CAPRIN1 — 178 ClinVar variants
All ClinVar germline CAPRIN1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 106 flagged for review →
19 Pathogenic · 16 Likely pathogenic · 1 Conflicting · 1 Benign · 21 Likely benign · 120 Uncertain significance
Full CAPRIN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 106
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.
Predictors agree, ClinVar conflicts 1
ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.
-
CAPRIN1 p.Pro512Leu
Conflicting
Single submitter
cerebellar ataxia
Predictors lean, ClinVar uncertain 75
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- CAPRIN1 p.Arg132Cys Uncertain significance Multiple submitters
- CAPRIN1 p.Pro424Leu Uncertain significance Multiple submitters
- CAPRIN1 p.Ala265Thr Uncertain significance Single submitter
- CAPRIN1 p.Ala267Ser Uncertain significance Single submitter
- CAPRIN1 p.Ala333Ser Uncertain significance Single submitter
- CAPRIN1 p.Ala38Thr Uncertain significance Single submitter
- CAPRIN1 p.Ala38Val Uncertain significance Single submitter
- CAPRIN1 p.Ala469Thr Uncertain significance Single submitter
- CAPRIN1 p.Ala469Val Uncertain significance Single submitter
- CAPRIN1 p.Ala486Ser Uncertain significance Single submitter
- CAPRIN1 p.Ala486Thr Uncertain significance Single submitter
- CAPRIN1 p.Ala486Val Uncertain significance Single submitter
- CAPRIN1 p.Ala48Thr Uncertain significance Single submitter
- CAPRIN1 p.Ala543Pro Uncertain significance Single submitter
- CAPRIN1 p.Arg458Pro Uncertain significance Single submitter
- CAPRIN1 p.Asn204Ile Uncertain significance Single submitter
- CAPRIN1 p.Asn204Ser Uncertain significance Single submitter
- CAPRIN1 p.Asn325Ser Uncertain significance Single submitter
- CAPRIN1 p.Asn521Ser Uncertain significance Single submitter
- CAPRIN1 p.Asn594Asp Uncertain significance Single submitter
- CAPRIN1 p.Asn630Ser Uncertain significance Single submitter
- CAPRIN1 p.Asn645Ser Uncertain significance Single submitter
- CAPRIN1 p.Asp216Val Uncertain significance Single submitter
- CAPRIN1 p.Asp270Tyr Uncertain significance Single submitter
- CAPRIN1 p.Asp465Glu Uncertain significance Single submitter
- CAPRIN1 p.Gln286Pro Uncertain significance Single submitter
- CAPRIN1 p.Gln329Glu Uncertain significance Single submitter
- CAPRIN1 p.Gln330Arg Uncertain significance Single submitter
- CAPRIN1 p.Gln40Leu Uncertain significance Single submitter
- CAPRIN1 p.Gln494Arg Uncertain significance Single submitter
- CAPRIN1 p.Gln567His Uncertain significance Single submitter
- CAPRIN1 p.Gln79Arg Uncertain significance Single submitter
- CAPRIN1 p.Glu196Ala Uncertain significance Single submitter
- CAPRIN1 p.Glu281Lys Uncertain significance Single submitter
- CAPRIN1 p.Glu315Val Uncertain significance Single submitter
- CAPRIN1 p.Gly11Asp Uncertain significance Single submitter
- CAPRIN1 p.Gly16Arg Uncertain significance Single submitter
- CAPRIN1 p.Gly220Val Uncertain significance Single submitter
- CAPRIN1 p.Gly25Val Uncertain significance Single submitter
- CAPRIN1 p.Gly650Ser Uncertain significance Single submitter
- CAPRIN1 p.His209Arg Uncertain significance Single submitter
- CAPRIN1 p.His250Arg Uncertain significance Single submitter
- CAPRIN1 p.His412Leu Uncertain significance Single submitter
- CAPRIN1 p.His41Tyr Uncertain significance Single submitter
- CAPRIN1 p.His581Arg Uncertain significance Single submitter
- CAPRIN1 p.Leu185Trp Uncertain significance Single submitter
