BCL9L — 300 ClinVar variants

All ClinVar germline BCL9L variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 262 flagged for review →

14 Benign · 8 Likely benign · 278 Uncertain significance

Full BCL9L gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 262

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 lean, ClinVar uncertain 215

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification. · showing the 150 best-reviewed of 215

Predictors split 47

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

All BCL9L variants

Benign 14

p.Gln1340= Multiple submitters
p.Gly437= Multiple submitters
p.Leu256= Multiple submitters
p.Met646Val Multiple submitters
p.Pro1394= Multiple submitters
p.Pro1455= Multiple submitters
p.Pro764= Multiple submitters
p.Pro790= Multiple submitters
p.Ser424= Multiple submitters
p.Ser543Gly Multiple submitters
p.Val1441Met Multiple submitters
p.Val902Ala Multiple submitters
p.Leu812Phe Single submitter
p.Ser1345= Single submitter

Likely benign 8

p.Ala1292Thr Single submitter
p.Asn843Ser Single submitter
p.Gly1493Ser Single submitter
p.Pro1126= Single submitter
p.Pro309= Single submitter
p.Pro434Thr Single submitter
p.Pro455= Single submitter
p.Thr1242Ser Single submitter

Uncertain significance 278

p.Pro1161Ser Multiple submitters ⚠
p.Ala1009Ser Single submitter ⚠
p.Ala1058Thr Single submitter ⚠
p.Ala1151Thr Single submitter ⚠
p.Ala1191Thr Single submitter ⚠
p.Ala1260Gly Single submitter ⚠
p.Ala140Val Single submitter ⚠
p.Ala187Val Single submitter ⚠
p.Ala35Gly Single submitter ⚠
p.Ala438Thr Single submitter ⚠
p.Ala55Thr Single submitter ⚠
p.Ala698Val Single submitter ⚠
p.Ala714Val Single submitter ⚠
p.Ala734Val Single submitter ⚠
p.Ala82Thr Single submitter ⚠
p.Ala82Val Single submitter ⚠
p.Ala99fs Single submitter
p.Arg113Lys Single submitter ⚠
p.Arg1231Gln Single submitter ⚠
p.Arg125Gln Single submitter ⚠
p.Arg1373Gln Single submitter ⚠
p.Arg1373Trp Single submitter ⚠
p.Arg1475Trp Single submitter ⚠
p.Arg1477His Single submitter ⚠
p.Arg151Trp Single submitter ⚠
p.Arg15Gly Single submitter ⚠
p.Arg218Trp Single submitter ⚠
p.Arg259Gln Single submitter ⚠
p.Arg259Trp Single submitter ⚠
p.Arg273Trp Single submitter ⚠
p.Arg391Cys Single submitter ⚠
p.Arg544Cys Single submitter ⚠
p.Arg581Trp Single submitter ⚠
p.Arg593Gln Single submitter ⚠
p.Arg593Trp Single submitter
p.Arg610Gln Single submitter ⚠
p.Arg668Gln Single submitter ⚠
p.Arg687Gln Single submitter ⚠
p.Arg746Gln Single submitter ⚠
p.Arg819Gln Single submitter ⚠
p.Arg821Gln Single submitter ⚠
p.Arg908Trp Single submitter ⚠
p.Arg913Trp Single submitter ⚠
p.Arg986Cys Single submitter ⚠
p.Asn1029Thr Single submitter ⚠
p.Asn1038Tyr Single submitter ⚠
p.Asn1268Lys Single submitter ⚠
p.Asn388Ile Single submitter ⚠
p.Asn388Ser Single submitter ⚠
p.Asn46Asp Single submitter ⚠
p.Asn627Ile Single submitter ⚠
p.Asn6Asp Single submitter ⚠
p.Asn6Tyr Single submitter ⚠
p.Asn769Ser Single submitter ⚠
p.Asn91Ile Single submitter ⚠
p.Asp1114Tyr Single submitter ⚠
p.Asp1307Asn Single submitter ⚠
p.Asp1325Asn Single submitter ⚠
p.Asp133Asn Single submitter ⚠
p.Asp169Glu Single submitter ⚠
p.Asp170Asn Single submitter ⚠
p.Asp220Val Single submitter ⚠
p.Asp277Glu Single submitter ⚠
p.Asp585Gly Single submitter ⚠
p.Asp762Gly Single submitter
p.Asp805Tyr Single submitter
