CCM2 — 403 ClinVar variants

All ClinVar germline CCM2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 144 flagged for review →

75 Pathogenic · 10 Pathogenic/Likely pathogenic · 21 Likely pathogenic · 14 Conflicting · 36 Benign · 13 Benign/Likely benign · 88 Likely benign · 146 Uncertain significance

Full CCM2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 144

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 agree, ClinVar conflicts 4

ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.

Predictors lean, ClinVar uncertain 85

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.

Predictors split 55

The independent predictors disagree with each other — read with care.

All CCM2 variants

Pathogenic 75

  • c.30+1G>A Multiple submitters cerebral cavernous malformation 2
  • c.473-1G>T Multiple submitters cerebral cavernous malformation 2
  • c.745+1G>T Multiple submitters cerebral cavernous malformation 2
  • p.Arg19Ter Multiple submitters CCM2-related disorder
  • p.Arg57fs Multiple submitters cerebral cavernous malformation 2
  • p.Gln107Ter Multiple submitters cerebral cavernous malformation 2
  • p.Gln159Ter Multiple submitters cerebral cavernous malformation 2
  • p.Gln215Ter Multiple submitters cerebral cavernous malformation 2
  • p.Gln218Ter Multiple submitters cerebral cavernous malformation 2
  • p.Gln72Ter Multiple submitters cerebral cavernous malformation 2
  • p.Gly24fs Multiple submitters cerebral cavernous malformation 2
  • p.Met1Val Multiple submitters cerebral cavernous malformation 2
  • p.Ser280Ter Multiple submitters cerebral cavernous malformation 2
  • c.204+1G>A Single submitter cerebral cavernous malformation 2
  • c.289-1G>T Single submitter
  • c.289-2A>G Single submitter cerebral cavernous malformation 2
  • c.472+2_472+7del Single submitter
  • c.473-2A>G Single submitter cerebral cavernous malformation 2
  • c.610-1G>A Single submitter cerebral cavernous malformation 2
  • c.745+1G>C Single submitter cerebral cavernous malformation 2
  • c.745+2T>C Single submitter cerebral cavernous malformation 2
  • c.746-1G>A Single submitter cerebral cavernous malformation 2
  • p.Ala171fs Single submitter
  • p.Ala32fs Single submitter cerebral cavernous malformation 2
  • p.Arg28fs Single submitter cerebral cavernous malformation 2
  • p.Asp56fs Single submitter cerebral cavernous malformation 2
  • p.Cys211fs Single submitter cerebral cavernous malformation 2
  • p.Gln100Ter Single submitter cerebral cavernous malformation 2
  • p.Gln167fs Single submitter cerebral cavernous malformation 2
  • p.Gln167Ter Single submitter cerebral cavernous malformation 2
  • p.Gln218fs Single submitter cerebral cavernous malformation 2
  • p.Glu191fs Single submitter
  • p.Glu207fs Single submitter
  • p.Glu208Ter Single submitter
  • p.Glu324Ter Single submitter cerebral cavernous malformation 2
  • p.Glu359delinsProTer Single submitter cerebral cavernous malformation 2
  • p.Glu51Ter Single submitter cerebral cavernous malformation 2
  • p.Glu66fs Single submitter
  • p.Gly8fs Single submitter cerebral cavernous malformation 2
  • p.His104_Leu105insTer Single submitter
  • p.His104fs Single submitter cerebral cavernous malformation 2
  • p.His33fs Single submitter
  • p.His99fs Single submitter
  • p.Ile136fs Single submitter cerebral cavernous malformation 2
  • p.Leu113Pro Single submitter cerebral cavernous malformation 2
  • p.Leu177fs Single submitter cerebral cavernous malformation 2
  • p.Leu212fs Single submitter cerebral cavernous malformation 2
  • p.Leu349fs Single submitter cerebral cavernous malformation 2
  • p.Leu49fs Single submitter cerebral cavernous malformation
  • p.Leu58fs Single submitter Inborn genetic diseases
  • p.Leu59fs Single submitter
  • p.Leu73fs Single submitter cerebral cavernous malformation 2
  • p.Lys156fs Single submitter cerebral cavernous malformation 2
  • p.Phe17fs Single submitter cerebral cavernous malformation 2
  • p.Phe21fs Single submitter cerebral cavernous malformation 2
  • p.Phe228fs Single submitter
  • p.Pro16fs Single submitter cerebral cavernous malformation 2
  • p.Pro41fs Single submitter
  • p.Pro77fs Single submitter cerebral cavernous malformation 2
  • p.Ser15delinsIleTer Single submitter cerebral cavernous malformation 2
  • p.Ser174fs Single submitter cerebral cavernous malformation 2
  • p.Thr106fs Single submitter
  • p.Thr44fs Single submitter cerebral cavernous malformation 2
  • p.Trp124fs Single submitter cerebral cavernous malformation 2
  • p.Tyr118Ter Single submitter cavernous hemangioma
  • p.Val196fs Single submitter
  • p.Val220_Tyr221insTer Single submitter cerebral cavernous malformation 2
  • p.Val67fs Single submitter cerebral cavernous malformation 2
  • c.288+1G>A No assertion criteria cerebral cavernous malformation 2
  • p.Ala123Pro No assertion criteria cerebral cavernous malformation 2 ⚠
  • p.Ala98fs No assertion criteria cerebral cavernous malformation 2
  • p.Leu122Arg No assertion criteria cerebral cavernous malformation 2
  • p.Leu198Arg No assertion criteria cerebral cavernous malformation 2
  • p.Leu198Pro No assertion criteria cerebral cavernous malformation 2
  • p.Tyr79fs No assertion criteria

