EFNB1 — 193 ClinVar variants
All ClinVar germline EFNB1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 86 flagged for review →
41 Pathogenic · 4 Pathogenic/Likely pathogenic · 20 Likely pathogenic · 5 Conflicting · 8 Benign · 1 Benign/Likely benign · 28 Likely benign · 86 Uncertain significance
Full EFNB1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 86
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.
-
EFNB1 p.Arg109Gly
Conflicting
Single submitter
Inborn genetic diseases
-
EFNB1 p.Arg156Cys
Conflicting
Single submitter
craniofrontonasal syndrome
-
EFNB1 p.Gln115Arg
Conflicting
Single submitter
craniofrontonasal syndrome
- EFNB1 p.Met122Thr Conflicting Single submitter
Predictors lean, ClinVar uncertain 51
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
-
EFNB1 p.Arg180Ser
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
EFNB1 p.Asp206His
Uncertain significance
Multiple submitters
Inborn genetic diseases
- EFNB1 p.Pro34Ala Uncertain significance Multiple submitters
-
EFNB1 p.Thr294Ala
Uncertain significance
Multiple submitters
Inborn genetic diseases
- EFNB1 p.Ala279Thr Uncertain significance Single submitter
-
EFNB1 p.Ala340Val
Uncertain significance
Single submitter
Inborn genetic diseases
- EFNB1 p.Arg154Pro Uncertain significance Single submitter
- EFNB1 p.Arg156His Uncertain significance Single submitter
-
EFNB1 p.Arg199Gln
Uncertain significance
Single submitter
Inborn genetic diseases
- EFNB1 p.Arg268Trp Uncertain significance Single submitter
-
EFNB1 p.Arg270His
Uncertain significance
Single submitter
Inborn genetic diseases
- EFNB1 p.Arg307Gln Uncertain significance Single submitter
-
EFNB1 p.Arg71Gln
Uncertain significance
Single submitter
Inborn genetic diseases
- EFNB1 p.Asp61Val Uncertain significance Single submitter
- EFNB1 p.Cys153Tyr Uncertain significance Single submitter
- EFNB1 p.Cys89Ser Uncertain significance Single submitter
-
EFNB1 p.Gln332Arg
Uncertain significance
Single submitter
Inborn genetic diseases
- EFNB1 p.Glu310Asp Uncertain significance Single submitter
- EFNB1 p.Gly144Arg Uncertain significance Single submitter
- EFNB1 p.Gly144Glu Uncertain significance Single submitter
-
EFNB1 p.Gly290Glu
Uncertain significance
Single submitter
Inborn genetic diseases
-
EFNB1 p.Gly291Ser
Uncertain significance
Single submitter
Inborn genetic diseases
- EFNB1 p.Gly49Arg Uncertain significance Single submitter
- EFNB1 p.His130Arg Uncertain significance Single submitter
- EFNB1 p.Ile112Val Uncertain significance Single submitter
-
EFNB1 p.Ile250Ser
Uncertain significance
Single submitter
craniofrontonasal syndrome
-
EFNB1 p.Ile304Val
Uncertain significance
Single submitter
Inborn genetic diseases
- EFNB1 p.Ile342Val Uncertain significance Single submitter
-
EFNB1 p.Leu145Pro
Uncertain significance
Single submitter
craniofrontonasal syndrome
- EFNB1 p.Lys113Arg Uncertain significance Single submitter
-
EFNB1 p.Lys183Asn
Uncertain significance
Single submitter
Inborn genetic diseases
- EFNB1 p.Lys30Arg Uncertain significance Single submitter
-
EFNB1 p.Lys319Arg
Uncertain significance
Single submitter
