ARHGEF9 — 494 ClinVar variants

All ClinVar germline ARHGEF9 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 208 flagged for review →

25 Pathogenic · 6 Pathogenic/Likely pathogenic · 17 Likely pathogenic · 27 Conflicting · 27 Benign · 13 Benign/Likely benign · 165 Likely benign · 214 Uncertain significance

Full ARHGEF9 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 208

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 14

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

Predictors lean, ClinVar uncertain 125

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

Predictors split 69

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

All ARHGEF9 variants

Pathogenic 25

  • p.Arg296Ter Multiple submitters developmental and epileptic encephalopathy, 8
  • p.Gln259Ter Multiple submitters developmental and epileptic encephalopathy, 8
  • p.Glu436fs Multiple submitters developmental and epileptic encephalopathy, 8
  • p.Trp423Ter Multiple submitters developmental and epileptic encephalopathy, 8
  • c.1321+1G>A Single submitter
  • c.402+1G>C Single submitter developmental and epileptic encephalopathy, 8
  • p.Asn292fs Single submitter Inborn genetic diseases
  • p.Gln139Ter Single submitter Inborn genetic diseases
  • p.Gln308Ter Single submitter developmental and epileptic encephalopathy, 8
  • p.Gln344Ter Single submitter developmental and epileptic encephalopathy, 8
  • p.Gln451Ter Single submitter developmental and epileptic encephalopathy, 8
  • p.Glu315= Single submitter developmental and epileptic encephalopathy, 8
  • p.Glu384Ter Single submitter developmental and epileptic encephalopathy, 8
  • p.Glu60Ter Single submitter developmental and epileptic encephalopathy, 8
  • p.Gly330fs Single submitter developmental and epileptic encephalopathy, 8
  • p.His271fs Single submitter developmental and epileptic encephalopathy, 8
  • p.Leu367fs Single submitter developmental and epileptic encephalopathy, 8
  • p.Ser310fs Single submitter developmental and epileptic encephalopathy, 8
  • p.Ser470Ter Single submitter developmental and epileptic encephalopathy, 8
  • p.Trp314Ter Single submitter developmental and epileptic encephalopathy, 8
  • p.Trp72Ter Single submitter developmental and epileptic encephalopathy, 8
  • p.Tyr475fs Single submitter developmental and epileptic encephalopathy, 8
  • p.Val380fs Single submitter developmental and epileptic encephalopathy, 8
  • p.Gln2Ter No assertion criteria developmental and epileptic encephalopathy, 8
  • p.Gly62Ala No assertion criteria developmental and epileptic encephalopathy, 8

Pathogenic/Likely pathogenic 6

  • c.582+1G>A Multiple submitters developmental and epileptic encephalopathy, 8
  • p.Arg111Gln Multiple submitters developmental and epileptic encephalopathy, 8
  • p.Arg297His Multiple submitters Inborn genetic diseases
  • p.Arg345Trp Multiple submitters Inborn genetic diseases
  • p.Arg372His Multiple submitters Inborn genetic diseases ⚠
  • p.Glu186Lys Multiple submitters Inborn genetic diseases

Likely pathogenic 17

  • c.1078-1G>A Single submitter
  • c.1078-3T>G Single submitter developmental and epileptic encephalopathy, 8
  • c.1322-1G>A Single submitter
  • c.30+1G>A Single submitter developmental and epileptic encephalopathy, 8
  • c.402+1G>A Single submitter developmental and epileptic encephalopathy, 8
  • c.945+1G>A Single submitter Neurodevelopmental delay
  • c.946-8_949delinsATCCTAGAC Single submitter
  • p.Ala112fs Single submitter developmental and epileptic encephalopathy, 8
  • p.Arg345Gln Single submitter
  • p.Cys140Tyr Single submitter developmental and epileptic encephalopathy, 8
  • p.Gly188Arg Single submitter developmental and epileptic encephalopathy, 8
  • p.Ile421fs Single submitter
  • p.Lys359= Single submitter developmental and epileptic encephalopathy, 8
  • p.Trp24Ter Single submitter
  • p.Trp307Ter Single submitter developmental and epileptic encephalopathy, 8
  • p.Tyr125Ter Single submitter developmental and epileptic encephalopathy, 8
  • p.Val170fs Single submitter developmental and epileptic encephalopathy, 8

