EBP — 219 ClinVar variants
All ClinVar germline EBP variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 77 flagged for review →
41 Pathogenic · 6 Pathogenic/Likely pathogenic · 28 Likely pathogenic · 15 Conflicting · 13 Benign · 9 Benign/Likely benign · 42 Likely benign · 65 Uncertain significance
Full EBP gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 77
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 2
ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.
-
EBP p.Arg147Cys
Pathogenic/Likely pathogenic
Multiple submitters
MEND syndrome
-
EBP p.Arg62Trp
Pathogenic/Likely pathogenic
Multiple submitters
X-linked chondrodysplasia punctata 2
Predictors agree, ClinVar conflicts 5
ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.
-
EBP p.Asn20Thr
Conflicting
Single submitter
intellectual disability
-
EBP p.Gln143Arg
Conflicting
Single submitter
Inborn genetic diseases
-
EBP p.His76Asp
Conflicting
Single submitter
X-linked chondrodysplasia punctata 2
-
EBP p.His9Gln
Conflicting
Single submitter
X-linked chondrodysplasia punctata 2
- EBP p.Pro13Arg Conflicting Single submitter
Predictors lean, ClinVar uncertain 33
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
-
EBP p.Ala95Thr
Uncertain significance
Multiple submitters
MEND syndrome
-
EBP p.Arg62Gln
Uncertain significance
Multiple submitters
X-linked chondrodysplasia punctata 2
-
EBP p.Asn116Ser
Uncertain significance
Multiple submitters
X-linked chondrodysplasia punctata 2
-
EBP p.Trp186Arg
Uncertain significance
Multiple submitters
MEND syndrome
- EBP p.Ala139Pro Uncertain significance Single submitter
- EBP p.Ala214Val Uncertain significance Single submitter
-
EBP p.Arg142His
Uncertain significance
Single submitter
Inborn genetic diseases
-
EBP p.Arg17Thr
Uncertain significance
Single submitter
X-linked chondrodysplasia punctata 2
- EBP p.Arg26His Uncertain significance Single submitter
-
EBP p.Asn4Ile
Uncertain significance
Single submitter
Inborn genetic diseases
- EBP p.Asn4Ser Uncertain significance Single submitter
-
EBP p.Cys127Ser
Uncertain significance
Single submitter
Inborn genetic diseases
-
EBP p.Glu88Lys
Uncertain significance
Single submitter
Inborn genetic diseases
- EBP p.Gly40Arg Uncertain significance Single submitter
- EBP p.Gly73Arg Uncertain significance Single submitter
- EBP p.His9Asp Uncertain significance Single submitter
- EBP p.Ile159Leu Uncertain significance Single submitter
- EBP p.Ile31Leu Uncertain significance Single submitter
- EBP p.Leu128Arg Uncertain significance Single submitter
- EBP p.Leu146His Uncertain significance Single submitter
- EBP p.Leu218Val Uncertain significance Single submitter
-
EBP p.Lys209Thr
Uncertain significance
Single submitter
X-linked chondrodysplasia punctata 2
- EBP p.Phe189Leu Uncertain significance Single submitter
-
EBP p.Phe69Cys
Uncertain significance
Single submitter
X-linked chondrodysplasia punctata 2
- EBP p.Ser109Ile Uncertain significance Single submitter
- EBP p.Ser227Asn Uncertain significance Single submitter
- EBP p.Ser65Phe Uncertain significance Single submitter
- EBP p.Ser98Pro Uncertain significance Single submitter
- EBP p.Thr39Ile Uncertain significance Single submitter
- EBP p.Val163Leu Uncertain significance Single submitter
- EBP p.Val202Ile Uncertain significance Single submitter
-
EBP p.Val202Leu
Uncertain significance
Single submitter
X-linked chondrodysplasia punctata 2
- EBP p.Val44Gly Uncertain significance Single submitter
Predictors split 37
The independent predictors disagree with each other — read with care.