craniofrontonasal syndrome
- EFNB1 p.Lys59Gln Uncertain significance Single submitter
- EFNB1 p.Lys77Glu Uncertain significance Single submitter
-
EFNB1 p.Phe234Leu
Uncertain significance
Single submitter
Inborn genetic diseases
-
EFNB1 p.Pro119Thr
Uncertain significance
Single submitter
Inborn genetic diseases
-
EFNB1 p.Pro4Ser
Uncertain significance
Single submitter
Inborn genetic diseases
- EFNB1 p.Ser118Gly Uncertain significance Single submitter
-
EFNB1 p.Ser141Thr
Uncertain significance
Single submitter
Inborn genetic diseases
- EFNB1 p.Thr111Ala Uncertain significance Single submitter
- EFNB1 p.Thr137Ile Uncertain significance Single submitter
- EFNB1 p.Thr297Ile Uncertain significance Single submitter
-
EFNB1 p.Thr91Pro
Uncertain significance
Single submitter
craniofrontonasal syndrome
- EFNB1 p.Tyr121Cys Uncertain significance Single submitter
- EFNB1 p.Tyr132Cys Uncertain significance Single submitter
- EFNB1 p.Tyr75Cys Uncertain significance Single submitter
-
EFNB1 p.Val249Leu
Uncertain significance
Single submitter
Inborn genetic diseases
- EFNB1 p.Val331Phe Uncertain significance Single submitter
- EFNB1 p.Val51Gly Uncertain significance Single submitter
-
EFNB1 p.Lys59Glu
Uncertain significance
No assertion criteria
EFNB1-related disorder
Predictors split 31
The independent predictors disagree with each other — read with care.
-
EFNB1 p.Ala242Val
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
EFNB1 p.Arg199Trp
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
EFNB1 p.His272Tyr
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
EFNB1 p.Leu24Phe
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
EFNB1 p.Ala195Asp
Uncertain significance
Single submitter
Inborn genetic diseases
-
EFNB1 p.Ala243Thr
Uncertain significance
Single submitter
Inborn genetic diseases
- EFNB1 p.Ala243Val Uncertain significance Single submitter
- EFNB1 p.Ala277Val Likely benign Single submitter
-
EFNB1 p.Arg156Gly
Uncertain significance
Single submitter
Inborn genetic diseases
-
EFNB1 p.Arg3Trp
Uncertain significance
Single submitter
Inborn genetic diseases
-
EFNB1 p.Arg66Gln
Uncertain significance
Single submitter
Inborn genetic diseases
-
EFNB1 p.Asp131Asn
Uncertain significance
Single submitter
Inborn genetic diseases
- EFNB1 p.Asp229Tyr Uncertain significance Single submitter
-
EFNB1 p.Gly200Arg
Uncertain significance
Single submitter
Inborn genetic diseases
-
EFNB1 p.Gly232Cys
Uncertain significance
Single submitter
Inborn genetic diseases
- EFNB1 p.Gly245Ser Uncertain significance Single submitter
- EFNB1 p.Gly290Val Uncertain significance Single submitter
-
EFNB1 p.Ile250Met
Uncertain significance
Single submitter
Inborn genetic diseases
-
EFNB1 p.Ile254Thr
Uncertain significance
Single submitter
Inborn genetic diseases
-
EFNB1 p.Phe241Leu
Uncertain significance
Single submitter
Inborn genetic diseases
-
EFNB1 p.Pro173Ser
Uncertain significance
Single submitter
Inborn genetic diseases
-
EFNB1 p.Pro83Leu
Uncertain significance
Single submitter
Inborn genetic diseases
-
EFNB1 p.Ser198Ile
Uncertain significance
Single submitter
