SMAD9 — 285 ClinVar variants

All ClinVar germline SMAD9 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 115 flagged for review →

13 Pathogenic · 2 Pathogenic/Likely pathogenic · 11 Likely pathogenic · 11 Conflicting · 20 Benign · 6 Benign/Likely benign · 99 Likely benign · 123 Uncertain significance

Full SMAD9 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 115

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 7

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

Predictors lean, ClinVar uncertain 91

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

Predictors split 17

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

All SMAD9 variants

Pathogenic 13

  • p.Arg294Ter Multiple submitters pulmonary hypertension, primary, 2
  • p.Tyr129Ter Multiple submitters pulmonary hypertension, primary, 2
  • p.Ala233fs Single submitter pulmonary hypertension, primary, 2
  • p.Arg284Ter Single submitter pulmonary hypertension, primary, 2
  • p.Cys68fs Single submitter pulmonary hypertension, primary, 2
  • p.Leu229fs Single submitter pulmonary hypertension, primary, 2
  • p.Leu255_Ser256insTer Single submitter pulmonary hypertension, primary, 2
  • p.Lys67fs Single submitter pulmonary hypertension, primary, 2
  • p.Ser223Ter Single submitter pulmonary hypertension, primary, 2
  • p.Trp24Ter Single submitter pulmonary hypertension, primary, 2
  • p.Trp33Ter Single submitter pulmonary hypertension, primary, 2
  • p.Trp96fs Single submitter pulmonary hypertension, primary, 2
  • p.Cys202Ter No assertion criteria pulmonary hypertension, primary, 2

Pathogenic/Likely pathogenic 2

  • p.Cys68Ter Multiple submitters Pulmonary arterial hypertension associated with congenital heart disease
  • p.Gln271Ter Multiple submitters pulmonary hypertension, primary, 2

Likely pathogenic 11

  • p.Pro190fs Multiple submitters pulmonary hypertension, primary, 2
  • c.1004-2A>G Single submitter pulmonary hypertension, primary, 2
  • c.671-1G>A Single submitter pulmonary hypertension, primary, 2
  • p.Cys93fs Single submitter pulmonary hypertension, primary, 2
  • p.Gln271fs Single submitter pulmonary hypertension, primary, 2
  • p.Gln290Ter Single submitter pulmonary hypertension, primary, 2
  • p.Gln365fs Single submitter
  • p.Lys108delinsSerTer Single submitter pulmonary hypertension, primary, 2
  • p.Lys47fs Single submitter pulmonary hypertension, primary, 2
  • p.Tyr267Ter Single submitter pulmonary hypertension, primary, 2
  • p.Tyr346fs Single submitter pulmonary hypertension, primary, 2

Conflicting classifications of pathogenicity 11

  • c.781+2T>A Single submitter pulmonary hypertension, primary, 2
  • p.Arg263Gln Single submitter pulmonary hypertension, primary, 2 ⚠
  • p.Arg73Cys Single submitter pulmonary hypertension, primary, 2 ⚠
  • p.Asn307Ser Single submitter Inborn genetic diseases ⚠
  • p.Asn386Asp Single submitter Pulmonary arterial hypertension associated with congenital heart disease ⚠
  • p.Cys202= Single submitter pulmonary hypertension, primary, 2
  • p.His208Asp Single submitter Inborn genetic diseases ⚠
  • p.Ile332fs Single submitter pulmonary hypertension, primary, 2
  • p.Leu22Pro Single submitter pulmonary hypertension, primary, 2 ⚠
  • p.Lys46fs Single submitter pulmonary hypertension, primary, 2
  • p.Tyr150Cys Single submitter pulmonary hypertension, primary, 2 ⚠

Benign 20

Benign/Likely benign 6

  • c.1004-8G>A Multiple submitters pulmonary hypertension, primary, 2
  • c.1260+17A>C Multiple submitters pulmonary hypertension, primary, 2
  • p.His252= Multiple submitters pulmonary hypertension, primary, 2
  • p.Pro16= Multiple submitters pulmonary hypertension, primary, 2
  • p.Val276= Multiple submitters pulmonary hypertension, primary, 2
  • p.Val345= Multiple submitters pulmonary hypertension, primary, 2

