SET — 128 ClinVar variants
All ClinVar germline SET variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 41 flagged for review →
21 Pathogenic · 3 Pathogenic/Likely pathogenic · 17 Likely pathogenic · 1 Conflicting · 4 Benign · 1 Benign/Likely benign · 27 Likely benign · 54 Uncertain significance
Full SET gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 41
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.
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SET p.His105Arg
Likely pathogenic
Single submitter
intellectual disability, autosomal dominant 58
-
SET p.Asp236Gly
Likely pathogenic
No assertion criteria
intellectual disability, autosomal dominant 58
Predictors lean, ClinVar uncertain 25
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
-
SET p.Asp260Glu
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
SET p.Glu261Asp
Uncertain significance
Multiple submitters
Inborn genetic diseases
- SET p.Phe189Cys Uncertain significance Multiple submitters
- SET p.Ala103Gly Uncertain significance Single submitter
- SET p.Ala177Val Uncertain significance Single submitter
-
SET p.Arg64Cys
Uncertain significance
Single submitter
intellectual disability, autosomal dominant 58
- SET p.Arg64His Uncertain significance Single submitter
-
SET p.Asn80Tyr
Uncertain significance
Single submitter
intellectual disability, autosomal dominant 58
- SET p.Asp239Glu Uncertain significance Single submitter
- SET p.Asp255Val Uncertain significance Single submitter
- SET p.Asp260Gly Uncertain significance Single submitter
- SET p.Gln48Glu Uncertain significance Single submitter
- SET p.Glu116Asp Uncertain significance Single submitter
-
SET p.Glu271Asp
Uncertain significance
Single submitter
Inborn genetic diseases
-
SET p.Glu57Gln
Uncertain significance
Single submitter
intellectual disability, autosomal dominant 58
-
SET p.Leu95Pro
Uncertain significance
Single submitter
Inborn genetic diseases
-
SET p.Lys141Arg
Uncertain significance
Single submitter
intellectual disability, autosomal dominant 58
- SET p.Lys4Glu Uncertain significance Single submitter
- SET p.Pro132Ser Uncertain significance Single submitter
- SET p.Pro20Thr Uncertain significance Single submitter
- SET p.Pro90Gln Uncertain significance Single submitter
- SET p.Thr108Ser Uncertain significance Single submitter
-
SET p.Thr194Ile
Uncertain significance
Single submitter
intellectual disability, autosomal dominant 58
-
SET p.Tyr127His
Uncertain significance
Single submitter
intellectual disability, autosomal dominant 58
-
SET p.Asp202Gly
Uncertain significance
No assertion criteria
SET-related disorder
Predictors split 14
The independent predictors disagree with each other — read with care.
-
SET p.Asp224Asn
Uncertain significance
Multiple submitters
intellectual disability, autosomal dominant 58
- SET p.Asn40Ser Uncertain significance Single submitter
-
SET p.Asp263Asn
Uncertain significance
Single submitter
intellectual disability, autosomal dominant 58
- SET p.Glu157Lys Uncertain significance Single submitter
- SET p.Glu184Lys Uncertain significance Single submitter
- SET p.Glu187Asp Uncertain significance Single submitter
-
SET p.Glu233Gly
Uncertain significance
Single submitter
Inborn genetic diseases
- SET p.Glu270Gln Uncertain significance Single submitter
-
SET p.His196Arg
Uncertain significance
Single submitter
SET-related disorder
- SET p.Leu166Val Uncertain significance Single submitter
- SET p.Pro90Ser Uncertain significance Single submitter
-
SET p.Thr167Met
Uncertain significance
Single submitter
Inborn genetic diseases
