PER2 — 235 ClinVar variants
All ClinVar germline PER2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 155 flagged for review →
2 Pathogenic · 3 Conflicting · 15 Benign · 56 Likely benign · 159 Uncertain significance
Full PER2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 155
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.
-
PER2 p.Ser662Gly
Pathogenic
No assertion criteria
advanced sleep phase syndrome 1
Predictors agree, ClinVar conflicts 3
ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.
- PER2 p.Ala1206Pro Conflicting Single submitter
-
PER2 p.Asn598Ser
Conflicting
Single submitter
advanced sleep phase syndrome 1
- PER2 p.Pro72Leu Conflicting Single submitter
Predictors lean, ClinVar uncertain 136
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
-
PER2 p.Arg401His
Uncertain significance
Multiple submitters
advanced sleep phase syndrome 1
- PER2 p.Ala1160Val Uncertain significance Single submitter
- PER2 p.Ala128Asp Uncertain significance Single submitter
- PER2 p.Ala212Thr Uncertain significance Single submitter
- PER2 p.Ala572Val Uncertain significance Single submitter
-
PER2 p.Ala5Gly
Uncertain significance
Single submitter
advanced sleep phase syndrome 1
- PER2 p.Ala5Val Uncertain significance Single submitter
- PER2 p.Ala601Thr Uncertain significance Single submitter
- PER2 p.Ala632Thr Uncertain significance Single submitter
- PER2 p.Ala775Thr Uncertain significance Single submitter
- PER2 p.Ala819Ser Uncertain significance Single submitter
-
PER2 p.Ala848Thr
Uncertain significance
Single submitter
advanced sleep phase syndrome 1
-
PER2 p.Ala874Thr
Uncertain significance
Single submitter
advanced sleep phase syndrome 1
- PER2 p.Ala880Asp Uncertain significance Single submitter
- PER2 p.Ala999Val Uncertain significance Single submitter
- PER2 p.Arg273Cys Uncertain significance Single submitter
- PER2 p.Arg277Trp Uncertain significance Single submitter
- PER2 p.Arg285Cys Uncertain significance Single submitter
- PER2 p.Arg299Trp Uncertain significance Single submitter
- PER2 p.Arg403Gln Uncertain significance Single submitter
- PER2 p.Arg510Cys Uncertain significance Single submitter
- PER2 p.Arg51Gln Uncertain significance Single submitter
- PER2 p.Arg622Gln Uncertain significance Single submitter
- PER2 p.Arg801Trp Uncertain significance Single submitter
- PER2 p.Arg966Gln Uncertain significance Single submitter
- PER2 p.Arg984Ser Uncertain significance Single submitter
- PER2 p.Asn1111Lys Uncertain significance Single submitter
- PER2 p.Asn151Ser Uncertain significance Single submitter
- PER2 p.Asn189Asp Uncertain significance Single submitter
- PER2 p.Asn282Tyr Uncertain significance Single submitter
- PER2 p.Asn488Ser Uncertain significance Single submitter
- PER2 p.Asn91Ser Uncertain significance Single submitter
- PER2 p.Asp100Asn Uncertain significance Single submitter
- PER2 p.Asp1021Asn Uncertain significance Single submitter
- PER2 p.Asp1039Gly Uncertain significance Single submitter
- PER2 p.Asp191Asn Uncertain significance Single submitter
- PER2 p.Cys47Arg Uncertain significance Single submitter
- PER2 p.Cys962Arg Uncertain significance Single submitter
- PER2 p.Gln262Pro Uncertain significance Single submitter
- PER2 p.Glu1001Gly Uncertain significance Single submitter
- PER2 p.Glu1125Gly Uncertain significance Single submitter
- PER2 p.Glu559Val Uncertain significance Single submitter
- PER2 p.Glu699Lys Uncertain significance Single submitter
- PER2 p.Glu6Gly Uncertain significance Single submitter
- PER2 p.Glu940Lys Uncertain significance Single submitter
- PER2 p.Gly237Asp Uncertain significance Single submitter
- PER2 p.Gly697Trp Uncertain significance Single submitter
- PER2 p.Gly706Val Uncertain significance Single submitter
- PER2 p.Gly974Asp Uncertain significance Single submitter
- PER2 p.Gly974Ser Uncertain significance Single submitter
-
PER2 p.His1126Tyr
Uncertain significance
Single submitter
advanced sleep phase syndrome 1
- PER2 p.His41Arg Uncertain significance Single submitter
- PER2 p.His41Gln Uncertain significance Single submitter
- PER2 p.His456Pro Uncertain significance Single submitter
- PER2 p.His531Arg Uncertain significance Single submitter
- PER2 p.Ile429Val Uncertain significance Single submitter
- PER2 p.Leu1077Pro Uncertain significance Single submitter
- PER2 p.Leu563Pro Uncertain significance Single submitter
- PER2 p.Leu616Pro Uncertain significance Single submitter
- PER2 p.Leu65Pro Uncertain significance Single submitter
- PER2 p.Leu666Pro Uncertain significance Single submitter