Pathogenic/Likely pathogenic 10

  • c.289-1G>A Multiple submitters cerebral cavernous malformation 2
  • c.30+5_30+6delinsTT Multiple submitters Inborn genetic diseases
  • c.472+1G>C Multiple submitters cerebral cavernous malformation 2
  • p.Arg412fs Multiple submitters cerebral cavernous malformation 2
  • p.Arg57Ter Multiple submitters cerebral cavernous malformation 2
  • p.Glu264fs Multiple submitters cerebral cavernous malformation 2
  • p.Glu417fs Multiple submitters cerebral cavernous malformation 2
  • p.Lys203= Multiple submitters cerebral cavernous malformation 2
  • p.Lys360Ter Multiple submitters CCM2-related disorder
  • p.Val45fs Multiple submitters

Likely pathogenic 21

Conflicting classifications of pathogenicity 14

Benign 36

Benign/Likely benign 13

  • c.1054+12C>T Multiple submitters cerebral cavernous malformation 2
  • c.1055-6C>T Multiple submitters cerebral cavernous malformation 2
  • c.804-12del Multiple submitters cerebral cavernous malformation 2
  • c.804-5C>T Multiple submitters cerebral cavernous malformation 2
  • c.*14G>T Multiple submitters
  • p.Asn327Ser Multiple submitters cerebral cavernous malformation 2
  • p.Asn401= Multiple submitters cerebral cavernous malformation 2
  • p.Gly328= Multiple submitters cerebral cavernous malformation 2
  • p.His109= Multiple submitters cerebral cavernous malformation 2
  • p.Leu113= Multiple submitters cerebral cavernous malformation 2
  • p.Pro240= Multiple submitters cerebral cavernous malformation 2
  • p.Pro82= Multiple submitters Inborn genetic diseases
  • p.Thr74= Multiple submitters Inborn genetic diseases

