SUPT16H — 183 ClinVar variants
All ClinVar germline SUPT16H variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 116 flagged for review →
5 Pathogenic · 3 Likely pathogenic · 8 Benign · 16 Likely benign · 151 Uncertain significance
Full SUPT16H gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 116
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 87
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
-
SUPT16H p.Arg623Gln
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
SUPT16H p.Asn20Ser
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
SUPT16H p.Leu795Val
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
SUPT16H p.Ser188Asn
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
SUPT16H p.Ser420Phe
Uncertain significance
Multiple submitters
neurodevelopmental disorder with dysmorphic facies and thin corpus callosum
-
SUPT16H p.Ser986Asn
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
SUPT16H p.Val325Met
Uncertain significance
Multiple submitters
neurodevelopmental disorder with dysmorphic facies and thin corpus callosum
-
SUPT16H p.Ala173Ser
Uncertain significance
Single submitter
Inborn genetic diseases
- SUPT16H p.Ala33Gly Uncertain significance Single submitter
- SUPT16H p.Ala592Thr Uncertain significance Single submitter
-
SUPT16H p.Ala823Val
Uncertain significance
Single submitter
Inborn genetic diseases
-
SUPT16H p.Ala877Ser
Uncertain significance
Single submitter
Inborn genetic diseases
-
SUPT16H p.Ala970Val
Uncertain significance
Single submitter
Inborn genetic diseases
-
SUPT16H p.Arg12Trp
Uncertain significance
Single submitter
neurodevelopmental disorder with dysmorphic facies and thin corpus callosum
- SUPT16H p.Arg201Lys Uncertain significance Single submitter
- SUPT16H p.Arg278Cys Uncertain significance Single submitter
- SUPT16H p.Arg357Cys Uncertain significance Single submitter
- SUPT16H p.Arg357Leu Uncertain significance Single submitter
-
SUPT16H p.Arg506Cys
Uncertain significance
Single submitter
Li-Fraumeni syndrome 1
-
SUPT16H p.Arg631Cys
Uncertain significance
Single submitter
Inborn genetic diseases
- SUPT16H p.Arg668Cys Uncertain significance Single submitter
-
SUPT16H p.Asn111Thr
Uncertain significance
Single submitter
Inborn genetic diseases
-
SUPT16H p.Asn254Ser
Uncertain significance
Single submitter
Inborn genetic diseases
-
SUPT16H p.Asn30Ser
Uncertain significance
Single submitter
neurodevelopmental disorder with dysmorphic facies and thin corpus callosum
- SUPT16H p.Asn327Ser Uncertain significance Single submitter
-
SUPT16H p.Asn367Ser
Uncertain significance
Single submitter
Inborn genetic diseases
- SUPT16H p.Asn380Asp Uncertain significance Single submitter
-
SUPT16H p.Asp163Gly
Uncertain significance
Single submitter
neurodevelopmental disorder with dysmorphic facies and thin corpus callosum
- SUPT16H p.Asp209Tyr Uncertain significance Single submitter
- SUPT16H p.Asp449Asn Uncertain significance Single submitter
-
SUPT16H p.Asp838Val
Uncertain significance
Single submitter
Inborn genetic diseases
-
SUPT16H p.Cys323Arg
Uncertain significance
Single submitter
Inborn genetic diseases
- SUPT16H p.Gln503Lys Uncertain significance Single submitter
- SUPT16H p.Glu396Asp Uncertain significance Single submitter
- SUPT16H p.Glu495Lys Uncertain significance Single submitter
- SUPT16H p.Glu562Lys Uncertain significance Single submitter
-
SUPT16H p.Glu839Lys
Uncertain significance
Single submitter
neurodevelopmental disorder
- SUPT16H p.Gly93Ser Uncertain significance Single submitter
- SUPT16H p.His265Tyr Uncertain significance Single submitter
- SUPT16H p.His723Leu Uncertain significance Single submitter
-
SUPT16H p.Ile107Val
Uncertain significance
Single submitter
Inborn genetic diseases
- SUPT16H p.Ile122Val Uncertain significance Single submitter
- SUPT16H p.Ile125Val Uncertain significance Single submitter
- SUPT16H p.Ile172Val Uncertain significance Single submitter