- EBP p.Ala54Val Uncertain significance Multiple submitters
-
EBP p.Arg147His
Pathogenic
Multiple submitters
MEND syndrome
-
EBP p.Arg171His
Benign/Likely benign
Multiple submitters
Inborn genetic diseases
-
EBP p.Arg52Cys
Benign/Likely benign
Multiple submitters
Inborn genetic diseases
- EBP p.Gln94His Benign/Likely benign Multiple submitters
-
EBP p.Gly173Arg
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
EBP p.Gly177Arg
Uncertain significance
Multiple submitters
Inborn genetic diseases
- EBP p.Val208Met Uncertain significance Multiple submitters
- EBP p.Ala139Thr Uncertain significance Single submitter
-
EBP p.Arg142Cys
Conflicting
Single submitter
MEND syndrome
-
EBP p.Arg171Cys
Conflicting
Single submitter
MEND syndrome
- EBP p.Arg26Cys Uncertain significance Single submitter
- EBP p.Arg52Gly Uncertain significance Single submitter
-
EBP p.Arg63Gln
Conflicting
Single submitter
X-linked chondrodysplasia punctata 2
- EBP p.Asp219Asn Uncertain significance Single submitter
- EBP p.Asp93Gly Uncertain significance Single submitter
-
EBP p.Gly114Val
Conflicting
Single submitter
Inborn genetic diseases
- EBP p.Gly157Ser Pathogenic Single submitter
- EBP p.Gly180Arg Uncertain significance Single submitter
-
EBP p.Gly59Arg
Uncertain significance
Single submitter
X-linked chondrodysplasia punctata 2
- EBP p.Gly81Val Uncertain significance Single submitter
-
EBP p.His176Arg
Conflicting
Single submitter
X-linked chondrodysplasia punctata 2
-
EBP p.His9Tyr
Uncertain significance
Single submitter
X-linked chondrodysplasia punctata 2
- EBP p.Leu100Ile Uncertain significance Single submitter
- EBP p.Leu85Ile Uncertain significance Single submitter
-
EBP p.Met121Leu
Uncertain significance
Single submitter
X-linked chondrodysplasia punctata 2
- EBP p.Met121Val Uncertain significance Single submitter
- EBP p.Pro182Arg Uncertain significance Single submitter
-
EBP p.Ser65Pro
Uncertain significance
Single submitter
X-linked chondrodysplasia punctata 2
- EBP p.Val163Ala Uncertain significance Single submitter
-
EBP p.Val22Ile
Uncertain significance
Single submitter
Inborn genetic diseases
- EBP p.Val41Ile Uncertain significance Single submitter
- EBP p.Val44Met Benign Single submitter
-
EBP p.Val84Ile
Conflicting
Single submitter
X-linked chondrodysplasia punctata 2
- EBP p.Val84Leu Uncertain significance Single submitter
-
EBP p.Leu18Pro
Pathogenic
No assertion criteria
MEND syndrome
- EBP p.Phe140Cys Uncertain significance No assertion criteria
All EBP variants
Pathogenic 41
- p.Arg110Ter Multiple submitters X-linked chondrodysplasia punctata 2
- p.Arg147His Multiple submitters MEND syndrome ⚠
- p.Trp186Ter Multiple submitters X-linked chondrodysplasia punctata 2
- p.Tyr87Ter Multiple submitters X-linked chondrodysplasia punctata 2
- c.301+1G>A Single submitter
- c.301+2T>A Single submitter X-linked chondrodysplasia punctata 2
- c.338+1G>C Single submitter X-linked chondrodysplasia punctata 2
- p.Arg142fs Single submitter X-linked chondrodysplasia punctata 2
- p.Arg63Ter Single submitter X-linked chondrodysplasia punctata 2
- p.Asp162fs Single submitter
- p.Cys127Ter Single submitter