Likely benign 88

  • c.746-17C>T Multiple submitters cerebral cavernous malformation 2
  • c.804-12A>G Multiple submitters cerebral cavernous malformation 2
  • c.916-3C>T Multiple submitters cerebral cavernous malformation 2
  • c.*6A>G Multiple submitters
  • p.Arg378= Multiple submitters Inborn genetic diseases
  • p.Asn119= Multiple submitters cerebral cavernous malformation 2
  • p.Asp442= Multiple submitters Inborn genetic diseases
  • p.His388= Multiple submitters cerebral cavernous malformation 2
  • p.Ile428= Multiple submitters Inborn genetic diseases
  • p.Leu321= Multiple submitters Inborn genetic diseases
  • p.Leu42= Multiple submitters cerebral cavernous malformation 2
  • p.Phe228= Multiple submitters cerebral cavernous malformation 2
  • p.Ser183= Multiple submitters Inborn genetic diseases
  • p.Ser245= Multiple submitters cerebral cavernous malformation 2
  • p.Ser430= Multiple submitters Inborn genetic diseases
  • p.Ser60= Multiple submitters Inborn genetic diseases
  • c.204+11A>G Single submitter cerebral cavernous malformation 2
  • c.204+37C>T Single submitter
  • c.205-18T>G Single submitter cerebral cavernous malformation 2
  • c.288+11C>T Single submitter cerebral cavernous malformation 2
  • c.289-14G>A Single submitter cerebral cavernous malformation 2
  • c.30+14G>A Single submitter cerebral cavernous malformation 2
  • c.30+6C>T Single submitter
  • c.31-14G>A Single submitter cerebral cavernous malformation 2
  • c.472+13A>G Single submitter cerebral cavernous malformation 2
  • c.472+16G>A Single submitter cerebral cavernous malformation 2
  • c.472+17G>C Single submitter cerebral cavernous malformation 2
  • c.472+9G>C Single submitter cerebral cavernous malformation 2
  • c.609+18C>T Single submitter cerebral cavernous malformation 2
  • c.745+19G>A Single submitter cerebral cavernous malformation 2
  • c.746-13A>G Single submitter cerebral cavernous malformation 2
  • c.804-14A>T Single submitter cerebral cavernous malformation 2
  • c.915+16A>G Single submitter cerebral cavernous malformation 2
  • c.916-20C>G Single submitter cerebral cavernous malformation 2
  • c.916-7C>T Single submitter cerebral cavernous malformation 2
  • c.-27_-19dup Single submitter
  • c.*15G>A Single submitter
  • c.*20dup Single submitter
  • p.Ala141= Single submitter Inborn genetic diseases
  • p.Ala149Thr Single submitter
  • p.Ala171Val Single submitter Inborn genetic diseases
  • p.Ala295= Single submitter cerebral cavernous malformation 2
  • p.Ala434= Single submitter cerebral cavernous malformation 2
  • p.Arg146= Single submitter cerebral cavernous malformation 2
  • p.Arg19= Single submitter cerebral cavernous malformation 2
  • p.Arg389= Single submitter Inborn genetic diseases
  • p.Arg40= Single submitter cerebral cavernous malformation 2
  • p.Arg52= Single submitter cerebral cavernous malformation 2
  • p.Asn327Asp Single submitter Inborn genetic diseases ⚠
  • p.Asp431= Single submitter cerebral cavernous malformation 2
  • p.Glu259= Single submitter cerebral cavernous malformation 2
  • p.Glu433= Single submitter cerebral cavernous malformation 2
  • p.Gly180= Single submitter Inborn genetic diseases
  • p.Gly24= Single submitter cerebral cavernous malformation 2
  • p.His323= Single submitter Inborn genetic diseases
  • p.His33= Single submitter Inborn genetic diseases
  • p.Ile226= Single submitter
  • p.Ile226Val Single submitter Inborn genetic diseases
  • p.Leu115= Single submitter
  • p.Leu182= Single submitter cerebral cavernous malformation 2
  • p.Leu212= Single submitter cerebral cavernous malformation 2
  • p.Leu244= Single submitter cerebral cavernous malformation 2
  • p.Leu291= Single submitter
  • p.Leu298= Single submitter Inborn genetic diseases
  • p.Leu341= Single submitter cerebral cavernous malformation 2
  • p.Lys375= Single submitter
  • p.Phe270Leu Single submitter ⚠
  • p.Phe318= Single submitter cerebral cavernous malformation 2
  • p.Phe356= Single submitter cerebral cavernous malformation 2
  • p.Phe365= Single submitter cerebral cavernous malformation 2
  • p.Pro16= Single submitter cerebral cavernous malformation 2
  • p.Pro415= Single submitter Inborn genetic diseases
  • p.Pro50= Single submitter
  • p.Ser292= Single submitter Inborn genetic diseases
  • p.Ser408= Single submitter Inborn genetic diseases
  • p.Ser416= Single submitter cerebral cavernous malformation 2
  • p.Ser426= Single submitter cerebral cavernous malformation 2
  • p.Thr394Ser Single submitter Inborn genetic diseases
  • p.Tyr261= Single submitter cerebral cavernous malformation 2
  • p.Tyr342= Single submitter cerebral cavernous malformation 2
  • p.Val187= Single submitter Inborn genetic diseases
  • p.Val204= Single submitter cerebral cavernous malformation 2
  • p.Val220= Single submitter Inborn genetic diseases
  • p.Val53= Single submitter Inborn genetic diseases
  • c.31-10449G>T No assertion criteria CCM2-related disorder
  • c.915+10C>T No assertion criteria CCM2-related disorder
  • c.*19dup No assertion criteria CCM2-related disorder
  • p.Ser289= No assertion criteria CCM2-related disorder

Uncertain significance 146