Inborn genetic diseases
- EFNB1 p.Ser201Tyr Uncertain significance Single submitter
- EFNB1 p.Ser287Asn Uncertain significance Single submitter
- EFNB1 p.Thr135Asn Likely pathogenic Single submitter
- EFNB1 p.Tyr53Phe Uncertain significance Single submitter
-
EFNB1 p.Val164Ile
Uncertain significance
Single submitter
EFNB1-related disorder
- EFNB1 p.Val249Ile Uncertain significance Single submitter
- EFNB1 p.Val331Ile Uncertain significance Single submitter
-
EFNB1 p.Arg109His
Uncertain significance
No assertion criteria
EFNB1-related disorder
All EFNB1 variants
Pathogenic 41
- p.Arg66Ter Multiple submitters craniofrontonasal syndrome
- p.Gln85Ter Multiple submitters craniofrontonasal syndrome
- p.Gly10= Multiple submitters
- p.Gly151Ser Multiple submitters craniofrontonasal syndrome
- p.Met1Val Multiple submitters craniofrontonasal syndrome
- c.128+2T>A Single submitter craniofrontonasal syndrome
- c.129-1G>T Single submitter
- c.406+2T>C Single submitter craniofrontonasal syndrome
- p.Ala29fs Single submitter
- p.Ala87_Cys89del Single submitter
- p.Arg109fs Single submitter
- p.Arg66fs Single submitter craniofrontonasal syndrome
- p.Asn147fs Single submitter
- p.Asn187fs Single submitter craniofrontonasal syndrome
- p.Cys64Arg Single submitter Inborn genetic diseases
- p.Cys64Ter Single submitter craniofrontonasal syndrome
- p.Gln214Ter Single submitter
- p.Glu74Ter Single submitter
- p.Gly150fs Single submitter
- p.Ile52fs Single submitter
- p.Leu50Ter Single submitter craniofrontonasal syndrome
- p.Lys113Asn Single submitter
- p.Lys48fs Single submitter craniofrontonasal syndrome
- p.Lys48Ter Single submitter Inborn genetic diseases
- p.Met158Val Single submitter craniofrontonasal syndrome
- p.Pro54Arg Single submitter
- p.Ser205fs Single submitter
- p.Ser39fs Single submitter
- p.Thr111Ile Single submitter craniofrontonasal syndrome
- p.Thr135fs Single submitter
- p.Thr188fs Single submitter craniofrontonasal syndrome
- p.Trp19Ter Single submitter
- p.Trp37Ter Single submitter craniofrontonasal syndrome
- p.Tyr73Ter Single submitter
- p.Tyr79Ter Single submitter
- p.Val14fs Single submitter
- p.Val189fs Single submitter craniofrontonasal syndrome
- p.Gln166Ter No assertion criteria craniofrontonasal syndrome
- p.Gly151Val No assertion criteria craniofrontonasal syndrome
- p.Met158Ile No assertion criteria craniofrontonasal syndrome
- p.Trp37Gly No assertion criteria craniofrontonasal syndrome
Pathogenic/Likely pathogenic 4
- c.499+1G>A Multiple submitters craniofrontonasal syndrome
- p.Pro34fs Multiple submitters craniofrontonasal syndrome
- p.Pro54Leu Multiple submitters craniofrontonasal syndrome
- p.Trp12Ter Multiple submitters EFNB1-related disorder
Likely pathogenic 20
- c.128+1G>C Multiple submitters craniofrontonasal syndrome
- p.Gln175Ter Multiple submitters craniofrontonasal syndrome
- c.407-2A>G Single submitter
- c.499+2_499+7del Single submitter craniofrontonasal syndrome
- p.Arg109Cys Single submitter
- p.Arg154fs Single submitter craniofrontonasal syndrome
- p.Arg23fs Single submitter craniofrontonasal syndrome
- p.Asp204_Ser205insTer Single submitter
