CENPT — 133 ClinVar variants
All ClinVar germline CENPT variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 105 flagged for review →
1 Pathogenic · 11 Benign · 21 Likely benign · 100 Uncertain significance
Full CENPT gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 105
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 63
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- CENPT p.Ala208Thr Uncertain significance Single submitter
- CENPT p.Ala269Thr Uncertain significance Single submitter
- CENPT p.Ala293Thr Uncertain significance Single submitter
- CENPT p.Ala333Gly Uncertain significance Single submitter
- CENPT p.Ala333Thr Uncertain significance Single submitter
- CENPT p.Ala384Thr Uncertain significance Single submitter
- CENPT p.Ala41Thr Uncertain significance Single submitter
- CENPT p.Ala420Ser Uncertain significance Single submitter
- CENPT p.Ala426Ser Uncertain significance Single submitter
- CENPT p.Ala426Thr Uncertain significance Single submitter
- CENPT p.Ala471Val Uncertain significance Single submitter
- CENPT p.Ala479Val Uncertain significance Single submitter
- CENPT p.Ala551Val Uncertain significance Single submitter
- CENPT p.Arg122Lys Uncertain significance Single submitter
- CENPT p.Arg153Lys Uncertain significance Single submitter
- CENPT p.Arg215Gln Uncertain significance Single submitter
- CENPT p.Arg275Cys Uncertain significance Single submitter
- CENPT p.Arg394Gly Uncertain significance Single submitter
- CENPT p.Arg445Pro Uncertain significance Single submitter
- CENPT p.Arg452Gln Uncertain significance Single submitter
- CENPT p.Arg49Gly Uncertain significance Single submitter
- CENPT p.Arg520Gly Uncertain significance Single submitter
- CENPT p.Arg544Trp Uncertain significance Single submitter
- CENPT p.Asn190Ser Uncertain significance Single submitter
- CENPT p.Asn304Ser Uncertain significance Single submitter
- CENPT p.Asn5His Uncertain significance Single submitter
- CENPT p.Asp388Asn Uncertain significance Single submitter
- CENPT p.Cys127Trp Uncertain significance Single submitter
- CENPT p.Gln278Arg Uncertain significance Single submitter
- CENPT p.Gln353Glu Uncertain significance Single submitter
- CENPT p.Gln409His Uncertain significance Single submitter
- CENPT p.Glu136Ala Uncertain significance Single submitter
- CENPT p.Gly316Asp Uncertain significance Single submitter
- CENPT p.Gly316Val Uncertain significance Single submitter
- CENPT p.Gly329Val Uncertain significance Single submitter
- CENPT p.Gly387Arg Uncertain significance Single submitter
- CENPT p.Gly459Ala Uncertain significance Single submitter
- CENPT p.Gly79Glu Uncertain significance Single submitter
- CENPT p.His456Leu Uncertain significance Single submitter
- CENPT p.His493Leu Uncertain significance Single submitter
- CENPT p.His4Tyr Uncertain significance Single submitter
- CENPT p.His80Arg Uncertain significance Single submitter
- CENPT p.Ile58Met Uncertain significance Single submitter
- CENPT p.Leu132Val Uncertain significance Single submitter
- CENPT p.Leu20Val Uncertain significance Single submitter
- CENPT p.Lys465Gln Uncertain significance Single submitter
- CENPT p.Lys472Arg Uncertain significance Single submitter
- CENPT p.Pro140Arg Uncertain significance Single submitter
- CENPT p.Pro252Leu Uncertain significance Single submitter
- CENPT p.Pro25Ala Uncertain significance Single submitter
- CENPT p.Pro325Leu Uncertain significance Single submitter
- CENPT p.Pro432Leu Uncertain significance Single submitter
- CENPT p.Pro435Leu Uncertain significance Single submitter
- CENPT p.Pro451Thr Uncertain significance Single submitter
- CENPT p.Pro6Ala Uncertain significance Single submitter
- CENPT p.Pro98Ala Uncertain significance Single submitter
- CENPT p.Pro98Ser Uncertain significance Single submitter
- CENPT p.Thr261Ala Uncertain significance Single submitter
- CENPT p.Thr55Arg Uncertain significance Single submitter
- CENPT p.Thr57Arg Uncertain significance Single submitter
- CENPT p.Val533Leu Uncertain significance Single submitter
- CENPT p.Val533Met Uncertain significance Single submitter
- CENPT p.Val69Leu Uncertain significance Single submitter
Predictors split 42
The independent predictors disagree with each other — read with care.