- SUPT16H p.Ile247Thr Uncertain significance Single submitter
-
SUPT16H p.Ile322Met
Uncertain significance
Single submitter
Inborn genetic diseases
-
SUPT16H p.Ile34Val
Uncertain significance
Single submitter
Inborn genetic diseases
-
SUPT16H p.Ile44Met
Uncertain significance
Single submitter
neurodevelopmental disorder with dysmorphic facies and thin corpus callosum
-
SUPT16H p.Ile557Val
Uncertain significance
Single submitter
Inborn genetic diseases
-
SUPT16H p.Ile653Met
Uncertain significance
Single submitter
neurodevelopmental disorder with dysmorphic facies and thin corpus callosum
-
SUPT16H p.Ile882Val
Uncertain significance
Single submitter
Inborn genetic diseases
-
SUPT16H p.Leu316Ile
Uncertain significance
Single submitter
neurodevelopmental disorder with dysmorphic facies and thin corpus callosum
- SUPT16H p.Leu386Met Uncertain significance Single submitter
- SUPT16H p.Leu408Phe Uncertain significance Single submitter
-
SUPT16H p.Leu493Met
Uncertain significance
Single submitter
neurodevelopmental disorder with dysmorphic facies and thin corpus callosum
-
SUPT16H p.Leu980Met
Uncertain significance
Single submitter
Inborn genetic diseases
- SUPT16H p.Lys156Arg Uncertain significance Single submitter
- SUPT16H p.Lys184Arg Uncertain significance Single submitter
- SUPT16H p.Lys280Arg Uncertain significance Single submitter
-
SUPT16H p.Lys335Gln
Uncertain significance
Single submitter
neurodevelopmental disorder with dysmorphic facies and thin corpus callosum
-
SUPT16H p.Lys389Gln
Uncertain significance
Single submitter
Inborn genetic diseases
- SUPT16H p.Met147Leu Uncertain significance Single submitter
-
SUPT16H p.Met275Thr
Uncertain significance
Single submitter
Inborn genetic diseases
-
SUPT16H p.Met330Leu
Uncertain significance
Single submitter
Inborn genetic diseases
- SUPT16H p.Met330Thr Uncertain significance Single submitter
-
SUPT16H p.Phe304Cys
Uncertain significance
Single submitter
Inborn genetic diseases
- SUPT16H p.Phe689Val Uncertain significance Single submitter
- SUPT16H p.Phe855Leu Uncertain significance Single submitter
- SUPT16H p.Pro548Thr Uncertain significance Single submitter
-
SUPT16H p.Pro913Ser
Uncertain significance
Single submitter
Inborn genetic diseases
- SUPT16H p.Pro950Leu Uncertain significance Single submitter
-
SUPT16H p.Ser19Gly
Uncertain significance
Single submitter
neurodevelopmental disorder with dysmorphic facies and thin corpus callosum
- SUPT16H p.Ser19Thr Uncertain significance Single submitter
- SUPT16H p.Ser813Gly Uncertain significance Single submitter
-
SUPT16H p.Ser822Gly
Uncertain significance
Single submitter
Inborn genetic diseases
-
SUPT16H p.Thr461Ile
Uncertain significance
Single submitter
Inborn genetic diseases
- SUPT16H p.Thr4Ala Uncertain significance Single submitter
- SUPT16H p.Thr612Ile Uncertain significance Single submitter
- SUPT16H p.Thr736Ala Uncertain significance Single submitter
-
SUPT16H p.Tyr326Phe
Uncertain significance
Single submitter
Inborn genetic diseases
-
SUPT16H p.Tyr46Asp
Uncertain significance
Single submitter
neurodevelopmental disorder with dysmorphic facies and thin corpus callosum
-
SUPT16H p.Val31Ile
Uncertain significance
Single submitter
Inborn genetic diseases
-
SUPT16H p.Val332Met
Uncertain significance
Single submitter
Inborn genetic diseases
-
SUPT16H p.Val428Met
Uncertain significance
Single submitter
Inborn genetic diseases
-
SUPT16H p.Val542Met
Uncertain significance
Single submitter
Inborn genetic diseases
-
SUPT16H p.Val860Phe
Uncertain significance
Single submitter
neurodevelopmental disorder with dysmorphic facies and thin corpus callosum
-
SUPT16H p.Asn364Ser
Uncertain significance
No assertion criteria
neurodevelopmental disorder with dysmorphic facies and thin corpus callosum
Predictors split 29
The independent predictors disagree with each other — read with care.
