CST3 — 61 ClinVar variants
All ClinVar germline CST3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 35 flagged for review →
1 Pathogenic · 2 Conflicting · 8 Benign · 2 Benign/Likely benign · 12 Likely benign · 36 Uncertain significance
Full CST3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 35
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 12
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- CST3 p.Pro8Ser Uncertain significance Multiple submitters
- CST3 p.Ala121Val Uncertain significance Single submitter
- CST3 p.Cys109Tyr Uncertain significance Single submitter
- CST3 p.Gly3Arg Uncertain significance Single submitter
- CST3 p.Lys62Arg Uncertain significance Single submitter
- CST3 p.Pro23Leu Uncertain significance Single submitter
- CST3 p.Pro32Arg Uncertain significance Single submitter
- CST3 p.Pro4Ser Uncertain significance Single submitter
- CST3 p.Thr137Ala Uncertain significance Single submitter
- CST3 p.Thr97Ile Uncertain significance Single submitter
- CST3 p.Tyr88Cys Uncertain significance Single submitter
- CST3 p.Val44Leu Uncertain significance Single submitter
Predictors split 23
The independent predictors disagree with each other — read with care.
-
CST3 p.Ala25Thr
Benign/Likely benign
Multiple submitters
ACys amyloidosis
- CST3 p.Ala72Ser Benign Multiple submitters
-
CST3 p.Arg71His
Uncertain significance
Multiple submitters
ACys amyloidosis
- CST3 p.His112Arg Uncertain significance Multiple submitters
- CST3 p.Met67Val Uncertain significance Multiple submitters
- CST3 p.Thr142Ala Benign Multiple submitters
- CST3 p.Ala121Pro Uncertain significance Single submitter
- CST3 p.Ala16Gly Uncertain significance Single submitter
- CST3 p.Ala63Thr Uncertain significance Single submitter
- CST3 p.Arg79Ser Benign Single submitter
- CST3 p.Arg96Gln Uncertain significance Single submitter
- CST3 p.Asn65His Uncertain significance Single submitter
- CST3 p.Leu117Val Uncertain significance Single submitter
- CST3 p.Lys62Gln Uncertain significance Single submitter
-
CST3 p.Lys80Arg
Uncertain significance
Single submitter
ACys amyloidosis
- CST3 p.Met136Val Uncertain significance Single submitter
- CST3 p.Met40Leu Uncertain significance Single submitter
- CST3 p.Met67Ile Uncertain significance Single submitter
- CST3 p.Phe89Leu Uncertain significance Single submitter
- CST3 p.Pro39Arg Uncertain significance Single submitter
- CST3 p.Val75Met Uncertain significance Single submitter
- CST3 p.Val83Ile Uncertain significance Single submitter
- CST3 p.Val92Met Uncertain significance Single submitter
All CST3 variants
Pathogenic 1
- p.Leu94Gln No assertion criteria ACys amyloidosis
Conflicting classifications of pathogenicity 2
- p.Gln114Ter Single submitter ACys amyloidosis
- p.Gln126Ter Single submitter ACys amyloidosis
Benign 8
- p.Ala72Ser Multiple submitters ⚠
- p.Leu35= Multiple submitters
- p.Pro4= Multiple submitters
- p.Thr142Ala Multiple submitters ⚠
- p.Arg6= Single submitter
- p.Arg79Ser Single submitter ⚠
- p.Glu46= Single submitter
- p.Leu53= Single submitter
Benign/Likely benign 2
- p.Ala25Thr Multiple submitters ACys amyloidosis ⚠
- p.Ser139= Multiple submitters
Likely benign 12
- c.243+10G>A Single submitter
- c.243+11C>T Single submitter
- c.243+17G>T Single submitter
- p.Ala121= Single submitter
- p.Ala129Thr Single submitter
- p.Ala56= Single submitter
- p.Arg34= Single submitter
- p.Asp145= Single submitter
- p.Leu73= Single submitter
- p.Leu94= Single submitter
- p.Val21= Single submitter
- p.Val36= Single submitter
Uncertain significance 36
- c.357+1del Multiple submitters CST3-related Leukodystrophy
- p.Arg71His Multiple submitters ACys amyloidosis ⚠
- p.His112Arg Multiple submitters ⚠
- p.Met67Val Multiple submitters ⚠
- p.Pro8Ser Multiple submitters ⚠
- c.226_243+3del Single submitter
- p.Ala121fs Single submitter CST3-related Leukodystrophy
- p.Ala121Pro Single submitter ⚠
- p.Ala121Val Single submitter ⚠
- p.Ala16Gly Single submitter ⚠
- p.Ala63Thr Single submitter ⚠
- p.Arg96Gln Single submitter ⚠
- p.Asn65His Single submitter ⚠
- p.Asp66del Single submitter ACys amyloidosis
- p.Cys109Tyr Single submitter ⚠
- p.Gln114fs Single submitter
- p.Gly3Arg Single submitter ⚠
- p.Leu117Val Single submitter ⚠
- p.Lys62Arg Single submitter ⚠
- p.Lys62Gln Single submitter ⚠
- p.Lys80Arg Single submitter ACys amyloidosis ⚠
- p.Met136Val Single submitter ⚠
- p.Met40Leu Single submitter ⚠
- p.Met67Ile Single submitter ⚠
- p.Phe89Leu Single submitter ⚠
- p.Pro23Leu Single submitter ⚠
- p.Pro32Arg Single submitter ⚠
- p.Pro39Arg Single submitter ⚠
- p.Pro4Ser Single submitter ⚠
- p.Thr137Ala Single submitter ⚠
- p.Thr97Ile Single submitter ⚠
- p.Tyr88Cys Single submitter ⚠
- p.Val44Leu Single submitter ⚠
- p.Val75Met Single submitter ⚠
- p.Val83Ile Single submitter ⚠
- p.Val92Met Single submitter ⚠