- p.Glu169fs Single submitter X-linked chondrodysplasia punctata 2
- p.Gly157Ser Single submitter ⚠
- p.His76fs Single submitter X-linked chondrodysplasia punctata 2
- p.Leu85fs Single submitter
- p.Lys102Ter Single submitter X-linked chondrodysplasia punctata 2
- p.Phe36fs Single submitter
- p.Ser155fs Single submitter X-linked chondrodysplasia punctata 2
- p.Ser50Ter Single submitter
- p.Ser98fs Single submitter X-linked chondrodysplasia punctata 2
- p.Trp129Ter Single submitter
- p.Trp12Ter Single submitter
- p.Trp135Ter Single submitter
- p.Trp47Cys Single submitter X-linked chondrodysplasia punctata 2
- p.Trp47Ter Single submitter
- p.Trp61Ter Single submitter X-linked chondrodysplasia punctata 2
- p.Trp68Ter Single submitter X-linked chondrodysplasia punctata 2
- p.Trp82Ter Single submitter
- p.Tyr104His Single submitter X-linked chondrodysplasia punctata 2
- p.Tyr104Ter Single submitter X-linked chondrodysplasia punctata 2
- p.Tyr111Ter Single submitter X-linked chondrodysplasia punctata 2
- p.Tyr160Ter Single submitter X-linked chondrodysplasia punctata 2
- p.Val43fs Single submitter
- c.338+1G>T No assertion criteria X-linked chondrodysplasia punctata 2
- p.Gln175Ter No assertion criteria X-linked chondrodysplasia punctata 2
- p.Leu18Pro No assertion criteria MEND syndrome ⚠
- p.Pro131fs No assertion criteria X-linked chondrodysplasia punctata 2
- p.Trp196Ter No assertion criteria X-linked chondrodysplasia punctata 2
- p.Trp29Ter No assertion criteria X-linked chondrodysplasia punctata 2
- p.Trp47Arg No assertion criteria MEND syndrome
- p.Tyr11Ter No assertion criteria CHONDRODYSPLASIA PUNCTATA 2, X-LINKED DOMINANT, ATYPICAL
Pathogenic/Likely pathogenic 6
- p.Arg110Gln Multiple submitters X-linked chondrodysplasia punctata 2
- p.Arg147Cys Multiple submitters MEND syndrome ⚠
- p.Arg62Trp Multiple submitters X-linked chondrodysplasia punctata 2 ⚠
- p.Glu80Lys Multiple submitters connective tissue disorder
- p.Ser98Phe Multiple submitters
- p.Trp68Cys Multiple submitters X-linked chondrodysplasia punctata 2
Likely pathogenic 28
- c.301+2_301+3del Multiple submitters EBP-related disorder
- c.302-1G>A Single submitter
- c.469+3A>C Single submitter
- c.470-2A>C Single submitter X-linked chondrodysplasia punctata 2
- p.Ala105Asp Single submitter X-linked chondrodysplasia punctata 2
- p.Ala54fs Single submitter X-linked chondrodysplasia punctata 2
- p.Asp93Val Single submitter X-linked chondrodysplasia punctata 2
- p.Cys67dup Single submitter X-linked chondrodysplasia punctata 2
- p.Cys72Arg Single submitter X-linked chondrodysplasia punctata 2
- p.Cys72Tyr Single submitter
- p.Gly107Glu Single submitter X-linked chondrodysplasia punctata 2
- p.Gly161Arg Single submitter X-linked chondrodysplasia punctata 2
- p.Gly73Glu Single submitter X-linked chondrodysplasia punctata 2
- p.His76Tyr Single submitter
- p.Ile124_Cys127delinsGly Single submitter X-linked chondrodysplasia punctata 2
- p.Ile75Asn Single submitter MEND syndrome
- p.Leu100Pro Single submitter X-linked chondrodysplasia punctata 2
- p.Leu128Pro Single submitter
- p.Leu211Arg Single submitter X-linked chondrodysplasia punctata 2
- p.Phe96del Single submitter