Conflicting classifications of pathogenicity 27

  • c.816-9T>C Single submitter developmental and epileptic encephalopathy, 8
  • p.Ala261Ser Single submitter developmental and epileptic encephalopathy, 8 ⚠
  • p.Arg102Gln Single submitter Inborn genetic diseases ⚠
  • p.Arg111Trp Single submitter developmental and epileptic encephalopathy, 8 ⚠
  • p.Arg223Cys Single submitter developmental and epileptic encephalopathy, 8 ⚠
  • p.Arg297Cys Single submitter Inborn genetic diseases ⚠
  • p.Arg363Gln Single submitter developmental and epileptic encephalopathy, 8 ⚠
  • p.Asp491Asn Single submitter Inborn genetic diseases ⚠
  • p.Asp85Asn Single submitter developmental and epileptic encephalopathy, 8 ⚠
  • p.Gln225= Single submitter Inborn genetic diseases
  • p.Gln56Lys Single submitter developmental and epileptic encephalopathy, 8 ⚠
  • p.Glu117= Single submitter developmental and epileptic encephalopathy, 8
  • p.Glu150Lys Single submitter Inborn genetic diseases ⚠
  • p.Glu317Lys Single submitter Inborn genetic diseases ⚠
  • p.Glu60= Single submitter developmental and epileptic encephalopathy, 8
  • p.Gly168Asp Single submitter developmental and epileptic encephalopathy, 8 ⚠
  • p.Gly371= Single submitter Inborn genetic diseases
  • p.His124= Single submitter Inborn genetic diseases
  • p.Met213Ile Single submitter developmental and epileptic encephalopathy, 8 ⚠
  • p.Met354Leu Single submitter Inborn genetic diseases ⚠
  • p.Met395Val Single submitter Inborn genetic diseases ⚠
  • p.Phe499Leu Single submitter developmental and epileptic encephalopathy, 8 ⚠
  • p.Ser148Asn Single submitter developmental and epileptic encephalopathy, 8 ⚠
  • p.Ser516Gly Single submitter developmental and epileptic encephalopathy, 8 ⚠
  • p.Tyr339Cys Single submitter developmental and epileptic encephalopathy, 8 ⚠
  • p.Val498Ile Single submitter developmental and epileptic encephalopathy, 8 ⚠
  • p.Val86Leu Single submitter developmental and epileptic encephalopathy, 8 ⚠

Benign 27

Benign/Likely benign 13

  • c.816-12_816-11del Multiple submitters developmental and epileptic encephalopathy, 8
  • c.946-16C>T Multiple submitters developmental and epileptic encephalopathy, 8
  • c.946-4C>A Multiple submitters developmental and epileptic encephalopathy, 8
  • p.Ala35= Multiple submitters Inborn genetic diseases
  • p.Asp149= Multiple submitters developmental and epileptic encephalopathy, 8
  • p.Asp313Glu Multiple submitters Inborn genetic diseases ⚠
  • p.Asp491Glu Multiple submitters Inborn genetic diseases
  • p.Gly188= Multiple submitters developmental and epileptic encephalopathy, 8
  • p.His194= Multiple submitters Inborn genetic diseases
  • p.Ile17Val Multiple submitters Inborn genetic diseases
  • p.Ile444Val Multiple submitters developmental and epileptic encephalopathy, 8
  • p.Met10Thr Multiple submitters developmental and epileptic encephalopathy, 8
  • p.Ser185= Multiple submitters developmental and epileptic encephalopathy, 8