- SET p.Val222Phe Uncertain significance Single submitter
- SET p.Ala94Pro Uncertain significance No assertion criteria
All SET variants
Pathogenic 21
- c.663+5G>C Multiple submitters intellectual disability, autosomal dominant 58
- c.493-1G>A Single submitter intellectual disability, autosomal dominant 58
- c.493-3_504del Single submitter intellectual disability, autosomal dominant 58
- c.663+1G>C Single submitter
- p.Asn215fs Single submitter intellectual disability, autosomal dominant 58
- p.Asp36fs Single submitter intellectual disability, autosomal dominant 58
- p.Gln39Ter Single submitter SET-related disorder
- p.Glu206fs Single submitter
- p.Glu243fs Single submitter intellectual disability, autosomal dominant 58
- p.Gly163fs Single submitter
- p.Gly200fs Single submitter Inborn genetic diseases
- p.Lys26fs Single submitter intellectual disability, autosomal dominant 58
- p.Lys62fs Single submitter
- p.Pro151fs Single submitter Inborn genetic diseases
- p.Ser140fs Single submitter intellectual disability, autosomal dominant 58
- p.Ser148fs Single submitter intellectual disability, autosomal dominant 58
- p.Ser153Ter Single submitter intellectual disability, autosomal dominant 58
- p.Trp213Ter Single submitter intellectual disability, autosomal dominant 58
- p.Tyr220_Leu221delinsTer Single submitter intellectual disability, autosomal dominant 58
- p.Val110fs Single submitter intellectual disability, autosomal dominant 58
- p.Gln218fs No assertion criteria intellectual disability, autosomal dominant 58
Pathogenic/Likely pathogenic 3
- p.Arg44fs Multiple submitters intellectual disability, autosomal dominant 58
- p.Gln69fs Multiple submitters intellectual disability, autosomal dominant 58
- p.Trp82Gly No assertion criteria intellectual disability, autosomal dominant 58
Likely pathogenic 17
- p.His105Tyr Multiple submitters intellectual disability, autosomal dominant 58
- p.Asn80fs Single submitter
- p.Asn88Ser Single submitter
- p.Gln65Ter Single submitter intellectual disability, autosomal dominant 58
- p.Glu114fs Single submitter intellectual disability, autosomal dominant 58
- p.Glu47Ter Single submitter intellectual disability, autosomal dominant 58
- p.Glu73fs Single submitter intellectual disability, autosomal dominant 58
- p.His105Arg Single submitter intellectual disability, autosomal dominant 58 ⚠
- p.His34_Ile35insTer Single submitter intellectual disability, autosomal dominant 58
- p.Pro79fs Single submitter
- p.Trp192fs Single submitter intellectual disability, autosomal dominant 58
- c.378+1G>C No assertion criteria intellectual disability, autosomal dominant 58
- c.493-3T>A No assertion criteria intellectual disability, autosomal dominant 58
- p.Asp236Gly No assertion criteria intellectual disability, autosomal dominant 58 ⚠
- p.Lys141fs No assertion criteria intellectual disability, autosomal dominant 58
- p.Met1Ile No assertion criteria intellectual disability, autosomal dominant 58
- p.Thr85del No assertion criteria intellectual disability, autosomal dominant 58
Conflicting classifications of pathogenicity 1
- p.Gln91= Single submitter
Benign 4
- c.132-17C>T Multiple submitters intellectual disability, autosomal dominant 58
- c.493-14C>T Multiple submitters intellectual disability, autosomal dominant 58
- c.275-6G>A Single submitter
- c.810+65TA[11] Single submitter
Benign/Likely benign 1
- p.Leu22= Multiple submitters
Likely benign 27
- p.Asp202= Multiple submitters
- p.Asp235Glu Multiple submitters Inborn genetic diseases
- p.Asp264del Multiple submitters Inborn genetic diseases
