PRDM9 — 170 ClinVar variants
All ClinVar germline PRDM9 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 145 flagged for review →
3 Pathogenic · 11 Benign · 1 Benign/Likely benign · 19 Likely benign · 136 Uncertain significance
Full PRDM9 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 145
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.
-
PRDM9 p.Ile213Ser
Pathogenic
Single submitter
Genetic non-acquired premature ovarian failure
-
PRDM9 p.Lys226Met
Pathogenic
Single submitter
Genetic non-acquired premature ovarian failure
Predictors lean, ClinVar uncertain 41
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- PRDM9 p.Ala122Ser Uncertain significance Single submitter
- PRDM9 p.Arg459Lys Uncertain significance Single submitter
- PRDM9 p.Arg52Lys Uncertain significance Single submitter
- PRDM9 p.Asp443Asn Uncertain significance Single submitter
- PRDM9 p.Cys208Tyr Uncertain significance Single submitter
- PRDM9 p.Cys431Tyr Uncertain significance Single submitter
- PRDM9 p.Cys610Ser Uncertain significance Single submitter
- PRDM9 p.Cys862Phe Uncertain significance Single submitter
- PRDM9 p.Gln437Arg Uncertain significance Single submitter
- PRDM9 p.Gln7Arg Uncertain significance Single submitter
- PRDM9 p.Glu177Ala Uncertain significance Single submitter
- PRDM9 p.Glu19Lys Uncertain significance Single submitter
- PRDM9 p.Glu408Asp Uncertain significance Single submitter
- PRDM9 p.Glu471Lys Uncertain significance Single submitter
- PRDM9 p.Glu9Gly Uncertain significance Single submitter
- PRDM9 p.Gly257Trp Uncertain significance Single submitter
- PRDM9 p.Gly370Arg Uncertain significance Single submitter
- PRDM9 p.Gly433Arg Uncertain significance Single submitter
- PRDM9 p.Gly433Glu Uncertain significance Single submitter
- PRDM9 p.Gly515Glu Uncertain significance Single submitter
- PRDM9 p.Gly614Arg Uncertain significance Single submitter
- PRDM9 p.Gly670Arg Uncertain significance Single submitter
- PRDM9 p.His574Tyr Uncertain significance Single submitter
- PRDM9 p.His626Gln Uncertain significance Single submitter
- PRDM9 p.Ile280Val Uncertain significance Single submitter
- PRDM9 p.Ile569Leu Uncertain significance Single submitter
- PRDM9 p.Lys384Arg Uncertain significance Single submitter
- PRDM9 p.Met106Lys Uncertain significance Single submitter
- PRDM9 p.Met119Leu Uncertain significance Single submitter
- PRDM9 p.Met207Ile Uncertain significance Single submitter
- PRDM9 p.Met494Arg Uncertain significance Single submitter
- PRDM9 p.Met74Val Uncertain significance Single submitter
- PRDM9 p.Phe513Leu Uncertain significance Single submitter
- PRDM9 p.Ser128Ala Uncertain significance Single submitter
- PRDM9 p.Ser155Ala Uncertain significance Single submitter
- PRDM9 p.Ser486Arg Uncertain significance Single submitter
- PRDM9 p.Thr96Ile Uncertain significance Single submitter
- PRDM9 p.Trp315Gly Uncertain significance Single submitter
- PRDM9 p.Tyr291Ser Uncertain significance Single submitter
- PRDM9 p.Val516Ile Uncertain significance Single submitter
- PRDM9 p.Val535Ala Uncertain significance Single submitter
Predictors split 102
The independent predictors disagree with each other — read with care.