- p.Asp61Gly Single submitter craniofrontonasal syndrome
- p.Ile112fs Single submitter craniofrontonasal syndrome
- p.Met158Arg Single submitter craniofrontonasal syndrome
- p.Phe44Ser Single submitter craniofrontonasal syndrome
- p.Pro119Ala Single submitter
- p.Ser136Leu Single submitter craniofrontonasal syndrome
- p.Ser138Phe Single submitter craniofrontonasal syndrome
- p.Thr135Asn Single submitter ⚠
- p.Thr137Ala Single submitter
- p.Trp8Ter Single submitter craniofrontonasal syndrome
- p.Val212fs Single submitter craniofrontonasal syndrome
- p.Val51_Tyr53delinsGlyIlePhe Single submitter
Conflicting classifications of pathogenicity 5
- c.128+5G>A Single submitter craniofrontonasal syndrome
- p.Arg109Gly Single submitter Inborn genetic diseases ⚠
- p.Arg156Cys Single submitter craniofrontonasal syndrome ⚠
- p.Gln115Arg Single submitter craniofrontonasal syndrome ⚠
- p.Met122Thr Single submitter ⚠
Benign 8
- c.*6C>T Multiple submitters craniofrontonasal syndrome
- p.Ala170Val Multiple submitters
- p.Val189Ala Multiple submitters craniofrontonasal syndrome
- c.128+220C>G Single submitter
- c.128+235C>G Single submitter
- c.-385G>T Single submitter
- p.Glu143= Single submitter
- p.Thr297= Single submitter
Benign/Likely benign 1
- p.Leu253= Multiple submitters
Likely benign 28
- p.Ser281= Multiple submitters
- p.Val189Ile Multiple submitters Inborn genetic diseases
- c.128+16C>T Single submitter
- c.128+9C>T Single submitter
- c.129-299C>T Single submitter
- c.-279C>G Single submitter
- c.-588C>A Single submitter
- c.-695C>T Single submitter
- p.Ala246= Single submitter
- p.Ala277Val Single submitter ⚠
- p.Ala295= Single submitter
- p.Ala88Thr Single submitter Inborn genetic diseases
- p.Arg154His Single submitter
- p.Arg199= Single submitter
- p.Cys64= Single submitter
- p.His272= Single submitter
- p.Ile256= Single submitter
- p.Leu24= Single submitter
- p.Leu282= Single submitter
- p.Lys264= Single submitter
- p.Pro339= Single submitter
- p.Thr135= Single submitter
- p.Tyr324= Single submitter
- p.Val244= Single submitter
- p.Val81= Single submitter
- c.-6G>A No assertion criteria EFNB1-related disorder
- p.Gln6= No assertion criteria EFNB1-related disorder
- p.Pro335= No assertion criteria EFNB1-related disorder
Uncertain significance 86
- p.Ala242Val Multiple submitters Inborn genetic diseases ⚠
- p.Arg180Ser Multiple submitters Inborn genetic diseases ⚠
- p.Arg199Trp Multiple submitters Inborn genetic diseases ⚠
- p.Asp206His Multiple submitters Inborn genetic diseases ⚠
- p.His272Tyr Multiple submitters Inborn genetic diseases ⚠
- p.Leu24Phe Multiple submitters Inborn genetic diseases ⚠
- p.Pro34Ala Multiple submitters ⚠
- p.Thr294Ala Multiple submitters Inborn genetic diseases ⚠
- c.406+4A>G Single submitter craniofrontonasal syndrome
- c.500-3T>C Single submitter
- c.-95T>C Single submitter craniofrontonasal syndrome
- p.Ala195Asp Single submitter Inborn genetic diseases ⚠
- p.Ala242fs Single submitter
- p.Ala243Thr Single submitter Inborn genetic diseases ⚠
- p.Ala243Val Single submitter ⚠
- p.Ala279Thr Single submitter ⚠