- p.Trp101Cys Single submitter X-linked chondrodysplasia punctata 2
- p.Trp129Arg Single submitter
- p.Trp196Cys Single submitter
- p.Tyr104Cys Single submitter X-linked chondrodysplasia punctata 2
- p.Tyr111Asn Single submitter
- p.Tyr111His Single submitter X-linked chondrodysplasia punctata 2
- p.Val156fs Single submitter
- p.Val190fs Single submitter X-linked chondrodysplasia punctata 2
Conflicting classifications of pathogenicity 15
- c.301+3G>C Single submitter Inborn genetic diseases
- p.Arg142Cys Single submitter MEND syndrome ⚠
- p.Arg171Cys Single submitter MEND syndrome ⚠
- p.Arg63Gln Single submitter X-linked chondrodysplasia punctata 2 ⚠
- p.Asn20Thr Single submitter intellectual disability ⚠
- p.Gln143Arg Single submitter Inborn genetic diseases ⚠
- p.Gly114Val Single submitter Inborn genetic diseases ⚠
- p.Gly73= Single submitter
- p.His176Arg Single submitter X-linked chondrodysplasia punctata 2 ⚠
- p.His76Asp Single submitter X-linked chondrodysplasia punctata 2 ⚠
- p.His9Gln Single submitter X-linked chondrodysplasia punctata 2 ⚠
- p.Ile138= Single submitter X-linked chondrodysplasia punctata 2
- p.Leu128= Single submitter X-linked chondrodysplasia punctata 2
- p.Pro13Arg Single submitter ⚠
- p.Val84Ile Single submitter X-linked chondrodysplasia punctata 2 ⚠
Benign 13
- c.301+154C>T Multiple submitters
- c.469+9A>G Single submitter
- c.470-16del Single submitter
- c.470-54C>T Single submitter
- c.-43del Single submitter
- c.-43dup Single submitter
- c.-44_-43dup Single submitter
- c.-73-129dup Single submitter
- p.Asn20Ser Single submitter
- p.Leu58= Single submitter
- p.Phe185= Single submitter
- p.Val22= Single submitter
- p.Val44Met Single submitter ⚠
Benign/Likely benign 9
- c.-74+3G>C Multiple submitters connective tissue disorder
- p.Ala5Thr Multiple submitters Inborn genetic diseases
- p.Arg171= Multiple submitters
- p.Arg171His Multiple submitters Inborn genetic diseases ⚠
- p.Arg52Cys Multiple submitters Inborn genetic diseases ⚠
- p.Gln94His Multiple submitters ⚠
- p.Ile149Val Multiple submitters
- p.Leu97= Multiple submitters
- p.Thr217Met Multiple submitters Inborn genetic diseases
Likely benign 42
- c.469+222A>G Multiple submitters
- p.Tyr111= Multiple submitters
- c.301+19C>A Single submitter
- c.301+5G>C Single submitter
- c.302-11_302-9del Single submitter
- c.302-12T>C Single submitter
- c.302-16C>T Single submitter
- c.302-67C>A Single submitter
- c.338+10del Single submitter
- c.338+8T>G Single submitter
- c.339-16A>G Single submitter
- c.469+12G>A Single submitter
- c.-19G>A Single submitter
- c.-42A>T Single submitter
- c.-47_-43dup Single submitter
- c.-49T>C Single submitter
- c.-73-129del Single submitter
- c.-73-146G>A Single submitter
- p.Ala222= Single submitter
- p.Ala5= Single submitter
- p.Ala54= Single submitter
- p.Asn116= Single submitter
- p.Asp172= Single submitter
- p.Gln14Arg Single submitter Inborn genetic diseases
- p.Glu178= Single submitter
- p.Glu88Gln Single submitter Inborn genetic diseases
- p.Gly180Ser Single submitter
- p.His176= Single submitter
- p.His9= Single submitter
- p.Ile112= Single submitter
- p.Leu113Met Single submitter Developmental disorder