- SUPT16H p.Ala51Val Uncertain significance Single submitter
-
SUPT16H p.Ala592Val
Uncertain significance
Single submitter
neurodevelopmental disorder with dysmorphic facies and thin corpus callosum
- SUPT16H p.Ala637Asp Uncertain significance Single submitter
-
SUPT16H p.Ala873Thr
Uncertain significance
Single submitter
neurodevelopmental disorder with dysmorphic facies and thin corpus callosum
-
SUPT16H p.Asn388Ile
Uncertain significance
Single submitter
Inborn genetic diseases
- SUPT16H p.Asn582Asp Uncertain significance Single submitter
- SUPT16H p.Asn854Ser Uncertain significance Single submitter
-
SUPT16H p.Asp140Glu
Uncertain significance
Single submitter
SUPT16H-related disorder
- SUPT16H p.Asp890Glu Uncertain significance Single submitter
- SUPT16H p.Asp953Tyr Uncertain significance Single submitter
-
SUPT16H p.Glu918Val
Uncertain significance
Single submitter
Inborn genetic diseases
- SUPT16H p.His477Arg Uncertain significance Single submitter
- SUPT16H p.Ile624Asn Uncertain significance Single submitter
- SUPT16H p.Ile905Val Uncertain significance Single submitter
- SUPT16H p.Lys185Thr Uncertain significance Single submitter
- SUPT16H p.Lys372Glu Uncertain significance Single submitter
-
SUPT16H p.Met183Thr
Uncertain significance
Single submitter
neurodevelopmental disorder
-
SUPT16H p.Met203Val
Uncertain significance
Single submitter
Inborn genetic diseases
-
SUPT16H p.Met266Ile
Uncertain significance
Single submitter
Inborn genetic diseases
- SUPT16H p.Met352Ile Uncertain significance Single submitter
-
SUPT16H p.Met768Ile
Uncertain significance
Single submitter
neurodevelopmental disorder with dysmorphic facies and thin corpus callosum
-
SUPT16H p.Phe543Leu
Uncertain significance
Single submitter
Inborn genetic diseases
- SUPT16H p.Phe740Leu Uncertain significance Single submitter
- SUPT16H p.Ser577Asn Uncertain significance Single submitter
-
SUPT16H p.Ser982Asn
Uncertain significance
Single submitter
Inborn genetic diseases
- SUPT16H p.Thr171Ile Uncertain significance Single submitter
-
SUPT16H p.Thr54Ile
Uncertain significance
Single submitter
Inborn genetic diseases
- SUPT16H p.Thr749Ala Uncertain significance Single submitter
- SUPT16H p.Thr828Met Uncertain significance Single submitter
All SUPT16H variants
Pathogenic 5
- p.Arg492fs Single submitter neurodevelopmental disorder with dysmorphic facies and thin corpus callosum
- p.Arg693Gln Single submitter
- p.Arg847Trp Single submitter neurodevelopmental disorder with dysmorphic facies and thin corpus callosum
- p.Asn571Ser No assertion criteria neurodevelopmental disorder with dysmorphic facies and thin corpus callosum
- p.Leu432Pro No assertion criteria neurodevelopmental disorder with dysmorphic facies and thin corpus callosum
Likely pathogenic 3
- p.Arg693Ter Single submitter neurodevelopmental disorder with dysmorphic facies and thin corpus callosum
- p.Arg734Trp Single submitter neurodevelopmental disorder with dysmorphic facies and thin corpus callosum
