TDRD9 — 257 ClinVar variants

All ClinVar germline TDRD9 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 192 flagged for review →

5 Pathogenic · 7 Likely pathogenic · 1 Conflicting · 11 Benign · 1 Benign/Likely benign · 30 Likely benign · 202 Uncertain significance

Full TDRD9 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 192

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 agree, ClinVar conflicts 1

ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.

TDRD9 p.Pro111Leu Conflicting Single submitter

Predictors lean, ClinVar uncertain 165

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 165

Predictors split 26

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

All TDRD9 variants

Pathogenic 5

p.Arg259Ter Single submitter
p.Glu924fs Single submitter
p.Ser1202fs Single submitter
p.Ser1162fs No assertion criteria azoospermia
p.Ser241fs No assertion criteria spermatogenic failure 30

Likely pathogenic 7

c.3716+3A>G Single submitter male infertility
p.Arg499Ter Single submitter spermatogenic failure 30
p.Gln478fs Single submitter spermatogenic failure 30
p.Glu679fs Single submitter spermatogenic failure 30
p.Pro772fs Single submitter spermatogenic failure 30
p.Tyr506Ter Single submitter spermatogenic failure 30
p.Val1050fs Single submitter male infertility

Conflicting classifications of pathogenicity 1

p.Pro111Leu Single submitter ⚠

Benign 11

c.323-10C>T Multiple submitters
p.His1059= Multiple submitters
p.Leu936= Multiple submitters
p.Thr232Ala Multiple submitters
c.3509+4T>C Single submitter
p.Ala1313Val Single submitter
p.Thr120= Single submitter
c.2607-5T>C No assertion criteria TDRD9-related disorder
c.*1G>A No assertion criteria TDRD9-related disorder
p.Phe1278Cys No assertion criteria TDRD9-related disorder
p.Val303Leu No assertion criteria TDRD9-related disorder

Benign/Likely benign 1

p.Val651= Multiple submitters

Likely benign 30

p.Lys1335= Multiple submitters
c.2224-18A>C Single submitter
c.3439-19C>T Single submitter
c.642+14G>T Single submitter
c.642+9GGGA[3] Single submitter
p.Glu294= Single submitter
p.Ile1203Val Single submitter
p.Met1120Val Single submitter
p.Ser1330Leu Single submitter
p.Ser135Asn Single submitter
p.Thr1045Ala Single submitter
p.Thr6= Single submitter
p.Thr896= Single submitter
p.Val174Ile Single submitter
p.Val802= Single submitter
p.Val939Met Single submitter
c.2223+3G>A No assertion criteria TDRD9-related disorder
c.2719-5T>G No assertion criteria TDRD9-related disorder
c.3975-7A>T No assertion criteria TDRD9-related disorder
c.421-3T>C No assertion criteria TDRD9-related disorder
c.642+8T>G No assertion criteria TDRD9-related disorder
p.Ala1319= No assertion criteria TDRD9-related disorder
p.Gly208= No assertion criteria TDRD9-related disorder
p.Leu1040= No assertion criteria TDRD9-related disorder
p.Met368Thr No assertion criteria TDRD9-related disorder
p.Pro48= No assertion criteria TDRD9-related disorder
p.Ser177= No assertion criteria TDRD9-related disorder
p.Thr1087= No assertion criteria TDRD9-related disorder
p.Val1172Ile No assertion criteria TDRD9-related disorder
p.Val1312= No assertion criteria EBV-positive nodal T- and NK-cell lymphoma

