CBX2 — 190 ClinVar variants
All ClinVar germline CBX2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 126 flagged for review →
2 Pathogenic · 2 Conflicting · 15 Benign · 3 Benign/Likely benign · 41 Likely benign · 127 Uncertain significance
Full CBX2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 126
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.
-
CBX2 p.Arg443Pro
Pathogenic
No assertion criteria
46,XY sex reversal 5
-
CBX2 p.Pro98Leu
Pathogenic
No assertion criteria
46,XY sex reversal 5
Predictors agree, ClinVar conflicts 2
ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.
Predictors lean, ClinVar uncertain 75
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- CBX2 p.Gly133Ser Uncertain significance Multiple submitters
- CBX2 p.Met260Val Uncertain significance Multiple submitters
- CBX2 p.Met404Leu Uncertain significance Multiple submitters
- CBX2 p.Pro327Leu Uncertain significance Multiple submitters
- CBX2 p.Thr348Ser Uncertain significance Multiple submitters
- CBX2 p.Ala152Ser Uncertain significance Single submitter
- CBX2 p.Ala206Thr Uncertain significance Single submitter
- CBX2 p.Ala275Val Uncertain significance Single submitter
- CBX2 p.Ala278Val Uncertain significance Single submitter
- CBX2 p.Ala311Val Uncertain significance Single submitter
- CBX2 p.Ala460Ser Uncertain significance Single submitter
- CBX2 p.Ala460Thr Uncertain significance Single submitter
- CBX2 p.Ala474Thr Uncertain significance Single submitter
- CBX2 p.Ala474Val Uncertain significance Single submitter
- CBX2 p.Arg190Gln Uncertain significance Single submitter
- CBX2 p.Arg190Gly Uncertain significance Single submitter
- CBX2 p.Arg247Gln Uncertain significance Single submitter
- CBX2 p.Arg262Gln Uncertain significance Single submitter
- CBX2 p.Arg373His Uncertain significance Single submitter
- CBX2 p.Arg79Trp Uncertain significance Single submitter
- CBX2 p.Asn282Lys Uncertain significance Single submitter
- CBX2 p.Asp99Asn Uncertain significance Single submitter
- CBX2 p.Cys430Gly Uncertain significance Single submitter
- CBX2 p.Glu172Gln Uncertain significance Single submitter
- CBX2 p.Glu28Gln Uncertain significance Single submitter
- CBX2 p.Glu350Gln Uncertain significance Single submitter
- CBX2 p.Glu457Gln Uncertain significance Single submitter
- CBX2 p.Gly133Val Uncertain significance Single submitter
- CBX2 p.Gly194Glu Uncertain significance Single submitter
-
CBX2 p.Gly210Asp
Uncertain significance
Single submitter
46,XY complete gonadal dysgenesis
- CBX2 p.Gly249Ser Uncertain significance Single submitter
- CBX2 p.Gly297Arg Uncertain significance Single submitter
- CBX2 p.Gly322Arg Uncertain significance Single submitter
- CBX2 p.Gly325Glu Uncertain significance Single submitter
- CBX2 p.Gly326Ala Uncertain significance Single submitter
- CBX2 p.Gly367Arg Uncertain significance Single submitter
- CBX2 p.Gly380Asp Uncertain significance Single submitter
- CBX2 p.Gly447Arg Uncertain significance Single submitter
- CBX2 p.Gly73Arg Uncertain significance Single submitter
- CBX2 p.His217Gln Uncertain significance Single submitter
- CBX2 p.His331Arg Uncertain significance Single submitter
- CBX2 p.His374Arg Uncertain significance Single submitter
- CBX2 p.Leu396His Uncertain significance Single submitter
- CBX2 p.Lys103Glu Uncertain significance Single submitter
- CBX2 p.Lys413Glu Uncertain significance Single submitter
- CBX2 p.Lys451Arg Uncertain significance Single submitter
- CBX2 p.Lys71Arg Uncertain significance Single submitter
- CBX2 p.Met241Val Uncertain significance Single submitter
- CBX2 p.Met301Ile Uncertain significance Single submitter
- CBX2 p.Met86Val Uncertain significance Single submitter
- CBX2 p.Phe527Leu Uncertain significance Single submitter
- CBX2 p.Pro141Ala Uncertain significance Single submitter
- CBX2 p.Pro154Ser Uncertain significance Single submitter
- CBX2 p.Pro159Ser Uncertain significance Single submitter
- CBX2 p.Pro196Leu Uncertain significance Single submitter
- CBX2 p.Pro303Leu Uncertain significance Single submitter
- CBX2 p.Pro303Ser Uncertain significance Single submitter
- CBX2 p.Pro309Leu Uncertain significance Single submitter
- CBX2 p.Pro327Ser Uncertain significance Single submitter
- CBX2 p.Pro327Thr Uncertain significance Single submitter
- CBX2 p.Pro328Ala Uncertain significance Single submitter
- CBX2 p.Pro341Ala Uncertain significance Single submitter
- CBX2 p.Pro345Leu Uncertain significance Single submitter
- CBX2 p.Pro424Ser Uncertain significance Single submitter
- CBX2 p.Pro476Leu Uncertain significance Single submitter
- CBX2 p.Pro98Ala Uncertain significance Single submitter
- CBX2 p.Thr348Asn Uncertain significance Single submitter
- CBX2 p.Thr444Arg Uncertain significance Single submitter
- CBX2 p.Thr454Pro Uncertain significance Single submitter
- CBX2 p.Thr479Ser Uncertain significance Single submitter
- CBX2 p.Val142Leu Uncertain significance Single submitter
- CBX2 p.Val336Leu Uncertain significance Single submitter
- CBX2 p.Val487Ile Uncertain significance Single submitter
- CBX2 p.Val505Ile Uncertain significance Single submitter
-
CBX2 p.Arg135Gln
Uncertain significance
No assertion criteria
disorder of sexual differentiation
Predictors split 47
The independent predictors disagree with each other — read with care.