p.Asp873Gly Single submitter
p.Gln1269Lys Single submitter ⚠
p.Gln1278Glu Single submitter ⚠
p.Gln1340Arg Single submitter ⚠
p.Gln1384Arg Single submitter ⚠
p.Gln1409His Single submitter ⚠
p.Gln1430Glu Single submitter ⚠
p.Gln1465His Single submitter
p.Gln278Glu Single submitter ⚠
p.Gln412His Single submitter ⚠
p.Gln453Pro Single submitter ⚠
p.Gln477Arg Single submitter
p.Gln607Lys Single submitter ⚠
p.Gln692Arg Single submitter ⚠
p.Gln713Glu Single submitter ⚠
p.Gln717Glu Single submitter ⚠
p.Gln726Glu Single submitter ⚠
p.Gln853Arg Single submitter ⚠
p.Gln857Pro Single submitter ⚠
p.Gln874Glu Single submitter ⚠
p.Gln960Lys Single submitter ⚠
p.Glu1309Lys Single submitter ⚠
p.Glu1346Lys Single submitter ⚠
p.Glu623Lys Single submitter ⚠
p.Glu685Gln Single submitter
p.Glu707Lys Single submitter ⚠
p.Gly1006fs Single submitter
p.Gly100Val Single submitter ⚠
p.Gly1048Ser Single submitter ⚠
p.Gly1134Arg Single submitter ⚠
p.Gly1157Ser Single submitter ⚠
p.Gly1182Val Single submitter
p.Gly1246Arg Single submitter ⚠
p.Gly1247Arg Single submitter ⚠
p.Gly1300Arg Single submitter ⚠
p.Gly1382Val Single submitter ⚠
p.Gly1386Glu Single submitter ⚠
p.Gly1395Arg Single submitter ⚠
p.Gly1419Arg Single submitter ⚠
p.Gly194Ser Single submitter ⚠
p.Gly212Ala Single submitter ⚠
p.Gly212Ser Single submitter ⚠
p.Gly225Arg Single submitter ⚠
p.Gly227Arg Single submitter ⚠
p.Gly350Val Single submitter ⚠
p.Gly398Cys Single submitter
p.Gly481Ala Single submitter ⚠
p.Gly481Ser Single submitter ⚠
p.Gly54Arg Single submitter ⚠
p.Gly554Asp Single submitter
p.Gly613Val Single submitter ⚠
p.Gly636Val Single submitter ⚠
p.Gly699Ser Single submitter ⚠
p.Gly703Glu Single submitter ⚠
p.Gly730Asp Single submitter ⚠
p.Gly74Cys Single submitter ⚠
p.Gly76Arg Single submitter ⚠
p.Gly854Glu Single submitter
p.Gly928Val Single submitter ⚠
p.Gly971Val Single submitter ⚠
p.His1279Gln Single submitter ⚠
p.His1358Gln Single submitter ⚠
p.His681Tyr Single submitter ⚠
p.Leu1298Pro Single submitter
p.Leu1305Pro Single submitter ⚠
p.Leu1326Met Single submitter ⚠
p.Leu1357Val Single submitter ⚠
p.Leu1427Ile Single submitter ⚠
p.Leu1453Phe Single submitter ⚠
p.Leu291Arg Single submitter ⚠
p.Leu678Met Single submitter ⚠
p.Leu812Ile Single submitter ⚠
p.Lys1344Arg Single submitter ⚠
p.Lys432Arg Single submitter ⚠
p.Lys686Glu Single submitter ⚠
p.Lys83Glu Single submitter ⚠
p.Lys953Arg Single submitter ⚠
p.Met1156Val Single submitter ⚠
p.Met1158Ile Single submitter ⚠
p.Met1158Val Single submitter ⚠
p.Met1202Thr Single submitter ⚠
p.Met1274Ile Single submitter ⚠
p.Met1285Thr Single submitter ⚠
p.Met1391Val Single submitter ⚠
p.Met1469Leu Single submitter ⚠
p.Met503Ile Single submitter ⚠
p.Met503Val Single submitter ⚠
p.Met584Val Single submitter ⚠
p.Met622Val Single submitter ⚠
p.Met646Leu Single submitter ⚠
p.Met708Ile Single submitter ⚠
p.Met722Val Single submitter ⚠
p.Met727Ile Single submitter ⚠
p.Met753Val Single submitter ⚠
p.Met780Val Single submitter ⚠
p.Met863Val Single submitter ⚠
p.Met877Ile Single submitter ⚠
p.Met890Ile Single submitter ⚠
p.Phe104Leu Single submitter ⚠
p.Phe1433Ile Single submitter ⚠
p.Phe239fs Single submitter
p.Phe239Leu Single submitter ⚠
p.Phe849Leu Single submitter ⚠
p.Pro1003Arg Single submitter ⚠
p.Pro1026Leu Single submitter ⚠
p.Pro1056Ser Single submitter ⚠
