3C3 p.Gln877Pro Uncertain significance Single submitter
- GTF3C3 p.Glu108Lys Uncertain significance Single submitter
- GTF3C3 p.Glu327Val Uncertain significance Single submitter
- GTF3C3 p.Ile331Thr Uncertain significance Single submitter
- GTF3C3 p.Ile386Lys Uncertain significance Single submitter
- GTF3C3 p.Leu727Pro Uncertain significance Single submitter
- GTF3C3 p.Met692Ile Uncertain significance Single submitter
- GTF3C3 p.Phe238Leu Uncertain significance Single submitter
- GTF3C3 p.Ser308Pro Uncertain significance Single submitter
- GTF3C3 p.Ser325Phe Uncertain significance Single submitter
- GTF3C3 p.Tyr11Ser Uncertain significance Single submitter
- GTF3C3 p.Tyr655His Uncertain significance Single submitter
- GTF3C3 p.Val397Ala Uncertain significance Single submitter
- GTF3C3 p.Val786Leu Uncertain significance Single submitter
-
GTF3C3 p.Ala509Thr
Pathogenic
No assertion criteria
neurodevelopmental disorder with dysmorphic facies, brain anomalies, and seizures
-
GTF3C3 p.Pro842Ala
Likely benign
No assertion criteria
GTF3C3-related disorder
All GTF3C3 variants
Pathogenic 8
- p.Ala168Val No assertion criteria neurodevelopmental disorder with dysmorphic facies, brain anomalies, and seizures
- p.Ala509Thr No assertion criteria neurodevelopmental disorder with dysmorphic facies, brain anomalies, and seizures ⚠
- p.Arg717Ter No assertion criteria neurodevelopmental disorder with dysmorphic facies, brain anomalies, and seizures
- p.Arg807Cys No assertion criteria neurodevelopmental disorder with dysmorphic facies, brain anomalies, and seizures
- p.Arg807His No assertion criteria neurodevelopmental disorder with dysmorphic facies, brain anomalies, and seizures
- p.Cys172Gly No assertion criteria neurodevelopmental disorder with dysmorphic facies, brain anomalies, and seizures
- p.Tyr479Cys No assertion criteria neurodevelopmental disorder with dysmorphic facies, brain anomalies, and seizures
- p.Val427Phe No assertion criteria neurodevelopmental disorder with dysmorphic facies, brain anomalies, and seizures
Likely pathogenic 3
- c.1390+3A>G Single submitter chromosome 2q32-q33 deletion syndrome
- p.Arg570Ter Single submitter neurodevelopmental disorder with dysmorphic facies, brain anomalies, and seizures
- p.Pro180Ser Single submitter
Benign 3
- c.1115-11G>A Single submitter
- p.Ala876= Single submitter
- p.Asn70Ser No assertion criteria GTF3C3-related disorder
Likely benign 12
- c.412-4A>G Single submitter
- p.Ala118= Single submitter
- p.Asp49Asn Single submitter
- p.Leu409= Single submitter
- p.Pro113Arg Single submitter
- c.2069+10C>T No assertion criteria GTF3C3-related disorder
- p.Ala210= No assertion criteria GTF3C3-related disorder
- p.Glu111_Thr112insGlu No assertion criteria GTF3C3-related disorder
- p.Phe317= No assertion criteria EBV-positive nodal T- and NK-cell lymphoma
- p.Pro842Ala No assertion criteria GTF3C3-related disorder ⚠
- p.Ser618= No assertion criteria GTF3C3-related disorder
- p.Ser640= No assertion criteria GTF3C3-related disorder
Uncertain significance 75
- p.Ala118Val Single submitter ⚠
- p.Ala210Val Single submitter ⚠
- p.Ala243Gly Single submitter ⚠
- p.Ala293Val Single submitter ⚠
- p.Ala332Ser Single submitter ⚠
- p.Ala446Val Single submitter ⚠
- p.Ala752Gly Single submitter ⚠
- p.Arg162Gln Single submitter ⚠
- p.Arg276His Single submitter ⚠
- p.Arg474Ter Single submitter neurodevelopmental disorder
- p.Arg641Pro Single submitter ⚠
- p.Arg717Gly Single submitter ⚠
- p.Arg761Cys Single submitter ⚠
- p.Arg761His Single submitter ⚠
- p.Arg79Thr Single submitter ⚠
- p.Arg819Cys Single submitter ⚠
- p.Asn232Ser Single submitter ⚠
- p.Asn400Lys Single submitter ⚠
- p.Asn698Ser Single submitter ⚠
- p.Asp120Asn Single submitter ⚠
- p.Asp419Val Single submitter ⚠
- p.Asp525Asn Single submitter ⚠
- p.Cys637Gly Single submitter ⚠
- p.Cys772Ser Single submitter ⚠
- p.Gln196Arg Single submitter ⚠
- p.Gln758His Single submitter ⚠
- p.Gln823His Single submitter chromosome 2q32-q33 deletion syndrome ⚠
- p.Gln877Leu Single submitter ⚠
- p.Gln877Pro Single submitter ⚠
- p.Glu105Asp Single submitter ⚠
- p.Glu108Lys Single submitter ⚠
- p.Glu327Val Single submitter ⚠
- p.Glu364Asp Single submitter ⚠
- p.Gly40Asp Single submitter ⚠
- p.His267Arg Single submitter ⚠
- p.His712Leu Single submitter ⚠
- p.His832Arg Single submitter ⚠
- p.Ile175Val Single submitter ⚠
- p.Ile331Thr Single submitter ⚠
- p.Ile386Lys Single submitter ⚠
- p.Leu647Met Single submitter ⚠
- p.Leu727Pro Single submitter ⚠
- p.Leu826Met Single submitter ⚠
- p.Met326Val Single submitter ⚠
- p.Met692Ile Single submitter ⚠
- p.Phe238Leu Single submitter ⚠
- p.Phe797Ser Single submitter ⚠
- p.Pro407Leu Single submitter ⚠
- p.Pro417Leu Single submitter ⚠
- p.Pro506Ser Single submitter ⚠
- p.Pro6Leu Single submitter ⚠
- p.Pro700Ser Single submitter ⚠
- p.Ser308Pro Single submitter ⚠
- p.Ser325Cys Single submitter ⚠
- p.Ser325Phe Single submitter ⚠
- p.Ser43Pro Single submitter ⚠
- p.Ser450Pro Single submitter ⚠
- p.Ser604Leu Single submitter ⚠
- p.Ser674Cys Single submitter ⚠
- p.Thr117Ser Single submitter ⚠
- p.Thr62Ile Single submitter ⚠
- p.Thr878Met Single submitter ⚠
- p.Thr882Ala Single submitter ⚠
- p.Thr882Asn Single submitter ⚠
- p.Tyr11Ser Single submitter ⚠
- p.Tyr655His Single submitter ⚠
- p.Tyr833Cys Single submitter neurodevelopmental disorder with dysmorphic facies, brain anomalies, and seizures ⚠
- p.Tyr861Cys Single submitter ⚠
- p.Val384Met Single submitter ⚠
- p.Val397Ala Single submitter ⚠
- p.Val483Ala Single submitter ⚠
- p.Val483Ile Single submitter ⚠
- p.Val615Met Single submitter ⚠
- p.Val619Ile Single submitter ⚠
- p.Val786Leu Single submitter ⚠