-
CENPT p.Ser8Arg
Benign
Multiple submitters
short stature and microcephaly with genital anomalies
- CENPT p.Arg13Gly Uncertain significance Single submitter
- CENPT p.Arg152Thr Uncertain significance Single submitter
- CENPT p.Arg153Gly Uncertain significance Single submitter
- CENPT p.Arg209Cys Uncertain significance Single submitter
- CENPT p.Arg209Pro Uncertain significance Single submitter
- CENPT p.Arg214Cys Uncertain significance Single submitter
- CENPT p.Arg39Gln Likely benign Single submitter
- CENPT p.Arg445Gln Uncertain significance Single submitter
- CENPT p.Arg445Trp Uncertain significance Single submitter
- CENPT p.Arg507Cys Likely benign Single submitter
- CENPT p.Arg537Gln Uncertain significance Single submitter
- CENPT p.Arg544Gln Uncertain significance Single submitter
- CENPT p.Arg62His Uncertain significance Single submitter
- CENPT p.Arg87Gln Uncertain significance Single submitter
- CENPT p.Arg87Trp Uncertain significance Single submitter
- CENPT p.Asp527Asn Uncertain significance Single submitter
- CENPT p.Glu99Gln Uncertain significance Single submitter
- CENPT p.Gly372Val Uncertain significance Single submitter
- CENPT p.Leu466Phe Uncertain significance Single submitter
- CENPT p.Lys489Asn Uncertain significance Single submitter
- CENPT p.Phe222Leu Likely benign Single submitter
- CENPT p.Phe244Leu Uncertain significance Single submitter
- CENPT p.Phe501Leu Uncertain significance Single submitter
- CENPT p.Pro139His Uncertain significance Single submitter
- CENPT p.Pro28Leu Uncertain significance Single submitter
- CENPT p.Pro474Arg Uncertain significance Single submitter
- CENPT p.Pro98Arg Uncertain significance Single submitter
- CENPT p.Ser230Phe Uncertain significance Single submitter
- CENPT p.Ser402Phe Uncertain significance Single submitter
- CENPT p.Ser429Phe Uncertain significance Single submitter
- CENPT p.Ser78Ile Uncertain significance Single submitter
- CENPT p.Ser8Asn Uncertain significance Single submitter
- CENPT p.Thr195Ile Uncertain significance Single submitter
- CENPT p.Thr368Ile Uncertain significance Single submitter
- CENPT p.Thr447Asn Uncertain significance Single submitter
- CENPT p.Thr45Met Uncertain significance Single submitter
- CENPT p.Thr509Ala Uncertain significance Single submitter
- CENPT p.Thr96Ile Uncertain significance Single submitter
- CENPT p.Tyr470Cys Uncertain significance Single submitter
- CENPT p.Val166Gly Uncertain significance Single submitter
-
CENPT p.Ser126Asn
Likely benign
No assertion criteria
CENPT-related disorder
All CENPT variants
Pathogenic 1
- c.1186+1G>A No assertion criteria short stature and microcephaly with genital anomalies
Benign 11
- c.1187-32A>G Multiple submitters short stature and microcephaly with genital anomalies
- c.703+46C>T Multiple submitters short stature and microcephaly with genital anomalies
- p.Ser8Arg Multiple submitters short stature and microcephaly with genital anomalies ⚠
- p.Ala180= Single submitter
- c.111-9T>A No assertion criteria CENPT-related disorder
- c.202-5G>A No assertion criteria CENPT-related disorder
- c.-6G>T No assertion criteria CENPT-related disorder
- p.Ala23Thr No assertion criteria CENPT-related disorder
- p.Arg122Gly No assertion criteria CENPT-related disorder
- p.Pro441Ala No assertion criteria CENPT-related disorder
- p.Ser121Ala No assertion criteria CENPT-related disorder
Likely benign 21
- c.386+7A>G Single submitter
- p.Arg224Gln Single submitter
- p.Arg39Gln Single submitter ⚠
- p.Arg507Cys Single submitter ⚠
- p.Asn253Ser Single submitter
- p.Asp380= Single submitter
- p.Gly274Ser Single submitter
- p.Leu524= Single submitter
- p.Phe222Leu Single submitter ⚠
- p.Pro120Ser Single submitter
- p.Ser400Leu Single submitter
- p.Ser8Gly Single submitter
- p.Tyr255His Single submitter