Likely benign 165

  • c.1078-18C>T Multiple submitters developmental and epileptic encephalopathy, 8
  • c.1390+163C>T Multiple submitters
  • c.1391-4C>G Multiple submitters developmental and epileptic encephalopathy, 8
  • c.31-29583C>A Multiple submitters developmental and epileptic encephalopathy, 8
  • c.403-4A>C Multiple submitters Inborn genetic diseases
  • c.583-11dup Multiple submitters developmental and epileptic encephalopathy, 8
  • c.583-18T>G Multiple submitters developmental and epileptic encephalopathy, 8
  • c.815+175T>C Multiple submitters
  • p.Ala494= Multiple submitters Inborn genetic diseases
  • p.Arg144= Multiple submitters Inborn genetic diseases
  • p.Arg506= Multiple submitters developmental and epileptic encephalopathy, 8
  • p.Asn88= Multiple submitters developmental and epileptic encephalopathy, 8
  • p.Cys97= Multiple submitters developmental and epileptic encephalopathy, 8
  • p.Gln259= Multiple submitters developmental and epileptic encephalopathy, 8
  • p.Gln337= Multiple submitters Inborn genetic diseases
  • p.Gln462= Multiple submitters developmental and epileptic encephalopathy, 8
  • p.Gln497Arg Multiple submitters developmental and epileptic encephalopathy, 8
  • p.Glu122= Multiple submitters developmental and epileptic encephalopathy, 8
  • p.Glu193= Multiple submitters developmental and epileptic encephalopathy, 8
  • p.Glu78= Multiple submitters developmental and epileptic encephalopathy, 8
  • p.His484= Multiple submitters Inborn genetic diseases
  • p.Ile240= Multiple submitters developmental and epileptic encephalopathy, 8
  • p.Ile409Val Multiple submitters developmental and epileptic encephalopathy, 8
  • p.Ile493= Multiple submitters developmental and epileptic encephalopathy, 8
  • p.Lys295= Multiple submitters developmental and epileptic encephalopathy, 8
  • p.Pro478= Multiple submitters developmental and epileptic encephalopathy, 8
  • p.Pro510= Multiple submitters Inborn genetic diseases
  • p.Ser496= Multiple submitters developmental and epileptic encephalopathy, 8
  • p.Ser84= Multiple submitters developmental and epileptic encephalopathy, 8
  • p.Thr502= Multiple submitters developmental and epileptic encephalopathy, 8
  • c.1077+10C>T Single submitter developmental and epileptic encephalopathy, 8
  • c.1077+11C>A Single submitter developmental and epileptic encephalopathy, 8
  • c.1077+18T>C Single submitter developmental and epileptic encephalopathy, 8
  • c.1077+19T>G Single submitter developmental and epileptic encephalopathy, 8
  • c.1077+7C>G Single submitter developmental and epileptic encephalopathy, 8
  • c.1077+8T>C Single submitter developmental and epileptic encephalopathy, 8
  • c.1078-13C>T Single submitter developmental and epileptic encephalopathy, 8
  • c.1078-18C>A Single submitter developmental and epileptic encephalopathy, 8
  • c.1078-19C>T Single submitter developmental and epileptic encephalopathy, 8
  • c.1078-324C>A Single submitter
  • c.1321+18A>G Single submitter developmental and epileptic encephalopathy, 8
  • c.1322-10T>C Single submitter developmental and epileptic encephalopathy, 8
  • c.1322-120del Single submitter
  • c.1322-17A>T Single submitter developmental and epileptic encephalopathy, 8
  • c.1322-19A>G Single submitter developmental and epileptic encephalopathy, 8
  • c.1322-31A>G Single submitter
  • c.1390+11C>T Single submitter developmental and epileptic encephalopathy, 8
  • c.1390+13C>T Single submitter developmental and epileptic encephalopathy, 8
  • c.1390+18A>G Single submitter developmental and epileptic encephalopathy, 8
  • c.1390+262del Single submitter
  • c.1391-12C>T Single submitter developmental and epileptic encephalopathy, 8
  • c.1391-14C>A Single submitter developmental and epileptic encephalopathy, 8
  • c.1391-16C>T Single submitter developmental and epileptic encephalopathy, 8
  • c.1391-5T>C Single submitter developmental and epileptic encephalopathy, 8
  • c.1391-7A>G Single submitter developmental and epileptic encephalopathy, 8
