NCOA3 — 173 ClinVar variants

All ClinVar germline NCOA3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 151 flagged for review →

1 Pathogenic · 1 Benign · 12 Likely benign · 159 Uncertain significance

Full NCOA3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 151

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.

NCOA3 p.Ser937Cys Pathogenic Single submitter
Bilateral sensorineural hearing impairment

Predictors lean, ClinVar uncertain 130

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

Predictors split 20

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

All NCOA3 variants

Pathogenic 1

p.Ser937Cys Single submitter Bilateral sensorineural hearing impairment ⚠

Benign 1

p.Pro559Ser Multiple submitters

Likely benign 12

p.Pro1351= Multiple submitters
p.Ala416Thr Single submitter
p.Arg36Trp Single submitter ⚠
p.Asn1333Ser Single submitter
p.Asn159Ser Single submitter
p.Gln1118Pro Single submitter
p.Gln1312Pro Single submitter
p.Gly928Ser Single submitter
p.Ile817Val Single submitter
p.Ile848Val Single submitter
p.Leu1044= Single submitter
p.Pro412Leu Single submitter

Uncertain significance 159

p.Ala1001Glu Single submitter ⚠
p.Ala1052Thr Single submitter ⚠
p.Ala1190Pro Single submitter ⚠
p.Ala1203Thr Single submitter ⚠
p.Ala120Val Single submitter ⚠
p.Ala1382Pro Single submitter ⚠
p.Ala525Thr Single submitter ⚠
p.Ala971Val Single submitter ⚠
p.Arg1156Gln Single submitter
p.Arg1163Gln Single submitter ⚠
p.Arg1163Trp Single submitter
p.Arg1229Cys Single submitter ⚠
p.Arg1229His Single submitter ⚠
p.Arg1239Gln Single submitter ⚠
p.Arg1242Ser Single submitter ⚠
p.Arg16Gln Single submitter ⚠
p.Arg18Cys Single submitter ⚠
p.Arg220Ile Single submitter ⚠
p.Arg251Cys Single submitter ⚠
p.Arg317Cys Single submitter ⚠
p.Arg334Gln Single submitter ⚠
p.Arg360Pro Single submitter ⚠
p.Arg36Gln Single submitter ⚠
p.Arg38Trp Single submitter ⚠
p.Arg590Gly Single submitter ⚠
p.Arg632Gln Single submitter ⚠
p.Arg632Pro Single submitter ⚠
p.Arg632Trp Single submitter ⚠
p.Asn1083Ser Single submitter ⚠
p.Asn1136Asp Single submitter ⚠
p.Asn1143Asp Single submitter ⚠
p.Asn1333Ile Single submitter ⚠
p.Asn140Ser Single submitter ⚠
p.Asn263Lys Single submitter ⚠
p.Asn279Ser Single submitter ⚠
p.Asn325Asp Single submitter ⚠
p.Asn550Lys Single submitter ⚠
p.Asn55Ser Single submitter ⚠
p.Asn672Ser Single submitter ⚠
p.Asn7Lys Single submitter ⚠
p.Asn835Thr Single submitter ⚠
p.Asn872Asp Single submitter ⚠
p.Asn91Ile Single submitter ⚠
p.Asn966His Single submitter ⚠
p.Asn966Ile Single submitter ⚠
p.Asp1065Gly Single submitter ⚠
p.Asp1420Ala Single submitter ⚠
p.Asp295Glu Single submitter ⚠
p.Asp576Asn Single submitter ⚠
p.Asp576Glu Single submitter ⚠
p.Cys769Arg Single submitter ⚠
p.Gln1000His Single submitter ⚠
p.Gln1006Ter Single submitter
p.Gln1129Glu Single submitter ⚠
p.Gln1181His Single submitter ⚠
p.Gln1218Arg Single submitter ⚠
p.Gln1224Lys Single submitter
p.Gln1228His Single submitter ⚠
p.Gln1320Pro Single submitter ⚠
p.Gln976Glu Single submitter ⚠
p.Gln979Arg Single submitter ⚠