Likely benign 99

  • c.1004-6C>T Multiple submitters pulmonary hypertension, primary, 2
  • c.781+18A>G Multiple submitters pulmonary hypertension, primary, 2
  • p.Ala163Thr Multiple submitters pulmonary hypertension, primary, 2
  • p.Arg146Lys Multiple submitters pulmonary hypertension, primary, 2
  • p.Cys349= Multiple submitters pulmonary hypertension, primary, 2
  • p.Pro62= Multiple submitters pulmonary hypertension, primary, 2
  • p.Thr203= Multiple submitters pulmonary hypertension, primary, 2
  • c.1004-15T>G Single submitter pulmonary hypertension, primary, 2
  • c.1004-221G>A Single submitter
  • c.1260+10G>A Single submitter pulmonary hypertension, primary, 2
  • c.1260+139C>T Single submitter
  • c.1261-19C>G Single submitter pulmonary hypertension, primary, 2
  • c.1261-265G>C Single submitter
  • c.1261-267G>A Single submitter
  • c.412+15C>T Single submitter pulmonary hypertension, primary, 2
  • c.412+16G>A Single submitter pulmonary hypertension, primary, 2
  • c.412+18C>T Single submitter pulmonary hypertension, primary, 2
  • c.412+7C>G Single submitter pulmonary hypertension, primary, 2
  • c.412+7C>T Single submitter
  • c.413-206A>G Single submitter
  • c.413-6T>C Single submitter pulmonary hypertension, primary, 2
  • c.413-7A>G Single submitter pulmonary hypertension, primary, 2
  • c.670+14A>G Single submitter pulmonary hypertension, primary, 2
  • c.670+33G>A Single submitter
  • c.670+7A>G Single submitter pulmonary hypertension, primary, 2
  • c.671-11C>T Single submitter pulmonary hypertension, primary, 2
  • c.781+15A>T Single submitter
  • c.781+17C>T Single submitter pulmonary hypertension, primary, 2
  • c.781+9C>T Single submitter pulmonary hypertension, primary, 2
  • c.782-17G>T Single submitter pulmonary hypertension, primary, 2
  • c.-186-157T>C Single submitter
  • p.Ala163= Single submitter pulmonary hypertension, primary, 2
  • p.Ala196= Single submitter pulmonary hypertension, primary, 2
  • p.Ala236= Single submitter pulmonary hypertension, primary, 2
  • p.Ala37= Single submitter pulmonary hypertension, primary, 2
  • p.Arg161= Single submitter pulmonary hypertension, primary, 2
  • p.Arg284= Single submitter pulmonary hypertension, primary, 2
  • p.Arg360= Single submitter pulmonary hypertension, primary, 2
  • p.Arg94= Single submitter pulmonary hypertension, primary, 2
  • p.Asn174= Single submitter pulmonary hypertension, primary, 2
  • p.Asn322= Single submitter pulmonary hypertension, primary, 2
  • p.Asp303= Single submitter
  • p.Asp76= Single submitter pulmonary hypertension, primary, 2
  • p.Cys112= Single submitter pulmonary hypertension, primary, 2
  • p.Cys380= Single submitter pulmonary hypertension, primary, 2
  • p.Cys61= Single submitter
  • p.Gln221= Single submitter pulmonary hypertension, primary, 2
  • p.His105= Single submitter pulmonary hypertension, primary, 2
  • p.His195= Single submitter pulmonary hypertension, primary, 2
  • p.His366= Single submitter pulmonary hypertension, primary, 2
  • p.Leu110= Single submitter pulmonary hypertension, primary, 2
  • p.Leu139= Single submitter pulmonary hypertension, primary, 2
  • p.Leu143= Single submitter pulmonary hypertension, primary, 2
  • p.Leu154= Single submitter pulmonary hypertension, primary, 2
  • p.Leu189= Single submitter pulmonary hypertension, primary, 2
  • p.Leu229= Single submitter pulmonary hypertension, primary, 2
  • p.Leu382= Single submitter pulmonary hypertension, primary, 2
  • p.Leu45= Single submitter pulmonary hypertension, primary, 2
  • p.Leu55= Single submitter pulmonary hypertension, primary, 2
  • p.Leu59= Single submitter pulmonary hypertension, primary, 2
  • p.Leu79= Single submitter pulmonary hypertension, primary, 2
  • p.Leu87= Single submitter
  • p.Lys43Glu Single submitter pulmonary hypertension, primary, 2
  • p.Lys67= Single submitter pulmonary hypertension, primary, 2
  • p.Phe117= Single submitter pulmonary hypertension, primary, 2
  • p.Phe390= Single submitter pulmonary hypertension, primary, 2
  • p.Pro145Gln Single submitter pulmonary hypertension, primary, 2
  • p.Pro152= Single submitter pulmonary hypertension, primary, 2
  • p.Pro169= Single submitter pulmonary hypertension, primary, 2
  • p.Pro185= Single submitter pulmonary hypertension, primary, 2
  • p.Pro201= Single submitter pulmonary hypertension, primary, 2
  • p.Pro213= Single submitter pulmonary hypertension, primary, 2
  • p.Pro230= Single submitter pulmonary hypertension, primary, 2
  • p.Pro264= Single submitter pulmonary hypertension, primary, 2
  • p.Pro445= Single submitter pulmonary hypertension, primary, 2
  • p.Pro99= Single submitter pulmonary hypertension, primary, 2
  • p.Ser103= Single submitter pulmonary hypertension, primary, 2
  • p.Ser162= Single submitter pulmonary hypertension, primary, 2
  • p.Ser180= Single submitter pulmonary hypertension, primary, 2
  • p.Ser214= Single submitter
  • p.Ser256= Single submitter pulmonary hypertension, primary, 2
  • p.Ser275= Single submitter pulmonary hypertension, primary, 2
  • p.Ser293= Single submitter pulmonary hypertension, primary, 2
  • p.Ser295= Single submitter pulmonary hypertension, primary, 2
  • p.Ser317= Single submitter pulmonary hypertension, primary, 2
  • p.Ser378= Single submitter pulmonary hypertension, primary, 2
  • p.Ser397= Single submitter
  • p.Thr288= Single submitter pulmonary hypertension, primary, 2
  • p.Thr302= Single submitter pulmonary hypertension, primary, 2
  • p.Thr324= Single submitter pulmonary hypertension, primary, 2
  • p.Thr5= Single submitter pulmonary hypertension, primary, 2
  • p.Tyr150= Single submitter pulmonary hypertension, primary, 2
  • p.Val144Leu Single submitter pulmonary hypertension, primary, 2
  • p.Val18= Single submitter pulmonary hypertension, primary, 2
  • p.Val319= Single submitter pulmonary hypertension, primary, 2
  • p.Val336= Single submitter pulmonary hypertension, primary, 2
  • p.Val341= Single submitter pulmonary hypertension, primary, 2
  • p.Val404= Single submitter pulmonary hypertension, primary, 2
  • p.Val69= Single submitter pulmonary hypertension, primary, 2

Uncertain significance 123