  • c.211-13C>A Single submitter developmental and epileptic encephalopathy, 8
  • c.211-5C>T Single submitter developmental and epileptic encephalopathy, 8
  • c.30+20G>A Single submitter developmental and epileptic encephalopathy, 8
  • c.30+9A>C Single submitter developmental and epileptic encephalopathy, 8
  • c.31-10G>T Single submitter developmental and epileptic encephalopathy, 8
  • c.31-29459T>C Single submitter epilepsy
  • c.31-29577C>T Single submitter developmental and epileptic encephalopathy, 8
  • c.31-29579C>T Single submitter developmental and epileptic encephalopathy, 8
  • c.31-29596G>C Single submitter developmental and epileptic encephalopathy, 8
  • c.31-29639A>T Single submitter
  • c.31-29642del Single submitter
  • c.31-5C>T Single submitter developmental and epileptic encephalopathy, 8
  • c.31-6C>T Single submitter developmental and epileptic encephalopathy, 8
  • c.402+15T>C Single submitter developmental and epileptic encephalopathy, 8
  • c.402+20T>C Single submitter developmental and epileptic encephalopathy, 8
  • c.402+7A>T Single submitter developmental and epileptic encephalopathy, 8
  • c.402+8T>C Single submitter developmental and epileptic encephalopathy, 8
  • c.403-12C>G Single submitter developmental and epileptic encephalopathy, 8
  • c.403-16T>A Single submitter developmental and epileptic encephalopathy, 8
  • c.403-17T>C Single submitter developmental and epileptic encephalopathy, 8
  • c.582+10_582+14del Single submitter developmental and epileptic encephalopathy, 8
  • c.582+10T>A Single submitter developmental and epileptic encephalopathy, 8
  • c.582+18T>C Single submitter developmental and epileptic encephalopathy, 8
  • c.583-14T>C Single submitter developmental and epileptic encephalopathy, 8
  • c.583-17T>G Single submitter developmental and epileptic encephalopathy, 8
  • c.583-296del Single submitter
  • c.815+10C>T Single submitter developmental and epileptic encephalopathy, 8
  • c.815+11G>A Single submitter developmental and epileptic encephalopathy, 8
  • c.815+18T>C Single submitter developmental and epileptic encephalopathy, 8
  • c.815+302C>T Single submitter
  • c.815+8A>G Single submitter developmental and epileptic encephalopathy, 8
  • c.815+8A>T Single submitter developmental and epileptic encephalopathy, 8
  • c.816-10G>A Single submitter developmental and epileptic encephalopathy, 8
  • c.816-16T>C Single submitter developmental and epileptic encephalopathy, 8
  • c.816-18A>C Single submitter developmental and epileptic encephalopathy, 8
  • c.946-13A>C Single submitter developmental and epileptic encephalopathy, 8
  • c.946-17T>A Single submitter developmental and epileptic encephalopathy, 8
  • c.946-18A>G Single submitter developmental and epileptic encephalopathy, 8
  • c.946-19C>A Single submitter developmental and epileptic encephalopathy, 8
  • c.946-333AG[13] Single submitter
  • c.*146G>C Single submitter epilepsy
  • c.*7C>G Single submitter
  • p.Ala112= Single submitter developmental and epileptic encephalopathy, 8
  • p.Ala22= Single submitter developmental and epileptic encephalopathy, 8
  • p.Ala305= Single submitter developmental and epileptic encephalopathy, 8
  • p.Ala398= Single submitter developmental and epileptic encephalopathy, 8
  • p.Ala66= Single submitter developmental and epileptic encephalopathy, 8
  • p.Arg223= Single submitter
  • p.Arg296= Single submitter developmental and epileptic encephalopathy, 8
  • p.Arg372= Single submitter developmental and epileptic encephalopathy, 8
  • p.Arg431= Single submitter developmental and epileptic encephalopathy, 8
  • p.Arg517= Single submitter developmental and epileptic encephalopathy, 8
  • p.Asn31= Single submitter developmental and epileptic encephalopathy, 8
  • p.Asp313= Single submitter developmental and epileptic encephalopathy, 8
  • p.Asp318= Single submitter developmental and epileptic encephalopathy, 8