Uncertain significance 202

p.Ile16Leu Multiple submitters spermatogenic failure 30 ⚠
p.Val150Met Multiple submitters spermatogenic failure 30
c.2106+2T>A Single submitter spermatogenic failure 30
p.Ala1020Thr Single submitter ⚠
p.Ala1071Val Single submitter ⚠
p.Ala1084Gly Single submitter ⚠
p.Ala1205Val Single submitter ⚠
p.Ala1273Val Single submitter ⚠
p.Ala1359Thr Single submitter ⚠
p.Ala37Val Single submitter ⚠
p.Ala47Ser Single submitter ⚠
p.Ala551Val Single submitter ⚠
p.Ala67Val Single submitter ⚠
p.Ala69Val Single submitter ⚠
p.Ala704Pro Single submitter ⚠
p.Ala763Thr Single submitter ⚠
p.Ala763Val Single submitter ⚠
p.Arg1129Gln Single submitter ⚠
p.Arg1320His Single submitter ⚠
p.Arg1361Cys Single submitter ⚠
p.Arg1361His Single submitter ⚠
p.Arg136Gln Single submitter ⚠
p.Arg188Trp Single submitter ⚠
p.Arg197Gly Single submitter ⚠
p.Arg226Gly Single submitter ⚠
p.Arg271Cys Single submitter ⚠
p.Arg271His Single submitter ⚠
p.Arg279His Single submitter ⚠
p.Arg279Pro Single submitter ⚠
p.Arg412Gly Single submitter
p.Arg481Gln Single submitter ⚠
p.Arg496His Single submitter ⚠
p.Arg528Cys Single submitter ⚠
p.Arg564His Single submitter ⚠
p.Arg641Gln Single submitter ⚠
p.Arg641Trp Single submitter ⚠
p.Arg65Gln Single submitter ⚠
p.Arg681Gln Single submitter ⚠
p.Arg681Trp Single submitter ⚠
p.Arg737Gln Single submitter ⚠
p.Arg962His Single submitter ⚠
p.Arg99Cys Single submitter ⚠
p.Arg99Leu Single submitter ⚠
p.Asn1138Asp Single submitter ⚠
p.Asn1138Lys Single submitter ⚠
p.Asn974Ser Single submitter ⚠
p.Asn985Ser Single submitter ⚠
p.Asp1031Glu Single submitter ⚠
p.Asp1123Asn Single submitter ⚠
p.Asp1186Asn Single submitter ⚠
p.Asp1351Ala Single submitter ⚠
p.Asp297Gly Single submitter ⚠
p.Asp515Glu Single submitter ⚠
p.Asp685Glu Single submitter ⚠
p.Asp880Tyr Single submitter ⚠
p.Asp919Asn Single submitter ⚠
p.Asp990Gly Single submitter ⚠
p.Cys121Tyr Single submitter ⚠
p.Cys1328Phe Single submitter ⚠
p.Cys1328Tyr Single submitter ⚠
p.Cys292Tyr Single submitter ⚠
p.Gln164Arg Single submitter ⚠
p.Gln580Lys Single submitter ⚠
p.Gln793Pro Single submitter ⚠
p.Gln875Arg Single submitter ⚠
p.Gln961His Single submitter ⚠
p.Glu1092Lys Single submitter ⚠
p.Glu1124Lys Single submitter ⚠
p.Glu1281Lys Single submitter ⚠
p.Glu1285Lys Single submitter ⚠
p.Glu146Gln Single submitter ⚠
p.Glu247Gly Single submitter ⚠
p.Glu258Lys Single submitter ⚠
p.Glu323Lys Single submitter ⚠
p.Glu852Lys Single submitter ⚠
p.Gly106Glu Single submitter ⚠
p.Gly1253Ser Single submitter ⚠
p.Gly1253Val Single submitter ⚠
p.Gly1261Arg Single submitter ⚠
p.Gly1381Arg Single submitter ⚠
p.Gly17Cys Single submitter ⚠
p.Gly233Ala Single submitter ⚠
p.Gly317Ser Single submitter ⚠
p.Gly378Ala Single submitter ⚠
p.Gly394Val Single submitter ⚠
p.Gly437Val Single submitter spermatogenic failure 30 ⚠
p.Gly49Ser Single submitter ⚠
p.Gly51Asp Single submitter ⚠
p.Gly544Asp Single submitter ⚠
p.Gly558Val Single submitter ⚠
p.Gly655Asp Single submitter ⚠
p.Gly915Arg Single submitter ⚠
p.His1097Tyr Single submitter ⚠
p.His1268Asn Single submitter ⚠
p.His1375Gln Single submitter ⚠
p.His172Arg Single submitter ⚠
p.His172Gln Single submitter ⚠
p.His320Arg Single submitter ⚠
p.His341Arg Single submitter ⚠