p.Pro1075Leu Single submitter ⚠
p.Pro1125His Single submitter ⚠
p.Pro1126Ala Single submitter ⚠
p.Pro1127Gln Single submitter ⚠
p.Pro1127Ser Single submitter ⚠
p.Pro1206Leu Single submitter ⚠
p.Pro1229Ser Single submitter ⚠
p.Pro1249Leu Single submitter ⚠
p.Pro1256Leu Single submitter ⚠
p.Pro1270Leu Single submitter ⚠
p.Pro1273Ser Single submitter ⚠
p.Pro1295Gln Single submitter ⚠
p.Pro1295Ser Single submitter ⚠
p.Pro1350Arg Single submitter ⚠
p.Pro1350Leu Single submitter ⚠
p.Pro1350Ser Single submitter ⚠
p.Pro1406Ser Single submitter ⚠
p.Pro141Leu Single submitter ⚠
p.Pro1449Leu Single submitter ⚠
p.Pro1455Ser Single submitter ⚠
p.Pro1463Leu Single submitter ⚠
p.Pro164Leu Single submitter ⚠
p.Pro210Leu Single submitter ⚠
p.Pro22Leu Single submitter ⚠
p.Pro286Ala Single submitter ⚠
p.Pro294Leu Single submitter ⚠
p.Pro299Leu Single submitter ⚠
p.Pro299Thr Single submitter ⚠
p.Pro307Thr Single submitter ⚠
p.Pro311Leu Single submitter ⚠
p.Pro312Leu Single submitter ⚠
p.Pro32Thr Single submitter ⚠
p.Pro34Leu Single submitter ⚠
p.Pro366Leu Single submitter ⚠
p.Pro367Ser Single submitter ⚠
p.Pro429Ala Single submitter ⚠
p.Pro443Leu Single submitter ⚠
p.Pro448Ser Single submitter ⚠
p.Pro450Thr Single submitter ⚠
p.Pro451Arg Single submitter ⚠
p.Pro455Leu Single submitter ⚠
p.Pro468Leu Single submitter ⚠
p.Pro468Ser Single submitter ⚠
p.Pro493Leu Single submitter ⚠
p.Pro568Ser Single submitter ⚠
p.Pro599Ser Single submitter ⚠
p.Pro612Leu Single submitter ⚠
p.Pro621Ala Single submitter ⚠
p.Pro632Thr Single submitter ⚠
p.Pro752Ser Single submitter ⚠
p.Pro764Leu Single submitter ⚠
p.Pro764Ser Single submitter ⚠
p.Pro832Leu Single submitter ⚠
p.Pro872Ser Single submitter ⚠
p.Pro927Leu Single submitter ⚠
p.Pro935Ser Single submitter ⚠
p.Pro969Leu Single submitter ⚠
p.Pro998Ser Single submitter ⚠
p.Ser1004Thr Single submitter ⚠
p.Ser1017Asn Single submitter ⚠
p.Ser1032Phe Single submitter ⚠
p.Ser1054Leu Single submitter ⚠
p.Ser106Leu Single submitter ⚠
p.Ser1138Gly Single submitter ⚠
p.Ser1222Phe Single submitter ⚠
p.Ser131Pro Single submitter ⚠
p.Ser1458Cys Single submitter ⚠
p.Ser1478Asn Single submitter ⚠
p.Ser205Gly Single submitter ⚠
p.Ser295Pro Single submitter ⚠
p.Ser316Cys Single submitter ⚠
p.Ser338Leu Single submitter ⚠
p.Ser471Pro Single submitter ⚠
p.Ser543Asn Single submitter ⚠
p.Ser700Ile Single submitter ⚠
p.Ser72Pro Single submitter ⚠
p.Ser797Leu Single submitter ⚠
p.Ser904Leu Single submitter ⚠
p.Ser915Leu Single submitter ⚠
p.Ser942Thr Single submitter
p.Ser982Phe Single submitter ⚠
p.Ser982Pro Single submitter ⚠
p.Ser993Gly Single submitter ⚠
p.Thr1013Met Single submitter ⚠
p.Thr1194Ile Single submitter ⚠
p.Thr1319Ala Single submitter ⚠
p.Thr285Pro Single submitter ⚠
p.Thr298Ser Single submitter ⚠
p.Thr360Ala Single submitter ⚠
p.Thr456Met Single submitter ⚠
p.Thr67Ile Single submitter ⚠
p.Thr884Ala Single submitter ⚠
p.Tyr528Cys Single submitter ⚠
p.Tyr528His Single submitter ⚠
p.Val101Met Single submitter ⚠
p.Val1020Ile Single submitter ⚠
p.Val119Met Single submitter ⚠
p.Val1219Ala Single submitter ⚠
p.Val1405Met Single submitter ⚠
p.Val206Met Single submitter ⚠
p.Val240Ile Single submitter ⚠
p.Val633Met Single submitter ⚠
p.Val75Leu Single submitter ⚠
p.Val820Phe Single submitter ⚠
p.Val882Leu Single submitter ⚠
p.Val882Met Single submitter ⚠