DENND4A — 156 ClinVar variants

All ClinVar germline DENND4A variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 144 flagged for review →

1 Likely pathogenic · 5 Likely benign · 150 Uncertain significance

Full DENND4A gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 144

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.

DENND4A p.Ser696Arg Likely pathogenic Single submitter

Predictors lean, ClinVar uncertain 96

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

Predictors split 47

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

All DENND4A variants

Likely pathogenic 1

p.Ser696Arg Single submitter ⚠

Likely benign 5

p.Ala1476Thr Single submitter
p.Asn730Ser Single submitter
p.Leu1586Val Single submitter
p.Pro1130Ser Single submitter
p.Tyr1154Cys Single submitter

Uncertain significance 150

p.Ala1108Glu Single submitter ⚠
p.Ala1244Gly Single submitter ⚠
p.Ala1476Gly Single submitter ⚠
p.Ala1585Ser Single submitter ⚠
p.Ala1619Pro Single submitter ⚠
p.Ala324Gly Single submitter ⚠
p.Ala596Pro Single submitter ⚠
p.Ala937Val Single submitter
p.Arg1010Cys Single submitter ⚠
p.Arg1056Ser Single submitter ⚠
p.Arg1074Lys Single submitter ⚠
p.Arg1192Cys Single submitter ⚠
p.Arg1246His Single submitter ⚠
p.Arg1266Cys Single submitter ⚠
p.Arg1274Gln Single submitter ⚠
p.Arg1274Trp Single submitter ⚠
p.Arg127His Single submitter ⚠
p.Arg1293Ile Single submitter ⚠
p.Arg1496Gln Single submitter ⚠
p.Arg1607Gln Single submitter ⚠
p.Arg1630Gly Single submitter ⚠
p.Arg1875Cys Single submitter ⚠
p.Arg661Gln Single submitter ⚠
p.Arg762Ser Single submitter ⚠
p.Arg766Cys Single submitter ⚠
p.Arg831Gly Single submitter ⚠
p.Arg886Lys Single submitter ⚠
p.Arg8His Single submitter ⚠
p.Arg941Gly Single submitter
p.Asn1043Ser Single submitter ⚠
p.Asn1061Ser Single submitter ⚠
p.Asn1073Ile Single submitter ⚠
p.Asn1122Asp Single submitter ⚠
p.Asn1480Ser Single submitter ⚠
p.Asn1832Ser Single submitter ⚠
p.Asn375Lys Single submitter ⚠
p.Asn687Ser Single submitter ⚠
p.Asn844Ser Single submitter ⚠
p.Asp1107Asn Single submitter ⚠
p.Asp180Asn Single submitter ⚠
p.Asp180Glu Single submitter ⚠
p.Asp609Glu Single submitter ⚠
p.Asp67Ala Single submitter ⚠
p.Asp995Asn Single submitter ⚠
p.Cys1742Gly Single submitter ⚠
p.Cys996Tyr Single submitter ⚠
p.Gln1483Arg Single submitter ⚠
p.Gln1805Glu Single submitter ⚠
p.Gln602His Single submitter ⚠
p.Gln825Arg Single submitter ⚠
p.Glu1094Ala Single submitter ⚠
p.Glu988Lys Single submitter ⚠
p.Gly1024Arg Single submitter ⚠
p.Gly1466Arg Single submitter ⚠
p.Gly538Glu Single submitter ⚠
p.Gly658Ser Single submitter ⚠
p.Gly80Arg Single submitter ⚠
p.His1422Leu Single submitter ⚠
p.His1670Tyr Single submitter ⚠
p.His341Arg Single submitter ⚠
p.His373Tyr Single submitter ⚠
p.His747Arg Single submitter ⚠
