CCN2 — 59 ClinVar variants
All ClinVar germline CCN2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 52 flagged for review →
3 Pathogenic · 1 Benign · 7 Likely benign · 48 Uncertain significance
Full CCN2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 52
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 1
ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.
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CCN2 p.Arg22Pro
Pathogenic
No assertion criteria
spondyloepimetaphyseal dysplasia, Li-Shao-Li type
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.
- CCN2 p.Ala61Thr Uncertain significance Single submitter
- CCN2 p.Arg71His Uncertain significance Single submitter
- CCN2 p.Asp37Glu Uncertain significance Single submitter
- CCN2 p.Asp52Glu Uncertain significance Single submitter
- CCN2 p.Cys126Phe Uncertain significance Single submitter
- CCN2 p.Cys160Ser Uncertain significance Single submitter
- CCN2 p.Gln123Pro Uncertain significance Single submitter
- CCN2 p.Gln172Glu Uncertain significance Single submitter
- CCN2 p.Glu38Asp Uncertain significance Single submitter
- CCN2 p.Glu38Gln Uncertain significance Single submitter
- CCN2 p.Glu38Lys Uncertain significance Single submitter
- CCN2 p.Lys255Asn Uncertain significance Single submitter
- CCN2 p.Met238Val Uncertain significance Single submitter
- CCN2 p.Phe81Cys Uncertain significance Single submitter
- CCN2 p.Pro135Leu Uncertain significance Single submitter
- CCN2 p.Pro23Ser Uncertain significance Single submitter
- CCN2 p.Pro295Leu Uncertain significance Single submitter
- CCN2 p.Pro36Ser Uncertain significance Single submitter
- CCN2 p.Ser30Arg Uncertain significance Single submitter
- CCN2 p.Ser5Arg Uncertain significance Single submitter
- CCN2 p.Ser5Ile Uncertain significance Single submitter
- CCN2 p.Thr222Ala Uncertain significance Single submitter
- CCN2 p.Val174Ala Uncertain significance Single submitter
- CCN2 p.Val174Met Uncertain significance Single submitter
- CCN2 p.Val221Leu Uncertain significance Single submitter
Predictors split 26
The independent predictors disagree with each other — read with care.
- CCN2 p.Ala101Ser Uncertain significance Single submitter
- CCN2 p.Ala208Thr Uncertain significance Single submitter
- CCN2 p.Ala45Val Uncertain significance Single submitter
- CCN2 p.Arg34Gly Uncertain significance Single submitter
- CCN2 p.Arg42Gly Uncertain significance Single submitter
- CCN2 p.Arg58Gly Likely benign Single submitter
- CCN2 p.Asn333Ser Uncertain significance Single submitter
- CCN2 p.Gln233Lys Uncertain significance Single submitter
- CCN2 p.Gln27Arg Uncertain significance Single submitter
- CCN2 p.Glu163Asp Uncertain significance Single submitter
- CCN2 p.Glu311Gly Uncertain significance Single submitter
- CCN2 p.Glu70Gln Uncertain significance Single submitter
- CCN2 p.Gly100Ala Uncertain significance Single submitter
- CCN2 p.Gly100Ser Uncertain significance Single submitter
- CCN2 p.Leu17Ile Uncertain significance Single submitter
- CCN2 p.Leu49Arg Uncertain significance Single submitter
- CCN2 p.Lys252Glu Uncertain significance Single submitter
- CCN2 p.Met139Val Uncertain significance Single submitter
- CCN2 p.Met215Ile Likely benign Single submitter
- CCN2 p.Pro102Ser Likely benign Single submitter
- CCN2 p.Pro302Ala Uncertain significance Single submitter
- CCN2 p.Pro76Leu Uncertain significance Single submitter
- CCN2 p.Ser118Asn Uncertain significance Single submitter
- CCN2 p.Ser21Arg Uncertain significance Single submitter
- CCN2 p.Thr274Asn Uncertain significance Single submitter
- CCN2 p.Tyr340Phe Uncertain significance Single submitter
All CCN2 variants
Pathogenic 3
- p.Arg22Pro No assertion criteria spondyloepimetaphyseal dysplasia, Li-Shao-Li type ⚠
- p.Cys148Tyr No assertion criteria kyphomelic dysplasia
- p.Pro260fs No assertion criteria kyphomelic dysplasia
Benign 1
- c.290-6C>T Multiple submitters
Likely benign 7
- c.67-4G>A Multiple submitters
- p.Arg58Gly Single submitter ⚠
- p.Leu230= Single submitter
- p.Met134Val Single submitter
- p.Met215Ile Single submitter ⚠
- p.Phe305= Single submitter
- p.Pro102Ser Single submitter ⚠
Uncertain significance 48
- p.Ala101Ser Single submitter ⚠
- p.Ala208Thr Single submitter ⚠
- p.Ala45Val Single submitter ⚠
- p.Ala61Thr Single submitter ⚠
- p.Arg34Gly Single submitter ⚠
- p.Arg42Gly Single submitter ⚠
- p.Arg71His Single submitter ⚠
- p.Asn333Ser Single submitter ⚠
- p.Asp37Glu Single submitter ⚠
- p.Asp52Glu Single submitter ⚠
- p.Cys126Phe Single submitter ⚠
- p.Cys160Ser Single submitter ⚠
- p.Gln123Pro Single submitter ⚠
- p.Gln172Glu Single submitter ⚠
- p.Gln233Lys Single submitter ⚠
- p.Gln27Arg Single submitter ⚠
- p.Glu163Asp Single submitter ⚠
- p.Glu311Gly Single submitter ⚠
- p.Glu38Asp Single submitter ⚠
- p.Glu38Gln Single submitter ⚠
- p.Glu38Lys Single submitter ⚠
- p.Glu70Gln Single submitter ⚠
- p.Gly100Ala Single submitter ⚠
- p.Gly100Ser Single submitter ⚠
- p.Leu17Ile Single submitter ⚠
- p.Leu49Arg Single submitter ⚠
- p.Lys252Glu Single submitter ⚠
- p.Lys255Asn Single submitter ⚠
- p.Met139Val Single submitter ⚠
- p.Met238Val Single submitter ⚠
- p.Phe81Cys Single submitter ⚠
- p.Pro135Leu Single submitter ⚠
- p.Pro23Ser Single submitter ⚠
- p.Pro295Leu Single submitter ⚠
- p.Pro302Ala Single submitter ⚠
- p.Pro36Ser Single submitter ⚠
- p.Pro76Leu Single submitter ⚠
- p.Ser118Asn Single submitter ⚠
- p.Ser21Arg Single submitter ⚠
- p.Ser30Arg Single submitter ⚠
- p.Ser5Arg Single submitter ⚠
- p.Ser5Ile Single submitter ⚠
- p.Thr222Ala Single submitter ⚠
- p.Thr274Asn Single submitter ⚠
- p.Tyr340Phe Single submitter ⚠
- p.Val174Ala Single submitter ⚠
- p.Val174Met Single submitter ⚠
- p.Val221Leu Single submitter ⚠