- CAPRIN1 p.Leu501Ser Uncertain significance Single submitter
-
CAPRIN1 p.Lys231Glu
Uncertain significance
Single submitter
neurodevelopmental disorder with language impairment, autism, and attention deficit-hyperactivity disorder
- CAPRIN1 p.Met403Ile Uncertain significance Single submitter
- CAPRIN1 p.Met622Ile Uncertain significance Single submitter
- CAPRIN1 p.Pro279Ala Uncertain significance Single submitter
- CAPRIN1 p.Pro346Leu Uncertain significance Single submitter
- CAPRIN1 p.Pro352Ala Uncertain significance Single submitter
- CAPRIN1 p.Pro410Ala Uncertain significance Single submitter
- CAPRIN1 p.Pro659Ala Uncertain significance Single submitter
- CAPRIN1 p.Pro683Thr Uncertain significance Single submitter
- CAPRIN1 p.Ser10Asn Uncertain significance Single submitter
- CAPRIN1 p.Ser115Gly Uncertain significance Single submitter
- CAPRIN1 p.Ser26Gly Uncertain significance Single submitter
- CAPRIN1 p.Ser481Ala Uncertain significance Single submitter
- CAPRIN1 p.Ser503Asn Uncertain significance Single submitter
- CAPRIN1 p.Ser504Gly Uncertain significance Single submitter
- CAPRIN1 p.Ser615Ala Uncertain significance Single submitter
- CAPRIN1 p.Ser644Thr Uncertain significance Single submitter
- CAPRIN1 p.Thr126Ala Uncertain significance Single submitter
- CAPRIN1 p.Thr317Ala Uncertain significance Single submitter
- CAPRIN1 p.Thr317Ile Uncertain significance Single submitter
- CAPRIN1 p.Thr320Met Uncertain significance Single submitter
-
CAPRIN1 p.Thr478Ala
Uncertain significance
Single submitter
CAPRIN1-related disorder
- CAPRIN1 p.Thr568Arg Uncertain significance Single submitter
- CAPRIN1 p.Thr572Ile Uncertain significance Single submitter
- CAPRIN1 p.Tyr207Cys Uncertain significance Single submitter
- CAPRIN1 p.Tyr283Cys Uncertain significance Single submitter
- CAPRIN1 p.Val324Leu Uncertain significance Single submitter
-
CAPRIN1 p.Val175Leu
Uncertain significance
No assertion criteria
CAPRIN1-related disorder
Predictors split 29
The independent predictors disagree with each other — read with care.
- CAPRIN1 p.Gln206Arg Uncertain significance Multiple submitters
- CAPRIN1 p.Pro528Thr Uncertain significance Multiple submitters
- CAPRIN1 p.Ala109Ser Uncertain significance Single submitter
- CAPRIN1 p.Ala210Val Uncertain significance Single submitter
- CAPRIN1 p.Arg239Cys Uncertain significance Single submitter
- CAPRIN1 p.Arg297Thr Uncertain significance Single submitter
- CAPRIN1 p.Arg599Cys Uncertain significance Single submitter
- CAPRIN1 p.Arg612Gly Uncertain significance Single submitter
- CAPRIN1 p.Arg640His Uncertain significance Single submitter
- CAPRIN1 p.Arg660Gln Uncertain significance Single submitter
- CAPRIN1 p.Asp351Val Uncertain significance Single submitter
- CAPRIN1 p.Asp77Gly Uncertain significance Single submitter
- CAPRIN1 p.Gln393Lys Uncertain significance Single submitter
- CAPRIN1 p.Glu381Gln Uncertain significance Single submitter
- CAPRIN1 p.Ile57Phe Uncertain significance Single submitter
- CAPRIN1 p.Ile57Thr Uncertain significance Single submitter
- CAPRIN1 p.Leu183Phe Uncertain significance Single submitter
- CAPRIN1 p.Leu186Val Uncertain significance Single submitter
-
CAPRIN1 p.Leu362Phe
Likely benign
Single submitter
autism spectrum disorder
- CAPRIN1 p.Leu58Phe Uncertain significance Single submitter
- CAPRIN1 p.Met522Thr Uncertain significance Single submitter
- CAPRIN1 p.Phe189Leu Uncertain significance Single submitter