- p.Asn388fs Single submitter neurodevelopmental disorder with dysmorphic facies and thin corpus callosum
Benign 8
- c.783-6C>G Multiple submitters
- p.Ala727= Multiple submitters
- p.Asp991= Multiple submitters
- p.Ile44= Multiple submitters
- p.Lys92= Multiple submitters
- c.1234-4C>T No assertion criteria SUPT16H-related disorder
- p.Ala415Gly No assertion criteria SUPT16H-related disorder
- p.Arg456= No assertion criteria SUPT16H-related disorder
Likely benign 16
- c.1396-3C>T Multiple submitters
- p.Thr398= Multiple submitters
- c.1120+11C>T Single submitter
- p.Ala482= Single submitter
- p.Asn872= Single submitter
- p.Glu222= Single submitter
- p.His851= Single submitter
- p.Ile162= Single submitter
- p.Ile859= Single submitter
- p.Ser215= Single submitter
- p.Glu311= No assertion criteria SUPT16H-related disorder
- p.Gly576= No assertion criteria SUPT16H-related disorder
- p.Ile363Val No assertion criteria SUPT16H-related disorder
- p.Ile74Thr No assertion criteria SUPT16H-related disorder
- p.Leu17= No assertion criteria SUPT16H-related disorder
- p.Tyr632= No assertion criteria SUPT16H-related disorder
Uncertain significance 151
- p.Arg623Gln Multiple submitters Inborn genetic diseases ⚠
- p.Asn20Ser Multiple submitters Inborn genetic diseases ⚠
- p.Leu180Phe Multiple submitters neurodevelopmental disorder with dysmorphic facies and thin corpus callosum
- p.Leu795Val Multiple submitters Inborn genetic diseases ⚠
- p.Ser188Asn Multiple submitters Inborn genetic diseases ⚠
- p.Ser420Phe Multiple submitters neurodevelopmental disorder with dysmorphic facies and thin corpus callosum ⚠
- p.Ser986Asn Multiple submitters Inborn genetic diseases ⚠
- p.Thr566Ala Multiple submitters
- p.Val325Met Multiple submitters neurodevelopmental disorder with dysmorphic facies and thin corpus callosum ⚠
- c.1047-1G>A Single submitter
- c.2790+4C>T Single submitter
- c.2791-2A>C Single submitter
- c.2920+1G>A Single submitter neurodevelopmental disorder with dysmorphic facies and thin corpus callosum
- c.-1T>A Single submitter
- p.Ala173Ser Single submitter Inborn genetic diseases ⚠
- p.Ala270Gly Single submitter
- p.Ala33Gly Single submitter ⚠
- p.Ala415Pro Single submitter
- p.Ala51Val Single submitter ⚠
- p.Ala592Thr Single submitter ⚠
- p.Ala592Val Single submitter neurodevelopmental disorder with dysmorphic facies and thin corpus callosum ⚠
- p.Ala637Asp Single submitter ⚠
- p.Ala823Val Single submitter Inborn genetic diseases ⚠
- p.Ala873Thr Single submitter neurodevelopmental disorder with dysmorphic facies and thin corpus callosum ⚠
- p.Ala877Ser Single submitter Inborn genetic diseases ⚠
- p.Ala970Val Single submitter Inborn genetic diseases ⚠
- p.Arg12Trp Single submitter neurodevelopmental disorder with dysmorphic facies and thin corpus callosum ⚠
- p.Arg201Lys Single submitter ⚠
- p.Arg278Cys Single submitter ⚠
- p.Arg357Cys Single submitter ⚠
- p.Arg357Leu Single submitter ⚠
- p.Arg474Ter Single submitter