- c.387-10A>G No assertion criteria CENPT-related disorder
- c.524-5G>C No assertion criteria CENPT-related disorder
- p.Ala273= No assertion criteria CENPT-related disorder
- p.Ala422Val No assertion criteria CENPT-related disorder
- p.Asn253= No assertion criteria CENPT-related disorder
- p.Ile236Thr No assertion criteria CENPT-related disorder
- p.Ser126Asn No assertion criteria CENPT-related disorder ⚠
- p.Thr88= No assertion criteria CENPT-related disorder
Uncertain significance 100
- p.Ala208Thr Single submitter ⚠
- p.Ala269Thr Single submitter ⚠
- p.Ala293Thr Single submitter ⚠
- p.Ala333Gly Single submitter ⚠
- p.Ala333Thr Single submitter ⚠
- p.Ala384Thr Single submitter ⚠
- p.Ala41Thr Single submitter ⚠
- p.Ala420Ser Single submitter ⚠
- p.Ala426Ser Single submitter ⚠
- p.Ala426Thr Single submitter ⚠
- p.Ala471Val Single submitter ⚠
- p.Ala479Val Single submitter ⚠
- p.Ala551Val Single submitter ⚠
- p.Arg122Lys Single submitter ⚠
- p.Arg13Gly Single submitter ⚠
- p.Arg152Thr Single submitter ⚠
- p.Arg153Gly Single submitter ⚠
- p.Arg153Lys Single submitter ⚠
- p.Arg209Cys Single submitter ⚠
- p.Arg209Pro Single submitter ⚠
- p.Arg214Cys Single submitter ⚠
- p.Arg215Gln Single submitter ⚠
- p.Arg275Cys Single submitter ⚠
- p.Arg394Gly Single submitter ⚠
- p.Arg445Gln Single submitter ⚠
- p.Arg445Pro Single submitter ⚠
- p.Arg445Trp Single submitter ⚠
- p.Arg452Gln Single submitter ⚠
- p.Arg49Gly Single submitter ⚠
- p.Arg520Gly Single submitter ⚠
- p.Arg537Gln Single submitter ⚠
- p.Arg544Gln Single submitter ⚠
- p.Arg544Trp Single submitter ⚠
- p.Arg62His Single submitter ⚠
- p.Arg87Gln Single submitter ⚠
- p.Arg87Trp Single submitter ⚠
- p.Asn190Ser Single submitter ⚠
- p.Asn304Ser Single submitter ⚠
- p.Asn5His Single submitter ⚠
- p.Asp388Asn Single submitter ⚠
- p.Asp527Asn Single submitter ⚠
- p.Cys127Trp Single submitter ⚠
- p.Gln278Arg Single submitter ⚠
- p.Gln353Glu Single submitter ⚠
- p.Gln409His Single submitter ⚠
- p.Glu136Ala Single submitter ⚠
- p.Glu99Gln Single submitter ⚠
- p.Gly316Asp Single submitter ⚠
- p.Gly316Val Single submitter ⚠
- p.Gly329Val Single submitter ⚠
- p.Gly372Val Single submitter ⚠
- p.Gly387Arg Single submitter ⚠
- p.Gly459Ala Single submitter ⚠
- p.Gly79Glu Single submitter ⚠
- p.His456Leu Single submitter ⚠
- p.His493Leu Single submitter ⚠
- p.His4Tyr Single submitter ⚠
- p.His80Arg Single submitter ⚠
- p.Ile58Met Single submitter ⚠
- p.Leu132Val Single submitter ⚠
- p.Leu20Val Single submitter ⚠
- p.Leu466Phe Single submitter ⚠
- p.Lys465Gln Single submitter ⚠
- p.Lys472Arg Single submitter ⚠
- p.Lys489Asn Single submitter ⚠
- p.Phe244Leu Single submitter ⚠
- p.Phe501Leu Single submitter ⚠
- p.Pro139His Single submitter ⚠
- p.Pro140Arg Single submitter ⚠
- p.Pro252Leu Single submitter ⚠
- p.Pro25Ala Single submitter ⚠
- p.Pro28Leu Single submitter ⚠
- p.Pro325Leu Single submitter ⚠
- p.Pro432Leu Single submitter ⚠
- p.Pro435Leu Single submitter ⚠
- p.Pro451Thr Single submitter ⚠
- p.Pro474Arg Single submitter ⚠
- p.Pro6Ala Single submitter ⚠
- p.Pro98Ala Single submitter ⚠
- p.Pro98Arg Single submitter ⚠
- p.Pro98Ser Single submitter ⚠
- p.Ser230Phe Single submitter ⚠
- p.Ser402Phe Single submitter ⚠
- p.Ser429Phe Single submitter ⚠
- p.Ser78Ile Single submitter ⚠
- p.Ser8Asn Single submitter ⚠
- p.Thr195Ile Single submitter ⚠
- p.Thr261Ala Single submitter ⚠
- p.Thr368Ile Single submitter ⚠
- p.Thr447Asn Single submitter ⚠
- p.Thr45Met Single submitter ⚠
- p.Thr509Ala Single submitter ⚠
- p.Thr55Arg Single submitter ⚠
- p.Thr57Arg Single submitter ⚠
- p.Thr96Ile Single submitter ⚠
- p.Tyr470Cys Single submitter ⚠
- p.Val166Gly Single submitter ⚠
- p.Val533Leu Single submitter ⚠
- p.Val533Met Single submitter ⚠
- p.Val69Leu Single submitter ⚠