PER3 — 186 ClinVar variants
All ClinVar germline PER3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 126 flagged for review →
1 Pathogenic · 3 Likely pathogenic · 3 Conflicting · 8 Benign · 2 Benign/Likely benign · 42 Likely benign · 127 Uncertain significance
Full PER3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 126
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 2
ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.
-
PER3 p.His417Arg
Conflicting
Single submitter
advanced sleep phase syndrome 3
- PER3 p.Thr1049Ile Conflicting Single submitter
Predictors lean, ClinVar uncertain 108
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- PER3 p.Arg157His Uncertain significance Multiple submitters
-
PER3 p.Asn572Thr
Uncertain significance
Multiple submitters
advanced sleep phase syndrome 3
- PER3 p.Ala1050Val Uncertain significance Single submitter
- PER3 p.Ala105Val Uncertain significance Single submitter
- PER3 p.Ala1109Thr Uncertain significance Single submitter
- PER3 p.Ala122Thr Uncertain significance Single submitter
- PER3 p.Ala152Val Uncertain significance Single submitter
- PER3 p.Ala163Val Uncertain significance Single submitter
- PER3 p.Ala172Val Uncertain significance Single submitter
- PER3 p.Ala181Val Uncertain significance Single submitter
- PER3 p.Ala440Thr Uncertain significance Single submitter
- PER3 p.Ala627Val Uncertain significance Single submitter
- PER3 p.Ala92Gly Uncertain significance Single submitter
- PER3 p.Ala976Thr Uncertain significance Single submitter
- PER3 p.Arg1043Lys Uncertain significance Single submitter
- PER3 p.Arg1118Trp Uncertain significance Single submitter
- PER3 p.Arg1123His Uncertain significance Single submitter
- PER3 p.Arg1123Leu Uncertain significance Single submitter
- PER3 p.Arg12Leu Uncertain significance Single submitter
- PER3 p.Arg35Gly Uncertain significance Single submitter
- PER3 p.Arg378Gln Uncertain significance Single submitter
- PER3 p.Arg48Gly Uncertain significance Single submitter
- PER3 p.Arg494His Uncertain significance Single submitter
- PER3 p.Arg71Cys Uncertain significance Single submitter
- PER3 p.Arg85Cys Uncertain significance Single submitter
- PER3 p.Asn103Asp Uncertain significance Single submitter
- PER3 p.Asn192Ile Uncertain significance Single submitter
- PER3 p.Asn498Ser Uncertain significance Single submitter
- PER3 p.Asn81Ser Uncertain significance Single submitter
- PER3 p.Asn93Ser Uncertain significance Single submitter
- PER3 p.Asp289His Uncertain significance Single submitter
- PER3 p.Asp385Asn Uncertain significance Single submitter
- PER3 p.Asp532Tyr Uncertain significance Single submitter
- PER3 p.Asp78His Uncertain significance Single submitter
- PER3 p.Asp950Glu Uncertain significance Single submitter
- PER3 p.Asp950Val Uncertain significance Single submitter
- PER3 p.Gln1172Lys Uncertain significance Single submitter
- PER3 p.Gln1203Lys Uncertain significance Single submitter
- PER3 p.Gln34Arg Uncertain significance Single submitter
- PER3 p.Gln45Arg Uncertain significance Single submitter
- PER3 p.Gln45Lys Uncertain significance Single submitter
- PER3 p.Gln951Lys Uncertain significance Single submitter
- PER3 p.Glu1061Lys Uncertain significance Single submitter
- PER3 p.Glu1132Asp Uncertain significance Single submitter
- PER3 p.Glu149Gln Uncertain significance Single submitter
- PER3 p.Glu25Lys Uncertain significance Single submitter
- PER3 p.Gly1159Val Uncertain significance Single submitter
- PER3 p.Gly262Asp Uncertain significance Single submitter
- PER3 p.Gly970Ala Uncertain significance Single submitter
