NR2F1 — 484 ClinVar variants

All ClinVar germline NR2F1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 157 flagged for review →

54 Pathogenic · 10 Pathogenic/Likely pathogenic · 72 Likely pathogenic · 26 Conflicting · 6 Benign · 9 Benign/Likely benign · 140 Likely benign · 167 Uncertain significance

Full NR2F1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 157

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.

Predictors agree, ClinVar conflicts 16

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

Predicted LoF vs a conflicting call 1

ClinVar submitters conflict, and it's a predicted loss-of-function change in a gene where LoF causes disease — flagged for review, not resolved (verify NMD-escape for C-terminal truncations). Non-missense.

Predictors lean, ClinVar uncertain 115

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

Predictors split 24

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

All NR2F1 variants

Pathogenic 54

  • p.Met1Thr Multiple submitters Inborn genetic diseases
  • p.Phe110del Multiple submitters Inborn genetic diseases
  • c.991+2T>A Single submitter
  • p.Arg115Pro Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Arg135Cys Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Arg135Pro Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Arg235Leu Single submitter Neurodevelopmental delay
  • p.Arg373Ter Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Asn117fs Single submitter
  • p.Cys103Arg Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Cys122Phe Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Cys183fs Single submitter Inborn genetic diseases
  • p.Gln132Ter Single submitter
  • p.Gln139His Single submitter
  • p.Gln139Ter Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Gln303Ter Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Gln359Ter Single submitter Inborn genetic diseases
  • p.Gln40fs Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Gln41Ter Single submitter
  • p.Gln57Ter Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Gln81fs Single submitter
  • p.Glu346del Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Glu354_Tyr355insTer Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Glu39Ter Single submitter
  • p.Gly18fs Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Gly32fs Single submitter Inborn genetic diseases
  • p.Gly99fs Single submitter
  • p.His97Pro Single submitter
  • p.Leu118Ter Single submitter
  • p.Leu276Ter Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Leu282fs Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Lys144fs Single submitter
  • p.Lys145fs Single submitter
  • p.Lys148Ter Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Lys323fs Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Lys92Ter Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Met1Leu Single submitter
  • p.Met1Lys Single submitter
  • p.Met1Val Single submitter
  • p.Met406Thr Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Ser113Arg Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Thr200fs Single submitter
  • p.Thr255fs Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Thr63fs Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Tyr120Ter Single submitter
  • p.Tyr203Ter Single submitter
  • p.Tyr360fs Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Val88Met Single submitter
  • p.Cys138Tyr No assertion criteria Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Gln28Ter No assertion criteria Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Lys96Glu No assertion criteria Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Met151Lys No assertion criteria Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Met1Ile No assertion criteria Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Tyr171Ter No assertion criteria Bosch-Boonstra-Schaaf optic atrophy syndrome

Pathogenic/Likely pathogenic 10

  • p.Met151Ile Multiple submitters Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Arg142Cys Multiple submitters NR2F1-related disorder
  • p.Arg142His Multiple submitters Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Cys106Tyr Multiple submitters Inborn genetic diseases
  • p.Cys146Tyr Multiple submitters Inborn genetic diseases
  • p.Cys86Arg Multiple submitters Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Gly105Ser Multiple submitters Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Lys107Arg Multiple submitters
  • p.Lys107Glu Multiple submitters NR2F1-related disorder
  • p.Ser94Arg Multiple submitters Bosch-Boonstra-Schaaf optic atrophy syndrome

Likely pathogenic 72

  • c.463+1G>A Multiple submitters NR2F1-related disorder
  • p.Arg366Cys Multiple submitters Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Cys122Tyr Multiple submitters Inborn genetic diseases
  • p.Cys128Arg Multiple submitters Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Leu252Pro Multiple submitters Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Leu402fs Multiple submitters Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Met151Thr Multiple submitters Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Phe109Leu Multiple submitters Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Ala223fs Single submitter
  • p.Ala224fs Single submitter
  • p.Arg112Lys Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Arg112Thr Single submitter
  • p.Arg135His Single submitter Inborn genetic diseases
  • p.Arg135Leu Single submitter
  • p.Arg142Gly Single submitter
  • p.Arg142Leu Single submitter Inborn genetic diseases
  • p.Arg253Leu Single submitter
  • p.Arg31fs Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Asn362fs Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Cys122Arg Single submitter Seizure
  • p.Cys122Ser Single submitter
  • p.Cys128Tyr Single submitter NR2F1-related disorder
  • p.Cys141Gly Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Cys321Tyr Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Cys350Ter Single submitter
  • p.Cys89Gly Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Gln244Ter Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Gln345Ter Single submitter NR2F1-related disorder
  • p.Gln387Ter Single submitter
  • p.Gln82Ter Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Glu104Ala Single submitter Paediatric disorders
  • p.Glu104Gln Single submitter
  • p.Glu104Val Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Glu318Gly Single submitter
  • p.Glu318Ter Single submitter
  • p.Gly105Ala Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Gly105Val Single submitter NR2F1-related disorder
  • p.Gly395Ala Single submitter autism spectrum disorder
  • p.Gly47fs Single submitter NR2F1-related disorder
  • p.Gly65fs Single submitter
  • p.His134Pro Single submitter NR2F1-related disorder
  • p.His97Tyr Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Leu118fs Single submitter
  • p.Leu352fs Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Leu372Pro Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Lys111Glu Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Lys70fs Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Met151Ile Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Phe109Cys Single submitter NR2F1-related disorder
  • p.Phe109fs Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Phe110Leu Single submitter
  • p.Phe228dup Single submitter Inborn genetic diseases
  • p.Phe295fs Single submitter
  • p.Phe390del Single submitter
  • p.Phe390Ser Single submitter NR2F1-related disorder
  • p.Pro166Leu Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome ⚠
  • p.Ser108Asn Single submitter Neurodevelopmental delay
  • p.Ser108Ile Single submitter
  • p.Ser93Ter Single submitter
  • p.Thr329fs Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Tyr319Ter Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Tyr98Cys Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Tyr98His Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Val114Leu Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Val156Phe Single submitter Paediatric disorders
  • p.Val384fs Single submitter
  • p.Val394Gly Single submitter Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Gln349fs No assertion criteria optic atrophy
  • p.Gly95Asp No assertion criteria NR2F1-related disorder
  • p.His97Asp No assertion criteria Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Leu371Pro No assertion criteria Bosch-Boonstra-Schaaf optic atrophy syndrome
  • p.Ser93Leu No assertion criteria Seizure

Conflicting classifications of pathogenicity 26

Benign 6

Benign/Likely benign 9

Likely benign 140

Uncertain significance 167