- CBX2 p.Arg137His Uncertain significance Multiple submitters
- CBX2 p.Gln349His Uncertain significance Multiple submitters
- CBX2 p.Gly287Arg Uncertain significance Multiple submitters
- CBX2 p.Gly332Asp Uncertain significance Multiple submitters
- CBX2 p.Leu193Met Benign Multiple submitters
- CBX2 p.Ala270Pro Uncertain significance Single submitter
- CBX2 p.Arg137Cys Uncertain significance Single submitter
- CBX2 p.Arg161Trp Uncertain significance Single submitter
- CBX2 p.Arg247Trp Uncertain significance Single submitter
- CBX2 p.Arg373Cys Uncertain significance Single submitter
- CBX2 p.Arg443Cys Uncertain significance Single submitter
- CBX2 p.Arg450Cys Uncertain significance Single submitter
- CBX2 p.Arg450His Uncertain significance Single submitter
- CBX2 p.Arg70Trp Uncertain significance Single submitter
- CBX2 p.Arg91Trp Uncertain significance Single submitter
- CBX2 p.Asp470Asn Uncertain significance Single submitter
- CBX2 p.Gln267Arg Uncertain significance Single submitter
- CBX2 p.His258Tyr Uncertain significance Single submitter
- CBX2 p.Leu4Val Uncertain significance Single submitter
- CBX2 p.Lys162Asn Uncertain significance Single submitter
- CBX2 p.Lys167Arg Uncertain significance Single submitter
- CBX2 p.Lys61Gln Uncertain significance Single submitter
- CBX2 p.Pro159Leu Uncertain significance Single submitter
- CBX2 p.Pro179His Uncertain significance Single submitter
- CBX2 p.Pro437His Uncertain significance Single submitter
- CBX2 p.Pro477His Uncertain significance Single submitter
- CBX2 p.Ser106Cys Uncertain significance Single submitter
- CBX2 p.Ser109Tyr Uncertain significance Single submitter
-
CBX2 p.Ser111Phe
Likely benign
Single submitter
46,XY sex reversal 5
- CBX2 p.Ser119Pro Uncertain significance Single submitter
- CBX2 p.Ser126Arg Uncertain significance Single submitter
- CBX2 p.Ser198Asn Uncertain significance Single submitter
- CBX2 p.Ser19Arg Uncertain significance Single submitter
- CBX2 p.Ser251Cys Uncertain significance Single submitter
- CBX2 p.Ser306Asn Uncertain significance Single submitter
- CBX2 p.Ser416Phe Uncertain significance Single submitter
- CBX2 p.Ser438Ile Uncertain significance Single submitter
- CBX2 p.Ser459Arg Uncertain significance Single submitter
- CBX2 p.Ser467Leu Uncertain significance Single submitter
- CBX2 p.Ser90Asn Uncertain significance Single submitter
- CBX2 p.Thr294Met Uncertain significance Single submitter
- CBX2 p.Thr436Ile Uncertain significance Single submitter
- CBX2 p.Thr496Ile Uncertain significance Single submitter
- CBX2 p.Val208Ile Uncertain significance Single submitter
- CBX2 p.Val208Phe Uncertain significance Single submitter
- CBX2 p.Val503Ile Uncertain significance Single submitter
- CBX2 p.Val524Met Uncertain significance Single submitter
All CBX2 variants
Pathogenic 2
- p.Arg443Pro No assertion criteria 46,XY sex reversal 5 ⚠
- p.Pro98Leu No assertion criteria 46,XY sex reversal 5 ⚠
Conflicting classifications of pathogenicity 2
- p.Gly224Ser Single submitter ⚠
- p.Val257Met Single submitter ⚠
Benign 15
- p.Ala452Val Multiple submitters
- p.Glu448= Multiple submitters
- p.Gly314Ser Multiple submitters