- PRDM9 p.Thr681Ser Benign/Likely benign Multiple submitters
- PRDM9 p.Ala41Ser Uncertain significance Single submitter
- PRDM9 p.Arg113Cys Uncertain significance Single submitter
- PRDM9 p.Arg237Leu Uncertain significance Single submitter
- PRDM9 p.Arg323Trp Uncertain significance Single submitter
- PRDM9 p.Arg409His Uncertain significance Single submitter
- PRDM9 p.Arg559Gln Uncertain significance Single submitter
- PRDM9 p.Arg559Trp Uncertain significance Single submitter
- PRDM9 p.Arg647Gln Likely benign Single submitter
- PRDM9 p.Arg667Lys Uncertain significance Single submitter
- PRDM9 p.Arg684Lys Uncertain significance Single submitter
- PRDM9 p.Arg699Gln Uncertain significance Single submitter
- PRDM9 p.Arg70Gln Uncertain significance Single submitter
- PRDM9 p.Arg712Lys Uncertain significance Single submitter
- PRDM9 p.Arg712Ser Uncertain significance Single submitter
- PRDM9 p.Arg737Ser Likely benign Single submitter
- PRDM9 p.Arg751Lys Uncertain significance Single submitter
- PRDM9 p.Arg755Pro Uncertain significance Single submitter
- PRDM9 p.Arg783Trp Uncertain significance Single submitter
- PRDM9 p.Arg842Leu Uncertain significance Single submitter
- PRDM9 p.Arg867Gly Uncertain significance Single submitter
- PRDM9 p.Arg872Thr Uncertain significance Single submitter
- PRDM9 p.Asn57Ser Uncertain significance Single submitter
- PRDM9 p.Asn843Ser Uncertain significance Single submitter
- PRDM9 p.Asp324Glu Uncertain significance Single submitter
- PRDM9 p.Asp92Tyr Uncertain significance Single submitter
- PRDM9 p.Cys393Arg Uncertain significance Single submitter
- PRDM9 p.Gln255His Uncertain significance Single submitter
- PRDM9 p.Gln543Arg Uncertain significance Single submitter
- PRDM9 p.Gln571Pro Uncertain significance Single submitter
- PRDM9 p.Gln599Arg Uncertain significance Single submitter
- PRDM9 p.Gln627Pro Uncertain significance Single submitter
- PRDM9 p.Gln767Arg Uncertain significance Single submitter
- PRDM9 p.Glu13Gly Uncertain significance Single submitter
- PRDM9 p.Glu185Lys Uncertain significance Single submitter
- PRDM9 p.Glu193Lys Uncertain significance Single submitter
- PRDM9 p.Glu303Lys Uncertain significance Single submitter
- PRDM9 p.Glu47Gly Uncertain significance Single submitter
- PRDM9 p.Glu689Lys Uncertain significance Single submitter
- PRDM9 p.Glu696Gly Uncertain significance Single submitter
- PRDM9 p.Glu752Asp Uncertain significance Single submitter
- PRDM9 p.Glu773Asp Uncertain significance Single submitter
- PRDM9 p.Glu89Lys Uncertain significance Single submitter
- PRDM9 p.Gly188Arg Uncertain significance Single submitter
- PRDM9 p.Gly188Cys Uncertain significance Single submitter
- PRDM9 p.Gly350Asp Uncertain significance Single submitter
- PRDM9 p.Gly362Ser Uncertain significance Single submitter
- PRDM9 p.Gly588Ala Uncertain significance Single submitter
- PRDM9 p.Gly588Cys Uncertain significance Single submitter
- PRDM9 p.Gly632Val Uncertain significance Single submitter
- PRDM9 p.Gly698Arg Uncertain significance Single submitter