- PER3 p.His166Leu Uncertain significance Single submitter
- PER3 p.His240Asp Uncertain significance Single submitter
- PER3 p.Ile1078Met Uncertain significance Single submitter
- PER3 p.Ile1117Thr Uncertain significance Single submitter
- PER3 p.Ile1180Val Uncertain significance Single submitter
- PER3 p.Ile121Val Uncertain significance Single submitter
- PER3 p.Ile232Val Uncertain significance Single submitter
- PER3 p.Ile391Met Uncertain significance Single submitter
- PER3 p.Ile470Asn Uncertain significance Single submitter
- PER3 p.Leu1125Phe Uncertain significance Single submitter
- PER3 p.Leu1146Val Uncertain significance Single submitter
- PER3 p.Leu115Pro Uncertain significance Single submitter
- PER3 p.Leu253Val Uncertain significance Single submitter
- PER3 p.Leu296Val Uncertain significance Single submitter
- PER3 p.Leu411Pro Uncertain significance Single submitter
- PER3 p.Leu436Pro Uncertain significance Single submitter
- PER3 p.Leu533Met Uncertain significance Single submitter
- PER3 p.Leu80Phe Uncertain significance Single submitter
- PER3 p.Leu938Pro Uncertain significance Single submitter
- PER3 p.Lys488Thr Uncertain significance Single submitter
- PER3 p.Met1037Val Uncertain significance Single submitter
- PER3 p.Met1126Leu Uncertain significance Single submitter
- PER3 p.Met176Leu Uncertain significance Single submitter
- PER3 p.Met482Val Uncertain significance Single submitter
-
PER3 p.Met57Ile
Uncertain significance
Single submitter
advanced sleep phase syndrome 3
- PER3 p.Pro1058Ser Uncertain significance Single submitter
- PER3 p.Pro1063Ala Uncertain significance Single submitter
- PER3 p.Pro1063Ser Uncertain significance Single submitter
- PER3 p.Pro206Ala Uncertain significance Single submitter
- PER3 p.Pro228Ala Uncertain significance Single submitter
- PER3 p.Pro233Ala Uncertain significance Single submitter
- PER3 p.Pro2Leu Uncertain significance Single submitter
- PER3 p.Pro300Leu Uncertain significance Single submitter
- PER3 p.Pro650Gln Uncertain significance Single submitter
- PER3 p.Pro9Leu Uncertain significance Single submitter
- PER3 p.Ser1076Gly Uncertain significance Single submitter
- PER3 p.Ser114Arg Uncertain significance Single submitter
- PER3 p.Ser355Phe Uncertain significance Single submitter
- PER3 p.Ser40Thr Uncertain significance Single submitter
- PER3 p.Ser486Leu Uncertain significance Single submitter
- PER3 p.Ser515Tyr Uncertain significance Single submitter
- PER3 p.Ser68Leu Uncertain significance Single submitter
- PER3 p.Thr1066Asn Uncertain significance Single submitter
- PER3 p.Thr1187Ala Uncertain significance Single submitter
- PER3 p.Thr132Ser Uncertain significance Single submitter
- PER3 p.Thr453Met Uncertain significance Single submitter
- PER3 p.Thr574Ala Uncertain significance Single submitter
- PER3 p.Thr616Arg Uncertain significance Single submitter
- PER3 p.Thr616Ile Uncertain significance Single submitter
- PER3 p.Thr626Met Uncertain significance Single submitter
- PER3 p.Tyr113Cys Uncertain significance Single submitter
- PER3 p.Tyr180Cys Uncertain significance Single submitter
- PER3 p.Tyr180Ser Uncertain significance Single submitter
- PER3 p.Tyr202Ser Uncertain significance Single submitter
- PER3 p.Val1186Phe Uncertain significance Single submitter
- PER3 p.Val207Gly Uncertain significance Single submitter
- PER3 p.Val321Leu Uncertain significance Single submitter
- PER3 p.Val525Ala Uncertain significance Single submitter
- PER3 p.Val647Leu Uncertain significance Single submitter
Predictors split 16
The independent predictors disagree with each other — read with care.