- p.Leu217= Multiple submitters
- p.Tyr220= Multiple submitters
- c.112+13G>T Single submitter
- c.131+8T>G Single submitter
- c.492+15A>C Single submitter
- c.664-4del Single submitter
- c.664-4T>A Single submitter
- c.664-6_664-4del Single submitter
- c.73_73+1insAAAAAGAACAGCAAGAAGCGATTGAACACATTGATGAAGTACAAAATGAAATA Single submitter
- c.810+13T>A Single submitter
- p.Ala20Val Single submitter intellectual disability, autosomal dominant 58
- p.Gln12Pro Single submitter
- p.Gln218= Single submitter
- p.Glu234Asp Single submitter
- p.Ile75= Single submitter
- p.Leu22Pro Single submitter
- p.Phe143= Single submitter
- p.Pro10= Single submitter
- p.Pro79= Single submitter
- p.Thr156= Single submitter
- p.Thr167= Single submitter
- p.Thr173Met Single submitter Inborn genetic diseases
- c.664-5_664-4del No assertion criteria SET-related disorder
- p.Ser197= No assertion criteria SET-related disorder
Uncertain significance 54
- p.Asp224Asn Multiple submitters intellectual disability, autosomal dominant 58 ⚠
- p.Asp260Glu Multiple submitters Inborn genetic diseases ⚠
- p.Glu261Asp Multiple submitters Inborn genetic diseases ⚠
- p.Phe189Cys Multiple submitters ⚠
- c.112+5G>C Single submitter
- c.274+5G>A Single submitter
- c.378+3A>T Single submitter
- c.492+4T>C Single submitter Inborn genetic diseases
- c.73_73+1insAAAAAGAACAGCAAGAAGCGATTGAACACATTGAT Single submitter intellectual disability, autosomal dominant 58
- c.74-3C>G Single submitter intellectual disability, autosomal dominant 58
- c.811-6_811-3del Single submitter
- p.Ala103Gly Single submitter ⚠
- p.Ala177Val Single submitter ⚠
- p.Arg64Cys Single submitter intellectual disability, autosomal dominant 58 ⚠
- p.Arg64His Single submitter ⚠
- p.Asn40Ser Single submitter ⚠
- p.Asn80Tyr Single submitter intellectual disability, autosomal dominant 58 ⚠
- p.Asp211del Single submitter
- p.Asp239Glu Single submitter ⚠
- p.Asp255Val Single submitter ⚠
- p.Asp260Gly Single submitter ⚠
- p.Asp263Asn Single submitter intellectual disability, autosomal dominant 58 ⚠
- p.Asp36del Single submitter intellectual disability, autosomal dominant 58
- p.Gln48Glu Single submitter ⚠
- p.Glu116Asp Single submitter ⚠
- p.Glu157Lys Single submitter ⚠
- p.Glu184Lys Single submitter ⚠
- p.Glu187Asp Single submitter ⚠
- p.Glu229del Single submitter
- p.Glu233Gly Single submitter Inborn genetic diseases ⚠
- p.Glu261del Single submitter intellectual disability, autosomal dominant 58
- p.Glu267fs Single submitter
- p.Glu270Gln Single submitter ⚠
- p.Glu271Asp Single submitter Inborn genetic diseases ⚠
- p.Glu57Gln Single submitter intellectual disability, autosomal dominant 58 ⚠
- p.Gly232del Single submitter Inborn genetic diseases
- p.His196Arg Single submitter SET-related disorder ⚠
- p.Leu166Val Single submitter ⚠
- p.Leu95Pro Single submitter Inborn genetic diseases ⚠
- p.Lys141Arg Single submitter intellectual disability, autosomal dominant 58 ⚠
- p.Lys4Glu Single submitter ⚠
- p.Pro132Ser Single submitter ⚠
- p.Pro20Thr Single submitter ⚠
- p.Pro90Gln Single submitter ⚠
- p.Pro90Ser Single submitter ⚠
- p.Ser9fs Single submitter
- p.Thr108Ser Single submitter ⚠
- p.Thr167Met Single submitter Inborn genetic diseases ⚠
- p.Thr194Ile Single submitter intellectual disability, autosomal dominant 58 ⚠
- p.Tyr127His Single submitter intellectual disability, autosomal dominant 58 ⚠
- p.Val222Phe Single submitter ⚠
- p.Ala94Pro No assertion criteria ⚠
- p.Asp202Gly No assertion criteria SET-related disorder ⚠
- p.Asp247del No assertion criteria SET-related disorder