- PRDM9 p.Gly700Asp Uncertain significance Single submitter
- PRDM9 p.Gly840Ser Uncertain significance Single submitter
- PRDM9 p.His189Leu Uncertain significance Single submitter
- PRDM9 p.His219Gln Uncertain significance Single submitter
- PRDM9 p.His336Gln Uncertain significance Single submitter
- PRDM9 p.Ile295Val Uncertain significance Single submitter
- PRDM9 p.Leu258Phe Uncertain significance Single submitter
- PRDM9 p.Leu595Phe Uncertain significance Single submitter
- PRDM9 p.Leu875His Uncertain significance Single submitter
- PRDM9 p.Lys732Thr Uncertain significance Single submitter
- PRDM9 p.Lys830Glu Uncertain significance Single submitter
- PRDM9 p.Phe561Leu Uncertain significance Single submitter
- PRDM9 p.Phe645Ile Uncertain significance Single submitter
- PRDM9 p.Phe869Ile Uncertain significance Single submitter
- PRDM9 p.Pro635Ala Uncertain significance Single submitter
- PRDM9 p.Pro635His Uncertain significance Single submitter
- PRDM9 p.Pro719Ala Uncertain significance Single submitter
- PRDM9 p.Ser593Ala Uncertain significance Single submitter
- PRDM9 p.Ser621Ala Uncertain significance Single submitter
- PRDM9 p.Ser649Leu Uncertain significance Single submitter
- PRDM9 p.Ser730Cys Uncertain significance Single submitter
- PRDM9 p.Ser793Gly Uncertain significance Single submitter
- PRDM9 p.Ser817Pro Uncertain significance Single submitter
- PRDM9 p.Thr223Ile Uncertain significance Single submitter
- PRDM9 p.Thr575Ile Uncertain significance Single submitter
- PRDM9 p.Thr601Ile Uncertain significance Single submitter
- PRDM9 p.Thr603Lys Uncertain significance Single submitter
- PRDM9 p.Thr631Pro Uncertain significance Single submitter
- PRDM9 p.Thr659Ala Uncertain significance Single submitter
- PRDM9 p.Thr659Ile Uncertain significance Single submitter
- PRDM9 p.Thr681Ala Uncertain significance Single submitter
- PRDM9 p.Thr741Lys Uncertain significance Single submitter
- PRDM9 p.Thr825Ala Uncertain significance Single submitter
- PRDM9 p.Tyr191Cys Uncertain significance Single submitter
- PRDM9 p.Tyr51Cys Uncertain significance Single submitter
- PRDM9 p.Tyr58Cys Uncertain significance Single submitter
- PRDM9 p.Tyr636Phe Likely benign Single submitter
- PRDM9 p.Tyr692Ser Uncertain significance Single submitter
- PRDM9 p.Tyr776Cys Uncertain significance Single submitter
- PRDM9 p.Tyr804Ser Uncertain significance Single submitter
- PRDM9 p.Tyr860His Uncertain significance Single submitter
- PRDM9 p.Tyr860Ser Uncertain significance Single submitter
- PRDM9 p.Val194Ile Uncertain significance Single submitter
- PRDM9 p.Val230Met Uncertain significance Single submitter
- PRDM9 p.Val407Ala Uncertain significance Single submitter
- PRDM9 p.Val650Asp Uncertain significance Single submitter
- PRDM9 p.Val777Leu Uncertain significance Single submitter
- PRDM9 p.Val805Ala Uncertain significance Single submitter
-
PRDM9 p.Arg323Gln
Likely benign
No assertion criteria
PRDM9-related disorder
-
PRDM9 p.Lys232Asn
Likely benign
No assertion criteria
PRDM9-related disorder