- PER3 p.Arg1133Ser Uncertain significance Single submitter
- PER3 p.Arg267Gln Uncertain significance Single submitter
- PER3 p.Arg374Trp Uncertain significance Single submitter
- PER3 p.Asn156Thr Uncertain significance Single submitter
- PER3 p.Glu124Gly Uncertain significance Single submitter
- PER3 p.Glu264Lys Uncertain significance Single submitter
- PER3 p.Phe31Leu Uncertain significance Single submitter
- PER3 p.Phe66Leu Uncertain significance Single submitter
- PER3 p.Pro266Ser Uncertain significance Single submitter
- PER3 p.Pro269Leu Uncertain significance Single submitter
- PER3 p.Pro314Leu Uncertain significance Single submitter
-
PER3 p.Pro415Ala
Conflicting
Single submitter
advanced sleep phase syndrome 3
- PER3 p.Ser356Cys Uncertain significance Single submitter
- PER3 p.Ser426Arg Uncertain significance Single submitter
- PER3 p.Thr1127Ile Uncertain significance Single submitter
- PER3 p.Thr306Ile Uncertain significance Single submitter
All PER3 variants
Pathogenic 1
- c.3399-80_3399-77del Single submitter methylcobalamin deficiency type cblE
Likely pathogenic 3
- p.Glu61Ter Single submitter
- p.Met667fs Single submitter
- p.Pro250fs Single submitter
Conflicting classifications of pathogenicity 3
- p.His417Arg Single submitter advanced sleep phase syndrome 3 ⚠
- p.Pro415Ala Single submitter advanced sleep phase syndrome 3 ⚠
- p.Thr1049Ile Single submitter ⚠
Benign 8
- p.Ala980= Multiple submitters
- p.Cys1185Ser Multiple submitters
- p.Ile614= Multiple submitters
- p.Val420Met Multiple submitters
- p.998ALSTGSPPMKNPSHPTAS[1] Single submitter
- c.3550-5dup No assertion criteria PER3-related disorder
- p.Thr1019= No assertion criteria PER3-related disorder
- p.Thr978= No assertion criteria PER3-related disorder
Likely benign 42
- p.Leu937= Multiple submitters
- p.Thr527Ala Multiple submitters
- c.1137-13G>T Single submitter
- c.129-4C>T Single submitter
- c.1512_1522+10del Single submitter
- c.1957+17T>C Single submitter
- c.1958-4T>G Single submitter
- c.644+7A>G Single submitter
- c.794-7dup Single submitter
- c.872+8C>G Single submitter
- p.Ala181Thr Single submitter
- p.Ala504Val Single submitter
- p.Ala998= Single submitter
- p.Arg157Cys Single submitter
- p.Asp396Asn Single submitter
- p.Cys530Tyr Single submitter
- p.Gln405= Single submitter
- p.Gln543= Single submitter
- p.Gly639Ser Single submitter
- p.Gly970Ser Single submitter
- p.His260= Single submitter
- p.His538= Single submitter
- p.Ile147Val Single submitter
- p.Ile351Val Single submitter
- p.Ile479= Single submitter
- p.Leu1039Ser Single submitter
- p.Leu658= Single submitter
- p.Phe343= Single submitter
- p.Ser356= Single submitter
- p.Thr1013= Single submitter
- p.Thr1104Ala Single submitter
- p.Thr1120Ile Single submitter
- p.Tyr464Cys Single submitter
- c.129-10dup No assertion criteria PER3-related disorder
- c.275-9G>A No assertion criteria PER3-related disorder
- p.Ala163= No assertion criteria PER3-related disorder
- p.Ala18Ser No assertion criteria PER3-related disorder
- p.Gly1196= No assertion criteria PER3-related disorder
- p.Met1037Thr No assertion criteria PER3-related disorder
- p.Thr306= No assertion criteria PER3-related disorder
- p.Thr626= No assertion criteria PER3-related disorder
- p.Val647Gly No assertion criteria PER3-related disorder
Uncertain significance 127
- p.Arg157His Multiple submitters ⚠
- p.Asn572Thr Multiple submitters advanced sleep phase syndrome 3 ⚠
- c.3550-1G>A Single submitter advanced sleep phase syndrome 3
- p.Ala1050Val Single submitter ⚠
- p.Ala105Val Single submitter ⚠
- p.Ala1109Thr Single submitter ⚠
- p.Ala122Thr Single submitter ⚠
- p.Ala152Val Single submitter ⚠
- p.Ala163Val Single submitter ⚠
- p.Ala172Val Single submitter ⚠
- p.Ala181Val Single submitter ⚠
- p.Ala440Thr Single submitter ⚠
- p.Ala627Val Single submitter ⚠
