SP9 — 58 ClinVar variants
All ClinVar germline SP9 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 49 flagged for review →
4 Pathogenic · 2 Likely pathogenic · 3 Likely benign · 49 Uncertain significance
Full SP9 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 49
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 35
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
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SP9 p.Ser112Ala
Uncertain significance
Multiple submitters
SP9-related neurodevelopmental disorder with/without epileptic encephalopathy
- SP9 p.Ala176Val Uncertain significance Single submitter
- SP9 p.Ala241Ser Uncertain significance Single submitter
- SP9 p.Ala242Thr Uncertain significance Single submitter
- SP9 p.Ala393Ser Uncertain significance Single submitter
- SP9 p.Ala452Val Uncertain significance Single submitter
- SP9 p.Ala458Glu Uncertain significance Single submitter
- SP9 p.Ala463Val Uncertain significance Single submitter
- SP9 p.Ala468Ser Uncertain significance Single submitter
- SP9 p.Ala79Glu Uncertain significance Single submitter
- SP9 p.Ala79Val Uncertain significance Single submitter
- SP9 p.Arg52Gly Uncertain significance Single submitter
- SP9 p.Asp258Glu Uncertain significance Single submitter
- SP9 p.Cys394Ser Uncertain significance Single submitter
- SP9 p.Gln210His Uncertain significance Single submitter
- SP9 p.Glu359Lys Uncertain significance Single submitter
- SP9 p.Gly107Ser Uncertain significance Single submitter
- SP9 p.Gly170Ser Uncertain significance Single submitter
- SP9 p.Gly480Ala Uncertain significance Single submitter
- SP9 p.Gly72Ser Uncertain significance Single submitter
- SP9 p.Gly81Val Uncertain significance Single submitter
- SP9 p.His229Arg Uncertain significance Single submitter
- SP9 p.Leu167Val Uncertain significance Single submitter
- SP9 p.Leu63Pro Uncertain significance Single submitter
- SP9 p.Pro96Ser Uncertain significance Single submitter
- SP9 p.Ser240Ala Uncertain significance Single submitter
- SP9 p.Ser249Ala Uncertain significance Single submitter
- SP9 p.Ser251Gly Uncertain significance Single submitter
- SP9 p.Ser451Asn Uncertain significance Single submitter
- SP9 p.Ser54Leu Uncertain significance Single submitter
- SP9 p.Ser55Thr Uncertain significance Single submitter
- SP9 p.Ser64Leu Uncertain significance Single submitter
- SP9 p.Ser82Leu Uncertain significance Single submitter
- SP9 p.Thr428Met Uncertain significance Single submitter
- SP9 p.Thr70Ser Uncertain significance Single submitter
Predictors split 14
The independent predictors disagree with each other — read with care.
- SP9 p.Ala453Gly Uncertain significance Single submitter
- SP9 p.Ala455Thr Uncertain significance Single submitter
- SP9 p.Arg391Ser Uncertain significance Single submitter
- SP9 p.Asn25Lys Uncertain significance Single submitter
- SP9 p.Gly417Cys Uncertain significance Single submitter
- SP9 p.Met402Ile Uncertain significance Single submitter
- SP9 p.Pro10Leu Uncertain significance Single submitter
- SP9 p.Pro147Thr Uncertain significance Single submitter
- SP9 p.Pro395Ala Uncertain significance Single submitter
- SP9 p.Ser240Tyr Uncertain significance Single submitter
- SP9 p.Ser249Tyr Uncertain significance Single submitter
- SP9 p.Ser448Phe Uncertain significance Single submitter
- SP9 p.Ser62Arg Uncertain significance Single submitter
- SP9 p.Val396Leu Uncertain significance Single submitter
All SP9 variants
Pathogenic 4
- p.Glu378Gly Single submitter SP9-associated disorder
- p.Ser82Ter Single submitter neurodevelopmental disorder
- p.Arg403fs No assertion criteria intellectual disability
- p.His406fs No assertion criteria Convulsive status epilepticus
Likely pathogenic 2
- p.His410_Ile411insTer Single submitter Paediatric disorders
- p.Glu378Ala No assertion criteria intellectual disability
Uncertain significance 49
- p.Ser112Ala Multiple submitters SP9-related neurodevelopmental disorder with/without epileptic encephalopathy ⚠
- p.Ala176Val Single submitter ⚠
- p.Ala241Ser Single submitter ⚠
- p.Ala242Thr Single submitter ⚠
- p.Ala393Ser Single submitter ⚠
- p.Ala452Val Single submitter ⚠
- p.Ala453Gly Single submitter ⚠
- p.Ala455Thr Single submitter ⚠
- p.Ala458Glu Single submitter ⚠
- p.Ala463Val Single submitter ⚠
- p.Ala468Ser Single submitter ⚠
- p.Ala79Glu Single submitter ⚠
- p.Ala79Val Single submitter ⚠
- p.Arg391Ser Single submitter ⚠
- p.Arg52Gly Single submitter ⚠
- p.Asn25Lys Single submitter ⚠
- p.Asp258Glu Single submitter ⚠
- p.Cys394Ser Single submitter ⚠
- p.Gln210His Single submitter ⚠
- p.Glu359Lys Single submitter ⚠
- p.Gly107Ser Single submitter ⚠
- p.Gly170Ser Single submitter ⚠
- p.Gly417Cys Single submitter ⚠
- p.Gly480Ala Single submitter ⚠
- p.Gly72Ser Single submitter ⚠
- p.Gly81Val Single submitter ⚠
- p.His229Arg Single submitter ⚠
- p.Leu167Val Single submitter ⚠
- p.Leu63Pro Single submitter ⚠
- p.Met402Ile Single submitter ⚠
- p.Pro10Leu Single submitter ⚠
- p.Pro147Thr Single submitter ⚠
- p.Pro395Ala Single submitter ⚠
- p.Pro96Ser Single submitter ⚠
- p.Ser240Ala Single submitter ⚠
- p.Ser240Tyr Single submitter ⚠
- p.Ser249Ala Single submitter ⚠
- p.Ser249Tyr Single submitter ⚠
- p.Ser251Gly Single submitter ⚠
- p.Ser448Phe Single submitter ⚠
- p.Ser451Asn Single submitter ⚠
- p.Ser54Leu Single submitter ⚠
- p.Ser55Thr Single submitter ⚠
- p.Ser62Arg Single submitter ⚠
- p.Ser64Leu Single submitter ⚠
- p.Ser82Leu Single submitter ⚠
- p.Thr428Met Single submitter ⚠
- p.Thr70Ser Single submitter ⚠
- p.Val396Leu Single submitter ⚠