p.His918Tyr Single submitter
p.Ile1091Phe Single submitter ⚠
p.Ile1100Leu Single submitter ⚠
p.Ile1270Thr Single submitter ⚠
p.Ile1565Val Single submitter ⚠
p.Ile307Val Single submitter ⚠
p.Ile494Val Single submitter ⚠
p.Leu1124Phe Single submitter ⚠
p.Leu1124Pro Single submitter ⚠
p.Leu1155Trp Single submitter ⚠
p.Leu1306Phe Single submitter ⚠
p.Leu1459Val Single submitter ⚠
p.Leu560Phe Single submitter ⚠
p.Lys1021Glu Single submitter ⚠
p.Lys1134Glu Single submitter ⚠
p.Lys1140Glu Single submitter ⚠
p.Lys1380Glu Single submitter ⚠
p.Lys1461Thr Single submitter ⚠
p.Lys287Asn Single submitter ⚠
p.Lys5Glu Single submitter ⚠
p.Lys976Glu Single submitter ⚠
p.Met1087Ile Single submitter ⚠
p.Met1193Thr Single submitter ⚠
p.Met1367Ile Single submitter ⚠
p.Met1387Thr Single submitter ⚠
p.Met1487Val Single submitter ⚠
p.Met1620Ile Single submitter ⚠
p.Met1792Val Single submitter ⚠
p.Met1824Val Single submitter ⚠
p.Met187Thr Single submitter ⚠
p.Met540Thr Single submitter ⚠
p.Met759Leu Single submitter ⚠
p.Phe1385Leu Single submitter ⚠
p.Phe1462Leu Single submitter ⚠
p.Phe255Leu Single submitter ⚠
p.Phe321Leu Single submitter ⚠
p.Phe322Ser Single submitter ⚠
p.Phe352Leu Single submitter ⚠
p.Phe411Leu Single submitter ⚠
p.Pro1624Leu Single submitter ⚠
p.Pro227Ser Single submitter ⚠
p.Pro691Thr Single submitter ⚠
p.Pro729Arg Single submitter ⚠
p.Ser122Arg Single submitter ⚠
p.Ser1265Asn Single submitter ⚠
p.Ser1396Ile Single submitter ⚠
p.Ser1430Thr Single submitter ⚠
p.Ser1473Cys Single submitter ⚠
p.Ser1473Phe Single submitter ⚠
p.Ser1493Arg Single submitter ⚠
p.Ser1608Arg Single submitter ⚠
p.Ser1608Asn Single submitter ⚠
p.Ser1673Asn Single submitter ⚠
p.Ser1883Gly Single submitter ⚠
p.Ser379Arg Single submitter ⚠
p.Ser430Asn Single submitter ⚠
p.Ser49Leu Single submitter ⚠
p.Ser755Phe Single submitter ⚠
p.Ser904Cys Single submitter
p.Ser916Thr Single submitter
p.Ser943Ile Single submitter
p.Ser985Thr Single submitter ⚠
p.Thr1012Ile Single submitter ⚠
p.Thr1119Met Single submitter ⚠
p.Thr1184Ala Single submitter ⚠
p.Thr1307Asn Single submitter ⚠
p.Thr1354Ile Single submitter ⚠
p.Thr1389Asn Single submitter ⚠
p.Thr1413Asn Single submitter ⚠
p.Thr1471Arg Single submitter ⚠
p.Thr1499Ile Single submitter ⚠
p.Thr295Ile Single submitter ⚠
p.Thr46Ala Single submitter ⚠
p.Thr882Ile Single submitter ⚠
p.Thr898Pro Single submitter ⚠
p.Thr930Met Single submitter
p.Tyr1485Cys Single submitter ⚠
p.Tyr1548Cys Single submitter ⚠
p.Tyr208His Single submitter ⚠
p.Tyr547Cys Single submitter ⚠
p.Val1009Ile Single submitter ⚠
p.Val1362Ile Single submitter ⚠
p.Val1895Ala Single submitter ⚠
p.Val192Ile Single submitter ⚠
p.Val382Ala Single submitter ⚠
p.Val427Met Single submitter ⚠
p.Val459Ile Single submitter ⚠
p.Val796Met Single submitter ⚠