- PER2 p.Leu778Arg Uncertain significance Single submitter
- PER2 p.Lys1101Thr Uncertain significance Single submitter
- PER2 p.Lys126Arg Uncertain significance Single submitter
- PER2 p.Lys203Arg Uncertain significance Single submitter
- PER2 p.Lys297Glu Uncertain significance Single submitter
- PER2 p.Lys552Asn Uncertain significance Single submitter
- PER2 p.Lys683Arg Uncertain significance Single submitter
- PER2 p.Lys736Asn Uncertain significance Single submitter
- PER2 p.Lys750Gln Uncertain significance Single submitter
- PER2 p.Lys803Arg Uncertain significance Single submitter
- PER2 p.Lys87Asn Uncertain significance Single submitter
- PER2 p.Met1121Ile Uncertain significance Single submitter
- PER2 p.Met1121Lys Uncertain significance Single submitter
- PER2 p.Met1140Ile Uncertain significance Single submitter
- PER2 p.Met291Val Uncertain significance Single submitter
- PER2 p.Met558Lys Uncertain significance Single submitter
- PER2 p.Met690Val Uncertain significance Single submitter
- PER2 p.Met907Ile Uncertain significance Single submitter
- PER2 p.Met941Ile Uncertain significance Single submitter
- PER2 p.Met973Val Uncertain significance Single submitter
- PER2 p.Phe393Leu Uncertain significance Single submitter
- PER2 p.Phe745Ser Uncertain significance Single submitter
- PER2 p.Phe924Ser Uncertain significance Single submitter
- PER2 p.Phe924Val Uncertain significance Single submitter
- PER2 p.Phe949Leu Uncertain significance Single submitter
- PER2 p.Pro171Ser Uncertain significance Single submitter
- PER2 p.Pro328Thr Uncertain significance Single submitter
- PER2 p.Pro549Ala Uncertain significance Single submitter
- PER2 p.Pro628Ala Uncertain significance Single submitter
- PER2 p.Pro657Leu Uncertain significance Single submitter
- PER2 p.Pro684Leu Uncertain significance Single submitter
- PER2 p.Pro707Leu Uncertain significance Single submitter
- PER2 p.Pro71Ser Uncertain significance Single submitter
- PER2 p.Pro72Ser Uncertain significance Single submitter
- PER2 p.Pro770Ala Uncertain significance Single submitter
- PER2 p.Pro770Thr Uncertain significance Single submitter
- PER2 p.Pro851Ser Uncertain significance Single submitter
- PER2 p.Pro868Ser Uncertain significance Single submitter
- PER2 p.Pro869Leu Uncertain significance Single submitter
- PER2 p.Pro895Ser Uncertain significance Single submitter
- PER2 p.Pro929Ala Uncertain significance Single submitter
- PER2 p.Pro935Leu Uncertain significance Single submitter
- PER2 p.Pro950Ser Uncertain significance Single submitter
- PER2 p.Pro963Leu Uncertain significance Single submitter
- PER2 p.Ser103Leu Uncertain significance Single submitter
- PER2 p.Ser1089Gly Uncertain significance Single submitter
- PER2 p.Ser12Asn Uncertain significance Single submitter
- PER2 p.Ser180Asn Uncertain significance Single submitter
- PER2 p.Ser35Gly Uncertain significance Single submitter
- PER2 p.Ser61Gly Uncertain significance Single submitter
- PER2 p.Ser665Pro Uncertain significance Single submitter
- PER2 p.Ser756Phe Uncertain significance Single submitter
- PER2 p.Ser766Thr Uncertain significance Single submitter
- PER2 p.Ser810Asn Uncertain significance Single submitter
- PER2 p.Ser875Arg Uncertain significance Single submitter
- PER2 p.Ser915Leu Uncertain significance Single submitter
- PER2 p.Ser954Leu Uncertain significance Single submitter
- PER2 p.Ser987Leu Uncertain significance Single submitter
- PER2 p.Ser99Asn Uncertain significance Single submitter
- PER2 p.Thr1037Ile Uncertain significance Single submitter
- PER2 p.Thr1119Pro Uncertain significance Single submitter
- PER2 p.Thr1150Met Uncertain significance Single submitter
- PER2 p.Thr1196Met Uncertain significance Single submitter
- PER2 p.Thr134Met Uncertain significance Single submitter
- PER2 p.Thr811Asn Uncertain significance Single submitter
- PER2 p.Thr94Ile Uncertain significance Single submitter
- PER2 p.Tyr395His Uncertain significance Single submitter
- PER2 p.Val1131Ile Uncertain significance Single submitter
- PER2 p.Val170Leu Uncertain significance Single submitter
- PER2 p.Val181Ile Uncertain significance Single submitter
- PER2 p.Val474Leu Uncertain significance Single submitter
- PER2 p.Val565Ile Uncertain significance Single submitter
-
PER2 p.Val844Met
Uncertain significance
Single submitter
advanced sleep phase syndrome 1
- PER2 p.Val858Met Uncertain significance Single submitter
- PER2 p.Val865Met Uncertain significance Single submitter
Predictors split 15
The independent predictors disagree with each other — read with care.