  • p.Asp365= Single submitter developmental and epileptic encephalopathy, 8
  • p.Asp374= Single submitter developmental and epileptic encephalopathy, 8
  • p.Asp382Asn Single submitter developmental and epileptic encephalopathy, 8 ⚠
  • p.Asp491= Single submitter developmental and epileptic encephalopathy, 8
  • p.Asp58= Single submitter developmental and epileptic encephalopathy, 8
  • p.Asp58Asn Single submitter developmental and epileptic encephalopathy, 8
  • p.Cys97Arg Single submitter
  • p.Gln308= Single submitter developmental and epileptic encephalopathy, 8
  • p.Gln343= Single submitter developmental and epileptic encephalopathy, 8
  • p.Gln486= Single submitter developmental and epileptic encephalopathy, 8
  • p.Glu214= Single submitter developmental and epileptic encephalopathy, 8
  • p.Glu419= Single submitter developmental and epileptic encephalopathy, 8
  • p.Glu81= Single submitter developmental and epileptic encephalopathy, 8
  • p.Gly244= Single submitter developmental and epileptic encephalopathy, 8
  • p.Gly316= Single submitter
  • p.Gly340= Single submitter developmental and epileptic encephalopathy, 8
  • p.Gly386= Single submitter developmental and epileptic encephalopathy, 8
  • p.Gly39= Single submitter developmental and epileptic encephalopathy, 8
  • p.His128= Single submitter developmental and epileptic encephalopathy, 8
  • p.His352= Single submitter developmental and epileptic encephalopathy, 8
  • p.His402= Single submitter developmental and epileptic encephalopathy, 8
  • p.Ile187= Single submitter
  • p.Ile242= Single submitter developmental and epileptic encephalopathy, 8
  • p.Ile253= Single submitter developmental and epileptic encephalopathy, 8
  • p.Ile42= Single submitter developmental and epileptic encephalopathy, 8
  • p.Leu137= Single submitter developmental and epileptic encephalopathy, 8
  • p.Leu173= Single submitter developmental and epileptic encephalopathy, 8
  • p.Leu192= Single submitter developmental and epileptic encephalopathy, 8
  • p.Leu34= Single submitter developmental and epileptic encephalopathy, 8
  • p.Leu401= Single submitter developmental and epileptic encephalopathy, 8
  • p.Leu411= Single submitter developmental and epileptic encephalopathy, 8
  • p.Leu417= Single submitter developmental and epileptic encephalopathy, 8
  • p.Lys127= Single submitter developmental and epileptic encephalopathy, 8
  • p.Lys138= Single submitter developmental and epileptic encephalopathy, 8
  • p.Lys220= Single submitter developmental and epileptic encephalopathy, 8
  • p.Lys415= Single submitter developmental and epileptic encephalopathy, 8
  • p.Phe245= Single submitter developmental and epileptic encephalopathy, 8
  • p.Phe499= Single submitter developmental and epileptic encephalopathy, 8
  • p.Pro103= Single submitter developmental and epileptic encephalopathy, 8
  • p.Pro249= Single submitter developmental and epileptic encephalopathy, 8
  • p.Pro481= Single submitter developmental and epileptic encephalopathy, 8
  • p.Pro490= Single submitter developmental and epileptic encephalopathy, 8
  • p.Pro83= Single submitter developmental and epileptic encephalopathy, 8
  • p.Ser324= Single submitter developmental and epileptic encephalopathy, 8
  • p.Ser8= Single submitter developmental and epileptic encephalopathy, 8
  • p.Ser95= Single submitter developmental and epileptic encephalopathy, 8
  • p.Thr248= Single submitter
  • p.Thr406= Single submitter
  • p.Tyr136= Single submitter developmental and epileptic encephalopathy, 8
  • p.Tyr177= Single submitter developmental and epileptic encephalopathy, 8
  • p.Tyr339= Single submitter developmental and epileptic encephalopathy, 8
  • p.Tyr369= Single submitter developmental and epileptic encephalopathy, 8
  • p.Val489Leu Single submitter developmental and epileptic encephalopathy, 8
  • p.Val73= Single submitter developmental and epileptic encephalopathy, 8
  • p.Val79= Single submitter developmental and epileptic encephalopathy, 8

Uncertain significance 214