-
PRDM9 p.Thr709Ser
Likely benign
No assertion criteria
PRDM9-related disorder
All PRDM9 variants
Pathogenic 3
- p.Arg77Ter Single submitter Genetic non-acquired premature ovarian failure
- p.Ile213Ser Single submitter Genetic non-acquired premature ovarian failure ⚠
- p.Lys226Met Single submitter Genetic non-acquired premature ovarian failure ⚠
Benign 11
- c.301+67A>G Multiple submitters
- c.509-41C>T Multiple submitters
- c.883-52C>T Multiple submitters
- c.*125G>A Multiple submitters
- c.*37A>G Multiple submitters
- p.Asp30= Multiple submitters
- p.Gly144= Multiple submitters
- c.1145-188T>A Single submitter
- c.301+185G>T Single submitter
- c.301+43_301+44del Single submitter
- c.301+44del Single submitter
Benign/Likely benign 1
- p.Thr681Ser Multiple submitters ⚠
Likely benign 19
- p.Asn790His Multiple submitters
- p.Arg447Cys Single submitter
- p.Arg647Gln Single submitter ⚠
- p.Arg737Ser Single submitter ⚠
- p.Ile569Asn Single submitter
- p.Met106Val Single submitter
- p.Ser814Arg Single submitter
- p.Thr681= Single submitter
- p.Trp468Arg Single submitter
- p.Tyr636Phe Single submitter ⚠
- p.Tyr832= Single submitter
- p.Val331= Single submitter
- p.Val861= Single submitter
- p.Arg323Gln No assertion criteria PRDM9-related disorder ⚠
- p.Arg342Gly No assertion criteria PRDM9-related disorder
- p.Ile339Asn No assertion criteria PRDM9-related disorder
- p.Lys232Asn No assertion criteria PRDM9-related disorder ⚠
- p.Thr709= No assertion criteria PRDM9-related disorder
- p.Thr709Ser No assertion criteria PRDM9-related disorder ⚠
Uncertain significance 136
- p.Ala122Ser Single submitter ⚠
- p.Ala41Ser Single submitter ⚠
- p.Arg113Cys Single submitter ⚠
- p.Arg237Leu Single submitter ⚠
- p.Arg323Trp Single submitter ⚠
- p.Arg409His Single submitter ⚠
- p.Arg459Lys Single submitter ⚠
- p.Arg52Lys Single submitter ⚠
- p.Arg559Gln Single submitter ⚠
- p.Arg559Trp Single submitter ⚠
- p.Arg667Lys Single submitter ⚠
- p.Arg684Lys Single submitter ⚠
- p.Arg699Gln Single submitter ⚠
- p.Arg70Gln Single submitter ⚠
- p.Arg712Lys Single submitter ⚠
- p.Arg712Ser Single submitter ⚠
- p.Arg751Lys Single submitter ⚠
- p.Arg755Pro Single submitter ⚠
- p.Arg783Trp Single submitter ⚠
- p.Arg842Leu Single submitter ⚠
- p.Arg867Gly Single submitter ⚠
- p.Arg872Thr Single submitter ⚠
- p.Asn57Ser Single submitter ⚠
- p.Asn843Ser Single submitter ⚠
- p.Asp324Glu Single submitter ⚠
- p.Asp443Asn Single submitter ⚠
- p.Asp92Tyr Single submitter ⚠
- p.Cys208Tyr Single submitter ⚠
- p.Cys393Arg Single submitter ⚠
- p.Cys431Tyr Single submitter ⚠
- p.Cys610Ser Single submitter ⚠
- p.Cys862Phe Single submitter ⚠
- p.Gln255His Single submitter ⚠
- p.Gln437Arg Single submitter ⚠
- p.Gln543Arg Single submitter ⚠
- p.Gln571Pro Single submitter ⚠
- p.Gln599Arg Single submitter ⚠
- p.Gln627Pro Single submitter ⚠
- p.Gln767Arg Single submitter ⚠
- p.Gln7Arg Single submitter ⚠
- p.Glu13Gly Single submitter ⚠
- p.Glu177Ala Single submitter ⚠
- p.Glu185Lys Single submitter ⚠
- p.Glu193Lys Single submitter ⚠