- PER2 p.Glu184Ala Uncertain significance Multiple submitters
- PER2 p.Arg290Cys Uncertain significance Single submitter
- PER2 p.Arg290His Uncertain significance Single submitter
- PER2 p.Arg403Trp Uncertain significance Single submitter
- PER2 p.Asn404Ser Uncertain significance Single submitter
- PER2 p.Gly489Glu Uncertain significance Single submitter
- PER2 p.His121Pro Uncertain significance Single submitter
- PER2 p.Leu295Val Uncertain significance Single submitter
- PER2 p.Leu367Phe Uncertain significance Single submitter
- PER2 p.Met1149Ile Uncertain significance Single submitter
-
PER2 p.Pro988Leu
Uncertain significance
Single submitter
advanced sleep phase syndrome 1
- PER2 p.Ser477Cys Uncertain significance Single submitter
- PER2 p.Ser95Arg Uncertain significance Single submitter
- PER2 p.Thr364Ile Uncertain significance Single submitter
- PER2 p.Val590Leu Uncertain significance Single submitter
All PER2 variants
Pathogenic 2
- p.Leu199fs Single submitter advanced sleep phase syndrome 1
- p.Ser662Gly No assertion criteria advanced sleep phase syndrome 1 ⚠
Conflicting classifications of pathogenicity 3
- p.Ala1206Pro Single submitter ⚠
- p.Asn598Ser Single submitter advanced sleep phase syndrome 1 ⚠
- p.Pro72Leu Single submitter ⚠
Benign 15
- p.Ala655= Multiple submitters
- p.Arg401Cys Multiple submitters
- p.Phe393= Multiple submitters
- p.Pro822= Multiple submitters
- p.Ser180= Multiple submitters
- p.Ser665= Multiple submitters
- p.Thr134= Multiple submitters
- p.Val729Ile Multiple submitters
- p.Ala861Val Single submitter
- p.Leu603= Single submitter
- p.Lys226= Single submitter
- p.Ser103= Single submitter
- p.Tyr140= Single submitter
- p.Ala664= No assertion criteria PER2-related disorder
- p.Ala664Val No assertion criteria PER2-related disorder
Likely benign 56
- p.Arg820= Multiple submitters
- p.Cys1084Arg Multiple submitters
- p.His476Asn Multiple submitters
- c.1542+15A>G Single submitter
- c.1627+13dup Single submitter
- c.1775+4T>G Single submitter
- c.825-5C>T Single submitter
- p.Ala1012Thr Single submitter
- p.Ala225= Single submitter
- p.Ala695Val Single submitter
- p.Ala705Val Single submitter
- p.Ala732= Single submitter
- p.Arg1178= Single submitter
- p.Arg299Gln Single submitter
- p.Arg423= Single submitter
- p.Arg617= Single submitter
- p.Arg773Gln Single submitter
- p.Asp100Glu Single submitter
- p.Asp300Glu Single submitter
- p.Cys217Tyr Single submitter
- p.Cys309= Single submitter
- p.Cys841= Single submitter
- p.Glu1075Asp Single submitter
- p.Gly320Arg Single submitter autism spectrum disorder
- p.Gly658Ser Single submitter
- p.Gly768= Single submitter
- p.His631= Single submitter
- p.Ile418= Single submitter
- p.Leu157= Single submitter
- p.Leu993= Single submitter
- p.Lys682= Single submitter
- p.Lys800Arg Single submitter autism spectrum disorder
- p.Met1007Thr Single submitter
- p.Phe754Leu Single submitter
- p.Pro365= Single submitter
- p.Pro637= Single submitter
- p.Pro72= Single submitter
- p.Pro8Leu Single submitter
- p.Ser275= Single submitter
- p.Thr953= Single submitter
- p.Val1205Met Single submitter
- c.1153+10C>G No assertion criteria PER2-related disorder