- p.Arg506Cys Single submitter Li-Fraumeni syndrome 1 ⚠
- p.Arg569Ter Single submitter
- p.Arg601Ter Single submitter
- p.Arg631Cys Single submitter Inborn genetic diseases ⚠
- p.Arg635Ter Single submitter
- p.Arg668Cys Single submitter ⚠
- p.Arg760Ter Single submitter
- p.Arg770Ter Single submitter
- p.Asn111Thr Single submitter Inborn genetic diseases ⚠
- p.Asn254Ser Single submitter Inborn genetic diseases ⚠
- p.Asn30Ser Single submitter neurodevelopmental disorder with dysmorphic facies and thin corpus callosum ⚠
- p.Asn327Ser Single submitter ⚠
- p.Asn367Ser Single submitter Inborn genetic diseases ⚠
- p.Asn380Asp Single submitter ⚠
- p.Asn388Ile Single submitter Inborn genetic diseases ⚠
- p.Asn582Asp Single submitter ⚠
- p.Asn620_Ala621insAsp Single submitter
- p.Asn854Ser Single submitter ⚠
- p.Asp140Glu Single submitter SUPT16H-related disorder ⚠
- p.Asp163Gly Single submitter neurodevelopmental disorder with dysmorphic facies and thin corpus callosum ⚠
- p.Asp209Tyr Single submitter ⚠
- p.Asp449Asn Single submitter ⚠
- p.Asp838Val Single submitter Inborn genetic diseases ⚠
- p.Asp890Glu Single submitter ⚠
- p.Asp953Tyr Single submitter ⚠
- p.Cys323Arg Single submitter Inborn genetic diseases ⚠
- p.Gln503Lys Single submitter ⚠
- p.Glu396Asp Single submitter ⚠
- p.Glu439fs Single submitter neurodevelopmental disorder with dysmorphic facies and thin corpus callosum
- p.Glu495fs Single submitter
- p.Glu495Lys Single submitter ⚠
- p.Glu562Lys Single submitter ⚠
- p.Glu794del Single submitter neurodevelopmental disorder with dysmorphic facies and thin corpus callosum
- p.Glu839Lys Single submitter neurodevelopmental disorder ⚠
- p.Glu918Val Single submitter Inborn genetic diseases ⚠
- p.Gly896Ter Single submitter
- p.Gly93Ser Single submitter ⚠
- p.His265Tyr Single submitter ⚠
- p.His477Arg Single submitter ⚠
- p.His723Leu Single submitter ⚠
- p.Ile107Val Single submitter Inborn genetic diseases ⚠
- p.Ile122Val Single submitter ⚠
- p.Ile125Val Single submitter ⚠
- p.Ile172Val Single submitter ⚠
- p.Ile247Thr Single submitter ⚠
- p.Ile322Met Single submitter Inborn genetic diseases ⚠
- p.Ile34Val Single submitter Inborn genetic diseases ⚠
- p.Ile44Met Single submitter neurodevelopmental disorder with dysmorphic facies and thin corpus callosum ⚠
- p.Ile557Val Single submitter Inborn genetic diseases ⚠
- p.Ile624Asn Single submitter ⚠
- p.Ile653Met Single submitter neurodevelopmental disorder with dysmorphic facies and thin corpus callosum ⚠
- p.Ile882Val Single submitter Inborn genetic diseases ⚠
- p.Ile905Val Single submitter ⚠
- p.Leu106Gln Single submitter
- p.Leu316Ile Single submitter neurodevelopmental disorder with dysmorphic facies and thin corpus callosum ⚠
- p.Leu386Met Single submitter ⚠
- p.Leu408Phe Single submitter ⚠
- p.Leu493Met Single submitter neurodevelopmental disorder with dysmorphic facies and thin corpus callosum ⚠
- p.Leu980Met Single submitter Inborn genetic diseases ⚠
- p.Lys156Arg Single submitter ⚠