- p.Ala92Gly Single submitter ⚠
- p.Ala976Thr Single submitter ⚠
- p.Arg1043Lys Single submitter ⚠
- p.Arg1118Trp Single submitter ⚠
- p.Arg1123His Single submitter ⚠
- p.Arg1123Leu Single submitter ⚠
- p.Arg1133Ser Single submitter ⚠
- p.Arg12Leu Single submitter ⚠
- p.Arg267Gln Single submitter ⚠
- p.Arg35Gly Single submitter ⚠
- p.Arg374Trp Single submitter ⚠
- p.Arg378Gln Single submitter ⚠
- p.Arg48Gly Single submitter ⚠
- p.Arg494His Single submitter ⚠
- p.Arg50fs Single submitter advanced sleep phase syndrome 3
- p.Arg71Cys Single submitter ⚠
- p.Arg85Cys Single submitter ⚠
- p.Asn103Asp Single submitter ⚠
- p.Asn156Thr Single submitter ⚠
- p.Asn192Ile Single submitter ⚠
- p.Asn498Ser Single submitter ⚠
- p.Asn81Ser Single submitter ⚠
- p.Asn93Ser Single submitter ⚠
- p.Asp289His Single submitter ⚠
- p.Asp385Asn Single submitter ⚠
- p.Asp532Tyr Single submitter ⚠
- p.Asp78His Single submitter ⚠
- p.Asp950Glu Single submitter ⚠
- p.Asp950Val Single submitter ⚠
- p.Gln1172Lys Single submitter ⚠
- p.Gln1203Lys Single submitter ⚠
- p.Gln34Arg Single submitter ⚠
- p.Gln45Arg Single submitter ⚠
- p.Gln45Lys Single submitter ⚠
- p.Gln951Lys Single submitter ⚠
- p.Glu1061Lys Single submitter ⚠
- p.Glu1132Asp Single submitter ⚠
- p.Glu124Gly Single submitter ⚠
- p.Glu149Gln Single submitter ⚠
- p.Glu25Lys Single submitter ⚠
- p.Glu264Lys Single submitter ⚠
- p.Gly1159Val Single submitter ⚠
- p.Gly262Asp Single submitter ⚠
- p.Gly970Ala Single submitter ⚠
- p.His166Leu Single submitter ⚠
- p.His240Asp Single submitter ⚠
- p.Ile1078Met Single submitter ⚠
- p.Ile1117Thr Single submitter ⚠
- p.Ile1180Val Single submitter ⚠
- p.Ile121Val Single submitter ⚠
- p.Ile232Val Single submitter ⚠
- p.Ile391Met Single submitter ⚠
- p.Ile470Asn Single submitter ⚠
- p.Leu1125Phe Single submitter ⚠
- p.Leu1146Val Single submitter ⚠
- p.Leu115Pro Single submitter ⚠
- p.Leu253Val Single submitter ⚠
- p.Leu296Val Single submitter ⚠
- p.Leu411Pro Single submitter ⚠
- p.Leu436Pro Single submitter ⚠
- p.Leu533Met Single submitter ⚠
- p.Leu80Phe Single submitter ⚠
- p.Leu938Pro Single submitter ⚠
- p.Lys488Thr Single submitter ⚠
- p.Met1037Val Single submitter ⚠
- p.Met1126Leu Single submitter ⚠
- p.Met176Leu Single submitter ⚠
- p.Met482Val Single submitter ⚠
- p.Met57Ile Single submitter advanced sleep phase syndrome 3 ⚠
- p.Phe211Val Single submitter
- p.Phe31Leu Single submitter ⚠
- p.Phe66Leu Single submitter ⚠
- p.Pro1058Ser Single submitter ⚠
- p.Pro1063Ala Single submitter ⚠
- p.Pro1063Ser Single submitter ⚠
- p.Pro206Ala Single submitter ⚠
- p.Pro228Ala Single submitter ⚠
- p.Pro233Ala Single submitter ⚠
- p.Pro266Ser Single submitter ⚠
- p.Pro269Leu Single submitter ⚠
- p.Pro2Leu Single submitter ⚠
- p.Pro300Leu Single submitter ⚠
- p.Pro314Leu Single submitter ⚠
- p.Pro650Gln Single submitter ⚠
- p.Pro9Leu Single submitter ⚠
- p.Ser1076Gly Single submitter ⚠
- p.Ser114Arg Single submitter ⚠
- p.Ser355Phe Single submitter ⚠
- p.Ser356Cys Single submitter ⚠
- p.Ser40Thr Single submitter ⚠
- p.Ser426Arg Single submitter ⚠
- p.Ser486Leu Single submitter ⚠
- p.Ser515Tyr Single submitter ⚠
- p.Ser524fs Single submitter advanced sleep phase syndrome
- p.Ser68Leu Single submitter ⚠
- p.Thr1066Asn Single submitter ⚠
- p.Thr1127Ile Single submitter ⚠
- p.Thr1187Ala Single submitter ⚠
- p.Thr132Ser Single submitter ⚠
- p.Thr306Ile Single submitter ⚠
- p.Thr453Met Single submitter ⚠
- p.Thr574Ala Single submitter ⚠
- p.Thr616Arg Single submitter ⚠
- p.Thr616Ile Single submitter ⚠
- p.Thr626Met Single submitter ⚠
- p.Tyr113Cys Single submitter ⚠
- p.Tyr180Cys Single submitter ⚠
- p.Tyr180Ser Single submitter ⚠
- p.Tyr202Ser Single submitter ⚠
- p.Val1186Phe Single submitter ⚠
- p.Val207Gly Single submitter ⚠
- p.Val321Leu Single submitter ⚠
- p.Val525Ala Single submitter ⚠
- p.Val647Leu Single submitter ⚠