p.Glu321Gln Single submitter
p.Glu648Gln Single submitter ⚠
p.Glu788Gly Single submitter ⚠
p.Gly1125Asp Single submitter ⚠
p.Gly1201Asp Single submitter ⚠
p.Gly1298Arg Single submitter
p.Gly1318Arg Single submitter ⚠
p.Gly1385Arg Single submitter ⚠
p.Gly633Val Single submitter ⚠
p.Gly865Asp Single submitter ⚠
p.His468Arg Single submitter ⚠
p.His618Arg Single submitter
p.His618Tyr Single submitter ⚠
p.Ile1072Val Single submitter
p.Ile1159Met Single submitter ⚠
p.Ile1356Val Single submitter ⚠
p.Ile342Val Single submitter ⚠
p.Ile556Val Single submitter ⚠
p.Ile89Val Single submitter ⚠
p.Leu1037His Single submitter ⚠
p.Leu11Pro Single submitter ⚠
p.Leu173Phe Single submitter ⚠
p.Leu473Phe Single submitter ⚠
p.Leu678Val Single submitter ⚠
p.Leu727Gln Single submitter ⚠
p.Leu975Phe Single submitter ⚠
p.Lys110Glu Single submitter ⚠
p.Lys350Arg Single submitter ⚠
p.Met1122Val Single submitter ⚠
p.Met1138Val Single submitter ⚠
p.Met1142Arg Single submitter
p.Met1317Val Single submitter ⚠
p.Met1347Val Single submitter ⚠
p.Met401Thr Single submitter ⚠
p.Met403Val Single submitter ⚠
p.Met448Ile Single submitter ⚠
p.Met507Val Single submitter ⚠
p.Met554Thr Single submitter ⚠
p.Met902Ile Single submitter ⚠
p.Phe352Cys Single submitter ⚠
p.Phe352Leu Single submitter ⚠
p.Pro1079Ala Single submitter ⚠
p.Pro1120Leu Single submitter ⚠
p.Pro1167Arg Single submitter ⚠
p.Pro1198Ala Single submitter ⚠
p.Pro1290Leu Single submitter ⚠
p.Pro1299Leu Single submitter ⚠
p.Pro1351Ser Single submitter ⚠
p.Pro25Ser Single submitter ⚠
p.Pro380Leu Single submitter ⚠
p.Pro389Leu Single submitter ⚠
p.Pro444Ser Single submitter ⚠
p.Pro475Arg Single submitter ⚠
p.Pro552Ser Single submitter ⚠
p.Pro747Thr Single submitter ⚠
p.Pro775Arg Single submitter ⚠
p.Pro783Ala Single submitter ⚠
p.Pro950Thr Single submitter ⚠
p.Pro959Ala Single submitter ⚠
p.Ser1048Arg Single submitter ⚠
p.Ser1215Cys Single submitter ⚠
p.Ser1289Phe Single submitter ⚠
p.Ser1330Asn Single submitter ⚠
p.Ser1343Phe Single submitter ⚠
p.Ser2Thr Single submitter ⚠
p.Ser336Leu Single submitter ⚠
p.Ser402Thr Single submitter ⚠
p.Ser464Gly Single submitter ⚠
p.Ser505Phe Single submitter
p.Ser520Gly Single submitter ⚠
p.Ser530Arg Single submitter ⚠
p.Ser536Cys Single submitter ⚠
p.Ser640Pro Single submitter ⚠
p.Ser645Gly Single submitter ⚠
p.Ser657Cys Single submitter ⚠
p.Ser662Phe Single submitter ⚠
p.Ser752Phe Single submitter ⚠
p.Ser809Asn Single submitter ⚠
p.Ser863Cys Single submitter ⚠
p.Ser874Asn Single submitter ⚠
p.Ser917Leu Single submitter ⚠
p.Thr1114Arg Single submitter ⚠
p.Thr1277Ser Single submitter ⚠
p.Thr1300Ile Single submitter ⚠
p.Thr187Asn Single submitter ⚠
p.Thr282Arg Single submitter ⚠
p.Thr557Ile Single submitter ⚠
p.Thr960Ile Single submitter ⚠
p.Val1243Leu Single submitter ⚠
p.Val153Leu Single submitter ⚠
p.Val157Leu Single submitter ⚠
p.Val181Ile Single submitter ⚠
p.Val500Ile Single submitter ⚠
p.Val562Ala Single submitter ⚠
p.Val603Ile Single submitter ⚠
p.Val845Leu Single submitter ⚠
p.Val856Ala Single submitter ⚠
p.Val864Ile Single submitter ⚠