- p.Ala340Val Single submitter Inborn genetic diseases ⚠
- p.Ala88del Single submitter
- p.Arg154Pro Single submitter ⚠
- p.Arg156Gly Single submitter Inborn genetic diseases ⚠
- p.Arg156His Single submitter ⚠
- p.Arg199Gln Single submitter Inborn genetic diseases ⚠
- p.Arg268Trp Single submitter ⚠
- p.Arg270His Single submitter Inborn genetic diseases ⚠
- p.Arg307Gln Single submitter ⚠
- p.Arg3Trp Single submitter Inborn genetic diseases ⚠
- p.Arg66Gln Single submitter Inborn genetic diseases ⚠
- p.Arg71Gln Single submitter Inborn genetic diseases ⚠
- p.Asp131Asn Single submitter Inborn genetic diseases ⚠
- p.Asp229Tyr Single submitter ⚠
- p.Asp61Val Single submitter ⚠
- p.Cys153Tyr Single submitter ⚠
- p.Cys89Ser Single submitter ⚠
- p.Gln332Arg Single submitter Inborn genetic diseases ⚠
- p.Glu310Asp Single submitter ⚠
- p.Gly144Arg Single submitter ⚠
- p.Gly144Glu Single submitter ⚠
- p.Gly200Arg Single submitter Inborn genetic diseases ⚠
- p.Gly232Cys Single submitter Inborn genetic diseases ⚠
- p.Gly245Ser Single submitter ⚠
- p.Gly290Glu Single submitter Inborn genetic diseases ⚠
- p.Gly290Val Single submitter ⚠
- p.Gly291Ser Single submitter Inborn genetic diseases ⚠
- p.Gly49Arg Single submitter ⚠
- p.His130Arg Single submitter ⚠
- p.Ile112Val Single submitter ⚠
- p.Ile250Met Single submitter Inborn genetic diseases ⚠
- p.Ile250Ser Single submitter craniofrontonasal syndrome ⚠
- p.Ile254Thr Single submitter Inborn genetic diseases ⚠
- p.Ile304Val Single submitter Inborn genetic diseases ⚠
- p.Ile342Val Single submitter ⚠
- p.Leu145Pro Single submitter craniofrontonasal syndrome ⚠
- p.Leu252fs Single submitter
- p.Lys113Arg Single submitter ⚠
- p.Lys183Asn Single submitter Inborn genetic diseases ⚠
- p.Lys30Arg Single submitter ⚠
- p.Lys319Arg Single submitter craniofrontonasal syndrome ⚠
- p.Lys59Gln Single submitter ⚠
- p.Lys77Glu Single submitter ⚠
- p.Phe234Leu Single submitter Inborn genetic diseases ⚠
- p.Phe241Leu Single submitter Inborn genetic diseases ⚠
- p.Pro119Thr Single submitter Inborn genetic diseases ⚠
- p.Pro173Ser Single submitter Inborn genetic diseases ⚠
- p.Pro4Ser Single submitter Inborn genetic diseases ⚠
- p.Pro83Leu Single submitter Inborn genetic diseases ⚠
- p.Ser118Gly Single submitter ⚠
- p.Ser141Thr Single submitter Inborn genetic diseases ⚠
- p.Ser198Ile Single submitter Inborn genetic diseases ⚠
- p.Ser201Tyr Single submitter ⚠
- p.Ser287Asn Single submitter ⚠
- p.Thr111Ala Single submitter ⚠
- p.Thr137Ile Single submitter ⚠
- p.Thr297Ile Single submitter ⚠
- p.Thr91Pro Single submitter craniofrontonasal syndrome ⚠
- p.Tyr121Cys Single submitter ⚠
- p.Tyr132Cys Single submitter ⚠
- p.Tyr53Phe Single submitter ⚠
- p.Tyr75Cys Single submitter ⚠
- p.Val164Ile Single submitter EFNB1-related disorder ⚠
- p.Val249Ile Single submitter ⚠
- p.Val249Leu Single submitter Inborn genetic diseases ⚠
- p.Val331Ile Single submitter ⚠
- p.Val331Phe Single submitter ⚠
- p.Val51Gly Single submitter ⚠
- p.Arg109His No assertion criteria EFNB1-related disorder ⚠
- p.Lys59Glu No assertion criteria EFNB1-related disorder ⚠