p.His988Gln Single submitter ⚠
p.Ile1221Leu Single submitter ⚠
p.Ile1236Thr Single submitter ⚠
p.Ile1336Phe Single submitter ⚠
p.Ile360Leu Single submitter ⚠
p.Ile695Val Single submitter ⚠
p.Ile697Thr Single submitter ⚠
p.Ile700Leu Single submitter ⚠
p.Ile714Leu Single submitter ⚠
p.Ile781Val Single submitter ⚠
p.Ile997Ser Single submitter ⚠
p.Ile997Val Single submitter ⚠
p.Leu1023Val Single submitter ⚠
p.Leu1140Pro Single submitter ⚠
p.Leu1163Phe Single submitter ⚠
p.Leu1231Phe Single submitter
p.Leu1323Ile Single submitter ⚠
p.Leu132Met Single submitter ⚠
p.Leu235Val Single submitter ⚠
p.Leu274Val Single submitter ⚠
p.Leu540Phe Single submitter ⚠
p.Leu644Val Single submitter ⚠
p.Leu74Arg Single submitter ⚠
p.Leu898His Single submitter ⚠
p.Lys1101Glu Single submitter ⚠
p.Lys1125Arg Single submitter ⚠
p.Lys1353Glu Single submitter ⚠
p.Lys189Arg Single submitter ⚠
p.Lys18Asn Single submitter ⚠
p.Lys243Arg Single submitter ⚠
p.Lys374Glu Single submitter ⚠
p.Lys487Glu Single submitter
p.Lys790Asn Single submitter ⚠
p.Lys790Glu Single submitter ⚠
p.Lys840Gln Single submitter ⚠
p.Met286Leu Single submitter ⚠
p.Met368Val Single submitter ⚠
p.Met401Leu Single submitter ⚠
p.Met719Leu Single submitter ⚠
p.Met762Val Single submitter ⚠
p.Met836Ile Single submitter ⚠
p.Met860Lys Single submitter ⚠
p.Phe431Ser Single submitter ⚠
p.Phe513Val Single submitter
p.Pro1143Ala Single submitter ⚠
p.Pro1222Arg Single submitter ⚠
p.Pro1225Leu Single submitter ⚠
p.Pro1332Ser Single submitter ⚠
p.Pro309Thr Single submitter ⚠
p.Pro319Ser Single submitter ⚠
p.Pro33Leu Single submitter ⚠
p.Pro33Ser Single submitter ⚠
p.Pro340His Single submitter ⚠
p.Pro546Leu Single submitter ⚠
p.Pro556Leu Single submitter
p.Pro639Thr Single submitter ⚠
p.Pro66Gln Single submitter ⚠
p.Pro683Leu Single submitter ⚠
p.Ser1115Pro Single submitter ⚠
p.Ser1364Gly Single submitter ⚠
p.Ser200Ile Single submitter ⚠
p.Ser339Pro Single submitter ⚠
p.Ser657Ile Single submitter ⚠
p.Ser715Leu Single submitter ⚠
p.Ser723Phe Single submitter ⚠
p.Ser837Pro Single submitter ⚠
p.Thr1164Ala Single submitter ⚠
p.Thr1164Ser Single submitter ⚠
p.Thr1209Ala Single submitter ⚠
p.Thr1209Met Single submitter ⚠
p.Thr1215Ala Single submitter
p.Thr15Ala Single submitter ⚠
p.Thr552Ala Single submitter ⚠
p.Thr774Ala Single submitter ⚠
p.Trp205Ser Single submitter
p.Tyr1091Cys Single submitter ⚠
p.Tyr173Ser Single submitter ⚠
p.Tyr311His Single submitter ⚠
p.Tyr504Cys Single submitter ⚠
p.Tyr694His Single submitter ⚠
p.Tyr784Cys Single submitter ⚠
p.Tyr788Cys Single submitter
p.Tyr983Cys Single submitter ⚠
p.Val1024Ala Single submitter ⚠
p.Val1057Ile Single submitter ⚠
p.Val1276Phe Single submitter male infertility
p.Val1280Leu Single submitter ⚠
p.Val1280Met Single submitter ⚠
p.Val1297Ala Single submitter ⚠
p.Val150Leu Single submitter ⚠
p.Val256Ile Single submitter ⚠
p.Val281Leu Single submitter ⚠
p.Val390Gly Single submitter ⚠
p.Val415Phe Single submitter male infertility ⚠
p.Val538Glu Single submitter ⚠
p.Val603Ile Single submitter ⚠
p.Val612Ile Single submitter ⚠
p.Val764Glu Single submitter ⚠
p.Val814Met Single submitter ⚠
p.Val862Ile Single submitter ⚠
p.Val978Ile Single submitter ⚠
p.Val981Ile Single submitter ⚠
p.Cys98Gly No assertion criteria ⚠