- c.1542+4C>T No assertion criteria PER2-related disorder
- c.1775+4T>C No assertion criteria PER2-related disorder
- c.448+8G>T No assertion criteria PER2-related disorder
- p.Ala695= No assertion criteria PER2-related disorder
- p.Gln545= No assertion criteria PER2-related disorder
- p.Glu315= No assertion criteria PER2-related disorder
- p.Gly658= No assertion criteria PER2-related disorder
- p.Lys539= No assertion criteria PER2-related disorder
- p.Phe949Tyr No assertion criteria PER2-related disorder
- p.Pro816= No assertion criteria PER2-related disorder
- p.Ser971_Pro979del No assertion criteria PER2-related disorder
- p.Thr1004= No assertion criteria PER2-related disorder
- p.Tyr482= No assertion criteria PER2-related disorder
- p.Val844Leu No assertion criteria PER2-related disorder
Uncertain significance 159
- p.Arg401His Multiple submitters advanced sleep phase syndrome 1 ⚠
- p.Glu184Ala Multiple submitters ⚠
- c.293+1G>T Single submitter advanced sleep phase syndrome 1
- c.3275-1G>A Single submitter PER2-related disorder
- p.Ala1160Val Single submitter ⚠
- p.Ala128Asp Single submitter ⚠
- p.Ala212Thr Single submitter ⚠
- p.Ala572Val Single submitter ⚠
- p.Ala5Gly Single submitter advanced sleep phase syndrome 1 ⚠
- p.Ala5Val Single submitter ⚠
- p.Ala601Thr Single submitter ⚠
- p.Ala632Thr Single submitter ⚠
- p.Ala775Thr Single submitter ⚠
- p.Ala819Ser Single submitter ⚠
- p.Ala848Thr Single submitter advanced sleep phase syndrome 1 ⚠
- p.Ala874Thr Single submitter advanced sleep phase syndrome 1 ⚠
- p.Ala880Asp Single submitter ⚠
- p.Ala999Val Single submitter ⚠
- p.Arg273Cys Single submitter ⚠
- p.Arg277Trp Single submitter ⚠
- p.Arg285Cys Single submitter ⚠
- p.Arg290Cys Single submitter ⚠
- p.Arg290His Single submitter ⚠
- p.Arg299Trp Single submitter ⚠
- p.Arg403Gln Single submitter ⚠
- p.Arg403Trp Single submitter ⚠
- p.Arg510Cys Single submitter ⚠
- p.Arg51Gln Single submitter ⚠
- p.Arg622Gln Single submitter ⚠
- p.Arg801Trp Single submitter ⚠
- p.Arg966Gln Single submitter ⚠
- p.Arg984Ser Single submitter ⚠
- p.Asn1111Lys Single submitter ⚠
- p.Asn151Ser Single submitter ⚠
- p.Asn189Asp Single submitter ⚠
- p.Asn282Tyr Single submitter ⚠
- p.Asn404Ser Single submitter ⚠
- p.Asn488Ser Single submitter ⚠
- p.Asn91Ser Single submitter ⚠
- p.Asp100Asn Single submitter ⚠
- p.Asp1021Asn Single submitter ⚠
- p.Asp1039Gly Single submitter ⚠
- p.Asp191Asn Single submitter ⚠
- p.Asp31Val Single submitter
- p.Cys47Arg Single submitter ⚠
- p.Cys962Arg Single submitter ⚠
- p.Gln262Pro Single submitter ⚠
- p.Glu1001Gly Single submitter ⚠
- p.Glu1125Gly Single submitter ⚠
- p.Glu559Val Single submitter ⚠
- p.Glu699Lys Single submitter ⚠
- p.Glu6Gly Single submitter ⚠
- p.Glu940Lys Single submitter ⚠
- p.Gly237Asp Single submitter ⚠
- p.Gly489Glu Single submitter ⚠
- p.Gly697Trp Single submitter ⚠
- p.Gly706Val Single submitter ⚠
- p.Gly974Asp Single submitter ⚠
- p.Gly974Ser Single submitter ⚠
- p.His1126Tyr Single submitter advanced sleep phase syndrome 1 ⚠
- p.His121Pro Single submitter ⚠
- p.His41Arg Single submitter ⚠
- p.His41Gln Single submitter ⚠
- p.His456Pro Single submitter ⚠
- p.His531Arg Single submitter ⚠