- p.Ile49= Multiple submitters
- p.Leu193Met Multiple submitters ⚠
- p.Leu414= Multiple submitters
- p.Pro143= Multiple submitters
- p.Pro201= Multiple submitters
- p.Pro304= Multiple submitters
- p.Pro483= Multiple submitters
- c.182+20_182+21dup Single submitter
- c.72+25del Single submitter
- p.Ala452= Single submitter
- p.Ser42= Single submitter
- p.Thr376= Single submitter
Benign/Likely benign 3
- p.Arg23= Multiple submitters
- p.Lys283Asn Multiple submitters
- p.Thr114= Multiple submitters
Likely benign 41
- p.His140= Multiple submitters
- p.Pro471Ala Multiple submitters
- c.117-14C>T Single submitter
- c.288+147T>G Single submitter
- c.288+172del Single submitter
- c.288+43C>T Single submitter
- c.289-17del Single submitter
- c.73-19C>G Single submitter
- c.73-4G>T Single submitter
- c.73-7C>A Single submitter
- p.Ala189Thr Single submitter
- p.Ala195= Single submitter
- p.Ala375Thr Single submitter
- p.Ala420= Single submitter
- p.Ala474= Single submitter
- p.Arg92His Single submitter
- p.Cys16= Single submitter
- p.Cys89= Single submitter
- p.Gln173= Single submitter
- p.Gly223= Single submitter
- p.Gly246Ser Single submitter
- p.Gly285Ser Single submitter
- p.Leu211= Single submitter
- p.Pro179= Single submitter
- p.Pro366= Single submitter
- p.Pro382= Single submitter
- p.Pro483Leu Single submitter
- p.Ser111Phe Single submitter 46,XY sex reversal 5 ⚠
- p.Ser113= Single submitter
- p.Ser205= Single submitter
- p.Ser400= Single submitter
- p.Ser438= Single submitter
- p.Ser464= Single submitter
- p.Ser467= Single submitter
- p.Ser469= Single submitter
- p.Ser473= Single submitter
- p.Ser6= Single submitter
- p.Thr294= Single submitter
- p.Thr403Ser Single submitter
- p.Ala375= No assertion criteria CBX2-related disorder
- p.Pro476= No assertion criteria CBX2-related disorder
Uncertain significance 127
- c.117-18del Multiple submitters 46,XY sex reversal 5
- c.288+52G>T Multiple submitters 46,XY complete gonadal dysgenesis
- p.Arg137His Multiple submitters ⚠
- p.Gln349His Multiple submitters ⚠
- p.Gly133Ser Multiple submitters ⚠
- p.Gly287Arg Multiple submitters ⚠
- p.Gly332Asp Multiple submitters ⚠
- p.Met260Val Multiple submitters ⚠
- p.Met404Leu Multiple submitters ⚠
- p.Pro327Leu Multiple submitters ⚠
- p.Thr348Ser Multiple submitters ⚠
- p.Ala152Ser Single submitter ⚠
- p.Ala206Thr Single submitter ⚠
- p.Ala270Pro Single submitter ⚠
- p.Ala275Val Single submitter ⚠
- p.Ala278Val Single submitter ⚠
- p.Ala311Val Single submitter ⚠
- p.Ala415Ser Single submitter
- p.Ala460Ser Single submitter ⚠
- p.Ala460Thr Single submitter ⚠
- p.Ala474Thr Single submitter ⚠
- p.Ala474Val Single submitter ⚠
- p.Arg137Cys Single submitter ⚠
- p.Arg161Trp Single submitter ⚠
- p.Arg190Gln Single submitter ⚠
- p.Arg190Gly Single submitter ⚠
- p.Arg247Gln Single submitter ⚠
- p.Arg247Trp Single submitter ⚠
- p.Arg262Gln Single submitter ⚠
- p.Arg373Cys Single submitter ⚠
- p.Arg373His Single submitter ⚠
- p.Arg443Cys Single submitter ⚠
- p.Arg450Cys Single submitter ⚠
- p.Arg450His Single submitter ⚠
- p.Arg70Trp Single submitter ⚠
- p.Arg79Trp Single submitter ⚠