- p.Lys161= Single submitter
- p.Lys184Arg Single submitter ⚠
- p.Lys185Thr Single submitter ⚠
- p.Lys280Arg Single submitter ⚠
- p.Lys335Gln Single submitter neurodevelopmental disorder with dysmorphic facies and thin corpus callosum ⚠
- p.Lys343_Lys346del Single submitter
- p.Lys372Glu Single submitter ⚠
- p.Lys389Gln Single submitter Inborn genetic diseases ⚠
- p.Lys555= Single submitter
- p.Lys642_Glu643delinsGluVal Single submitter
- p.Lys696fs Single submitter neurodevelopmental disorder with dysmorphic facies and thin corpus callosum
- p.Met147Leu Single submitter ⚠
- p.Met183Thr Single submitter neurodevelopmental disorder ⚠
- p.Met203Val Single submitter Inborn genetic diseases ⚠
- p.Met266Ile Single submitter Inborn genetic diseases ⚠
- p.Met275Thr Single submitter Inborn genetic diseases ⚠
- p.Met330Leu Single submitter Inborn genetic diseases ⚠
- p.Met330Thr Single submitter ⚠
- p.Met352Ile Single submitter ⚠
- p.Met768Ile Single submitter neurodevelopmental disorder with dysmorphic facies and thin corpus callosum ⚠
- p.Phe304Cys Single submitter Inborn genetic diseases ⚠
- p.Phe543Leu Single submitter Inborn genetic diseases ⚠
- p.Phe689Val Single submitter ⚠
- p.Phe740Leu Single submitter ⚠
- p.Phe855Leu Single submitter ⚠
- p.Phe924fs Single submitter
- p.Pro548Thr Single submitter ⚠
- p.Pro913Ser Single submitter Inborn genetic diseases ⚠
- p.Pro950Leu Single submitter ⚠
- p.Ser19Gly Single submitter neurodevelopmental disorder with dysmorphic facies and thin corpus callosum ⚠
- p.Ser19Thr Single submitter ⚠
- p.Ser577Asn Single submitter ⚠
- p.Ser813Gly Single submitter ⚠
- p.Ser822Gly Single submitter Inborn genetic diseases ⚠
- p.Ser982Asn Single submitter Inborn genetic diseases ⚠
- p.Ser986fs Single submitter
- p.Thr171Ile Single submitter ⚠
- p.Thr272Ser Single submitter Inborn genetic diseases
- p.Thr461Ile Single submitter Inborn genetic diseases ⚠
- p.Thr494fs Single submitter
- p.Thr4Ala Single submitter ⚠
- p.Thr54Ile Single submitter Inborn genetic diseases ⚠
- p.Thr612Ile Single submitter ⚠
- p.Thr736Ala Single submitter ⚠
- p.Thr749Ala Single submitter ⚠
- p.Thr828Met Single submitter ⚠
- p.Tyr326Phe Single submitter Inborn genetic diseases ⚠
- p.Tyr46Asp Single submitter neurodevelopmental disorder with dysmorphic facies and thin corpus callosum ⚠
- p.Tyr864Ter Single submitter
- p.Val260Leu Single submitter
- p.Val31Ile Single submitter Inborn genetic diseases ⚠
- p.Val332Met Single submitter Inborn genetic diseases ⚠
- p.Val425Ter Single submitter
- p.Val428Met Single submitter Inborn genetic diseases ⚠
- p.Val542Met Single submitter Inborn genetic diseases ⚠
- p.Val860Phe Single submitter neurodevelopmental disorder with dysmorphic facies and thin corpus callosum ⚠
- c.956-1G>A No assertion criteria dextrocardia
- p.Asn364Ser No assertion criteria neurodevelopmental disorder with dysmorphic facies and thin corpus callosum ⚠
- p.Lys862fs No assertion criteria SUPT16H-related disorder