- p.Leu132= Single submitter
- p.Leu179= Single submitter
- p.Leu211= Single submitter
- p.Leu48= Single submitter
- p.Lys221= Single submitter
- p.Pro145= Single submitter
- p.Thr217= Single submitter Inborn genetic diseases
- p.Thr45= Single submitter
- p.Tyr188= Single submitter
- p.Tyr87= Single submitter
- p.Val43= Single submitter
Uncertain significance 65
- p.Ala54Val Multiple submitters ⚠
- p.Ala95Thr Multiple submitters MEND syndrome ⚠
- p.Arg62Gln Multiple submitters X-linked chondrodysplasia punctata 2 ⚠
- p.Asn116Ser Multiple submitters X-linked chondrodysplasia punctata 2 ⚠
- p.Gly173Arg Multiple submitters Inborn genetic diseases ⚠
- p.Gly177Arg Multiple submitters Inborn genetic diseases ⚠
- p.Lys229del Multiple submitters X-linked chondrodysplasia punctata 2
- p.Trp186Arg Multiple submitters MEND syndrome ⚠
- p.Val208Met Multiple submitters ⚠
- c.470-3C>G Single submitter X-linked chondrodysplasia punctata 2
- c.470-3C>T Single submitter
- p.Ala139Pro Single submitter ⚠
- p.Ala139Thr Single submitter ⚠
- p.Ala214Val Single submitter ⚠
- p.Ala225fs Single submitter
- p.Arg142His Single submitter Inborn genetic diseases ⚠
- p.Arg17Thr Single submitter X-linked chondrodysplasia punctata 2 ⚠
- p.Arg26Cys Single submitter ⚠
- p.Arg26His Single submitter ⚠
- p.Arg52Gly Single submitter ⚠
- p.Arg63del Single submitter
- p.Asn4Ile Single submitter Inborn genetic diseases ⚠
- p.Asn4Ser Single submitter ⚠
- p.Asp219Asn Single submitter ⚠
- p.Asp93Gly Single submitter ⚠
- p.Cys127Ser Single submitter Inborn genetic diseases ⚠
- p.Glu88Lys Single submitter Inborn genetic diseases ⚠
- p.Gly161= Single submitter connective tissue disorder
- p.Gly180Arg Single submitter ⚠
- p.Gly40Arg Single submitter ⚠
- p.Gly59Arg Single submitter X-linked chondrodysplasia punctata 2 ⚠
- p.Gly73Arg Single submitter ⚠
- p.Gly81Val Single submitter ⚠
- p.His9Asp Single submitter ⚠
- p.His9Tyr Single submitter X-linked chondrodysplasia punctata 2 ⚠
- p.Ile159Leu Single submitter ⚠
- p.Ile31Leu Single submitter ⚠
- p.Leu100Ile Single submitter ⚠
- p.Leu128Arg Single submitter ⚠
- p.Leu146His Single submitter ⚠
- p.Leu164= Single submitter
- p.Leu218Val Single submitter ⚠
- p.Leu85Ile Single submitter ⚠
- p.Lys209Thr Single submitter X-linked chondrodysplasia punctata 2 ⚠
- p.Met121Leu Single submitter X-linked chondrodysplasia punctata 2 ⚠
- p.Met121Val Single submitter ⚠
- p.Phe189Leu Single submitter ⚠
- p.Phe69Cys Single submitter X-linked chondrodysplasia punctata 2 ⚠
- p.Pro182Arg Single submitter ⚠
- p.Ser109Ile Single submitter ⚠
- p.Ser227Asn Single submitter ⚠
- p.Ser37del Single submitter
- p.Ser65Phe Single submitter ⚠
- p.Ser65Pro Single submitter X-linked chondrodysplasia punctata 2 ⚠
- p.Ser98Pro Single submitter ⚠
- p.Thr39Ile Single submitter ⚠
- p.Val163Ala Single submitter ⚠
- p.Val163Leu Single submitter ⚠
- p.Val202Ile Single submitter ⚠
- p.Val202Leu Single submitter X-linked chondrodysplasia punctata 2 ⚠
- p.Val22Ile Single submitter Inborn genetic diseases ⚠
- p.Val41Ile Single submitter ⚠
- p.Val44Gly Single submitter ⚠
- p.Val84Leu Single submitter ⚠
- p.Phe140Cys No assertion criteria ⚠