- p.Arg91Trp Single submitter ⚠
- p.Asn282Lys Single submitter ⚠
- p.Asp470Asn Single submitter ⚠
- p.Asp99Asn Single submitter ⚠
- p.Cys430Gly Single submitter ⚠
- p.Cys89fs Single submitter 46,XY sex reversal 5
- p.Gln267Arg Single submitter ⚠
- p.Glu172Gln Single submitter ⚠
- p.Glu28Gln Single submitter ⚠
- p.Glu350Gln Single submitter ⚠
- p.Glu457Gln Single submitter ⚠
- p.Gly133Val Single submitter ⚠
- p.Gly194Glu Single submitter ⚠
- p.Gly210Asp Single submitter 46,XY complete gonadal dysgenesis ⚠
- p.Gly249Ser Single submitter ⚠
- p.Gly297Arg Single submitter ⚠
- p.Gly322Arg Single submitter ⚠
- p.Gly325Glu Single submitter ⚠
- p.Gly326Ala Single submitter ⚠
- p.Gly367Arg Single submitter ⚠
- p.Gly380Asp Single submitter ⚠
- p.Gly447Arg Single submitter ⚠
- p.Gly73Arg Single submitter ⚠
- p.His217Gln Single submitter ⚠
- p.His258Tyr Single submitter ⚠
- p.His331Arg Single submitter ⚠
- p.His374Arg Single submitter ⚠
- p.Leu396His Single submitter ⚠
- p.Leu4Val Single submitter ⚠
- p.Leu56= Single submitter 46,XY sex reversal 5
- p.Lys103Glu Single submitter ⚠
- p.Lys162Asn Single submitter ⚠
- p.Lys167Arg Single submitter ⚠
- p.Lys379_Thr384del Single submitter
- p.Lys413Glu Single submitter ⚠
- p.Lys451Arg Single submitter ⚠
- p.Lys61Gln Single submitter ⚠
- p.Lys71Arg Single submitter ⚠
- p.Met241Val Single submitter ⚠
- p.Met301Ile Single submitter ⚠
- p.Met86Val Single submitter ⚠
- p.Phe527Leu Single submitter ⚠
- p.Pro141Ala Single submitter ⚠
- p.Pro154Ser Single submitter ⚠
- p.Pro159Leu Single submitter ⚠
- p.Pro159Ser Single submitter ⚠
- p.Pro179His Single submitter ⚠
- p.Pro196Leu Single submitter ⚠
- p.Pro303Leu Single submitter ⚠
- p.Pro303Ser Single submitter ⚠
- p.Pro309Leu Single submitter ⚠
- p.Pro327Ser Single submitter ⚠
- p.Pro327Thr Single submitter ⚠
- p.Pro328Ala Single submitter ⚠
- p.Pro341Ala Single submitter ⚠
- p.Pro345Leu Single submitter ⚠
- p.Pro424Ser Single submitter ⚠
- p.Pro437His Single submitter ⚠
- p.Pro476Leu Single submitter ⚠
- p.Pro477His Single submitter ⚠
- p.Pro98Ala Single submitter ⚠
- p.Ser106Cys Single submitter ⚠
- p.Ser109Tyr Single submitter ⚠
- p.Ser119Pro Single submitter ⚠
- p.Ser126Arg Single submitter ⚠
- p.Ser198Asn Single submitter ⚠
- p.Ser19Arg Single submitter ⚠
- p.Ser251Cys Single submitter ⚠
- p.Ser306Asn Single submitter ⚠
- p.Ser416Phe Single submitter ⚠
- p.Ser438Ile Single submitter ⚠
- p.Ser459Arg Single submitter ⚠
- p.Ser467Leu Single submitter ⚠
- p.Ser90Asn Single submitter ⚠
- p.Thr294Met Single submitter ⚠
- p.Thr348Asn Single submitter ⚠
- p.Thr436Ile Single submitter ⚠
- p.Thr444Arg Single submitter ⚠
- p.Thr454Pro Single submitter ⚠
- p.Thr479Ser Single submitter ⚠
- p.Thr496Ile Single submitter ⚠
- p.Val142Leu Single submitter ⚠
- p.Val208Ile Single submitter ⚠
- p.Val208Phe Single submitter ⚠
- p.Val336Leu Single submitter ⚠
- p.Val487Ile Single submitter ⚠
- p.Val503Ile Single submitter ⚠
- p.Val505Ile Single submitter ⚠
- p.Val524Met Single submitter ⚠
- c.117-3C>T No assertion criteria disorder of sexual differentiation
- p.Arg135Gln No assertion criteria disorder of sexual differentiation ⚠