- p.Glu19Lys Single submitter ⚠
- p.Glu303Lys Single submitter ⚠
- p.Glu408Asp Single submitter ⚠
- p.Glu471Lys Single submitter ⚠
- p.Glu47Gly Single submitter ⚠
- p.Glu689Lys Single submitter ⚠
- p.Glu696Gly Single submitter ⚠
- p.Glu752Asp Single submitter ⚠
- p.Glu773Asp Single submitter ⚠
- p.Glu89Lys Single submitter ⚠
- p.Glu9Gly Single submitter ⚠
- p.Gly188Arg Single submitter ⚠
- p.Gly188Cys Single submitter ⚠
- p.Gly257Trp Single submitter ⚠
- p.Gly350Asp Single submitter ⚠
- p.Gly362Ser Single submitter ⚠
- p.Gly370Arg Single submitter ⚠
- p.Gly433Arg Single submitter ⚠
- p.Gly433Glu Single submitter ⚠
- p.Gly515Glu Single submitter ⚠
- p.Gly588Ala Single submitter ⚠
- p.Gly588Cys Single submitter ⚠
- p.Gly614Arg Single submitter ⚠
- p.Gly632Val Single submitter ⚠
- p.Gly670Arg Single submitter ⚠
- p.Gly698Arg Single submitter ⚠
- p.Gly700Asp Single submitter ⚠
- p.Gly840Ser Single submitter ⚠
- p.His189Leu Single submitter ⚠
- p.His219Gln Single submitter ⚠
- p.His336Gln Single submitter ⚠
- p.His574Tyr Single submitter ⚠
- p.His626Gln Single submitter ⚠
- p.Ile280Val Single submitter ⚠
- p.Ile295Val Single submitter ⚠
- p.Ile569Leu Single submitter ⚠
- p.Leu258Phe Single submitter ⚠
- p.Leu595Phe Single submitter ⚠
- p.Leu875His Single submitter ⚠
- p.Lys384Arg Single submitter ⚠
- p.Lys732Thr Single submitter ⚠
- p.Lys830Glu Single submitter ⚠
- p.Met106Lys Single submitter ⚠
- p.Met119Leu Single submitter ⚠
- p.Met207Ile Single submitter ⚠
- p.Met494Arg Single submitter ⚠
- p.Met74Val Single submitter ⚠
- p.Phe513Leu Single submitter ⚠
- p.Phe561Leu Single submitter ⚠
- p.Phe645Ile Single submitter ⚠
- p.Phe869Ile Single submitter ⚠
- p.Pro635Ala Single submitter ⚠
- p.Pro635His Single submitter ⚠
- p.Pro719Ala Single submitter ⚠
- p.Ser128Ala Single submitter ⚠
- p.Ser155Ala Single submitter ⚠
- p.Ser486Arg Single submitter ⚠
- p.Ser593Ala Single submitter ⚠
- p.Ser621Ala Single submitter ⚠
- p.Ser649Leu Single submitter ⚠
- p.Ser730Cys Single submitter ⚠
- p.Ser793Gly Single submitter ⚠
- p.Ser817Pro Single submitter ⚠
- p.Thr223Ile Single submitter ⚠
- p.Thr575Ile Single submitter ⚠
- p.Thr601Ile Single submitter ⚠
- p.Thr603Lys Single submitter ⚠
- p.Thr631Pro Single submitter ⚠
- p.Thr659Ala Single submitter ⚠
- p.Thr659Ile Single submitter ⚠
- p.Thr681Ala Single submitter ⚠
- p.Thr741Lys Single submitter ⚠
- p.Thr825Ala Single submitter ⚠
- p.Thr96Ile Single submitter ⚠
- p.Trp315Gly Single submitter ⚠
- p.Tyr191Cys Single submitter ⚠
- p.Tyr291Ser Single submitter ⚠
- p.Tyr51Cys Single submitter ⚠
- p.Tyr58Cys Single submitter ⚠
- p.Tyr692Ser Single submitter ⚠
- p.Tyr776Cys Single submitter ⚠
- p.Tyr804Ser Single submitter ⚠
- p.Tyr860His Single submitter ⚠
- p.Tyr860Ser Single submitter ⚠
- p.Val194Ile Single submitter ⚠
- p.Val230Met Single submitter ⚠
- p.Val407Ala Single submitter ⚠
- p.Val516Ile Single submitter ⚠
- p.Val535Ala Single submitter ⚠
- p.Val650Asp Single submitter ⚠
- p.Val777Leu Single submitter ⚠
- p.Val805Ala Single submitter ⚠