- p.Ile429Val Single submitter ⚠
- p.Leu1077Pro Single submitter ⚠
- p.Leu295Val Single submitter ⚠
- p.Leu367Phe Single submitter ⚠
- p.Leu379Pro Single submitter
- p.Leu563Pro Single submitter ⚠
- p.Leu616Pro Single submitter ⚠
- p.Leu65Pro Single submitter ⚠
- p.Leu666Pro Single submitter ⚠
- p.Leu778Arg Single submitter ⚠
- p.Lys109Asn Single submitter
- p.Lys1101Thr Single submitter ⚠
- p.Lys126Arg Single submitter ⚠
- p.Lys203Arg Single submitter ⚠
- p.Lys297Glu Single submitter ⚠
- p.Lys552Asn Single submitter ⚠
- p.Lys683Arg Single submitter ⚠
- p.Lys736Asn Single submitter ⚠
- p.Lys750Gln Single submitter ⚠
- p.Lys803Arg Single submitter ⚠
- p.Lys87Asn Single submitter ⚠
- p.Met1121Ile Single submitter ⚠
- p.Met1121Lys Single submitter ⚠
- p.Met1140Ile Single submitter ⚠
- p.Met1149Ile Single submitter ⚠
- p.Met291Val Single submitter ⚠
- p.Met558Lys Single submitter ⚠
- p.Met690Val Single submitter ⚠
- p.Met907Ile Single submitter ⚠
- p.Met941Ile Single submitter ⚠
- p.Met973Val Single submitter ⚠
- p.Phe1179Tyr Single submitter
- p.Phe393Leu Single submitter ⚠
- p.Phe745Ser Single submitter ⚠
- p.Phe924Ser Single submitter ⚠
- p.Phe924Val Single submitter ⚠
- p.Phe949Leu Single submitter ⚠
- p.Pro171Ser Single submitter ⚠
- p.Pro328Thr Single submitter ⚠
- p.Pro473His Single submitter
- p.Pro549Ala Single submitter ⚠
- p.Pro628Ala Single submitter ⚠
- p.Pro657Leu Single submitter ⚠
- p.Pro684Leu Single submitter ⚠
- p.Pro707Leu Single submitter ⚠
- p.Pro71Ser Single submitter ⚠
- p.Pro72Ser Single submitter ⚠
- p.Pro770Ala Single submitter ⚠
- p.Pro770Thr Single submitter ⚠
- p.Pro851Ser Single submitter ⚠
- p.Pro868Ser Single submitter ⚠
- p.Pro869Leu Single submitter ⚠
- p.Pro895Ser Single submitter ⚠
- p.Pro929Ala Single submitter ⚠
- p.Pro935Leu Single submitter ⚠
- p.Pro950Ser Single submitter ⚠
- p.Pro963Leu Single submitter ⚠
- p.Pro988Leu Single submitter advanced sleep phase syndrome 1 ⚠
- p.Ser103Leu Single submitter ⚠
- p.Ser1089Gly Single submitter ⚠
- p.Ser12Asn Single submitter ⚠
- p.Ser180Asn Single submitter ⚠
- p.Ser35Gly Single submitter ⚠
- p.Ser426Tyr Single submitter
- p.Ser477Cys Single submitter ⚠
- p.Ser61Gly Single submitter ⚠
- p.Ser665Pro Single submitter ⚠
- p.Ser756Phe Single submitter ⚠
- p.Ser766Thr Single submitter ⚠
- p.Ser810Asn Single submitter ⚠
- p.Ser875Arg Single submitter ⚠
- p.Ser915Leu Single submitter ⚠
- p.Ser954Leu Single submitter ⚠
- p.Ser95Arg Single submitter ⚠
- p.Ser987Leu Single submitter ⚠
- p.Ser99Asn Single submitter ⚠
- p.Thr1037Ile Single submitter ⚠
- p.Thr1119Pro Single submitter ⚠
- p.Thr1150Met Single submitter ⚠
- p.Thr1196Met Single submitter ⚠
- p.Thr134Met Single submitter ⚠
- p.Thr364Ile Single submitter ⚠
- p.Thr811Asn Single submitter ⚠
- p.Thr94Ile Single submitter ⚠
- p.Tyr395His Single submitter ⚠
- p.Val1131Ile Single submitter ⚠
- p.Val170Leu Single submitter ⚠
- p.Val181Ile Single submitter ⚠
- p.Val474Leu Single submitter ⚠
- p.Val565Ile Single submitter ⚠
- p.Val590Leu Single submitter ⚠
- p.Val844Met Single submitter advanced sleep phase syndrome 1 ⚠
- p.Val858Met Single submitter ⚠
- p.Val865Met Single submitter ⚠