- CAPRIN1 p.Phe299Leu Uncertain significance Single submitter
- CAPRIN1 p.Phe372Ile Uncertain significance Single submitter
- CAPRIN1 p.Phe656Cys Uncertain significance Single submitter
- CAPRIN1 p.Ser15Phe Likely benign Single submitter
- CAPRIN1 p.Ser179Pro Uncertain significance Single submitter
- CAPRIN1 p.Val149Gly Uncertain significance Single submitter
- CAPRIN1 p.Val225Ala Uncertain significance Single submitter
All CAPRIN1 variants
Pathogenic 19
- p.Arg458Ter Multiple submitters neurodevelopmental disorder with language impairment, autism, and attention deficit-hyperactivity disorder
- p.Ala280fs Single submitter neurodevelopmental disorder with language impairment, autism, and attention deficit-hyperactivity disorder
- p.Arg297fs Single submitter juvenile myoclonic epilepsy
- p.Arg356Ter Single submitter neurodevelopmental disorder with language impairment, autism, and attention deficit-hyperactivity disorder
- p.Arg358Ter Single submitter neurodevelopmental disorder with language impairment, autism, and attention deficit-hyperactivity disorder
- p.Arg81Ter Single submitter
- p.Gln332fs Single submitter
- p.Glu282Ter Single submitter
- p.Glu564fs Single submitter neurodevelopmental disorder with language impairment, autism, and attention deficit-hyperactivity disorder
- p.Lys72fs Single submitter
- p.Ser326Ter Single submitter
- p.Ser498fs Single submitter CAPRIN1-related neurodevelopmental disorders
- p.Thr534_Leu535insTer Single submitter
- p.Thr559fs Single submitter
- p.Trp316Ter Single submitter
- p.Tyr545Ter Single submitter
- p.Gln399Ter No assertion criteria neurodevelopmental disorder with language impairment, autism, and attention deficit-hyperactivity disorder
- p.Gln582Ter No assertion criteria neurodevelopmental disorder with language impairment, autism, and attention deficit-hyperactivity disorder
- p.Glu293= No assertion criteria neurodevelopmental disorder with language impairment, autism, and attention deficit-hyperactivity disorder
Likely pathogenic 16
- c.217-5C>G Single submitter neurodegeneration, childhood-onset, with cerebellar ataxia and cognitive decline
- c.688+5G>A Single submitter
- p.Asp578fs Single submitter neurodevelopmental disorder with language impairment, autism, and attention deficit-hyperactivity disorder
- p.Gln419fs Single submitter CAPRIN1-related disorder
- p.Gln552Ter Single submitter Focal-onset seizure
- p.Gln92Ter Single submitter Autistic behavior
- p.Glu293fs Single submitter CAPRIN1-related disorder
- p.Gly31Ter Single submitter neurodevelopmental disorder with language impairment, autism, and attention deficit-hyperactivity disorder
- p.His554Tyr Single submitter ⚠
- p.Ile127fs Single submitter neurodevelopmental disorder with language impairment, autism, and attention deficit-hyperactivity disorder
- p.Ser264Ter Single submitter CAPRIN1-related disorder
- p.Ser482Ter Single submitter neurodevelopmental disorder with language impairment, autism, and attention deficit-hyperactivity disorder
- p.Tyr545fs Single submitter neurodevelopmental disorder with language impairment, autism, and attention deficit-hyperactivity disorder
- p.Gln271Ter No assertion criteria Moyamoya angiopathy
- p.Glu278Ter No assertion criteria neurodevelopmental disorder with language impairment, autism, and attention deficit-hyperactivity disorder
- p.Ser550fs No assertion criteria CAPRIN1-related disorder
Conflicting classifications of pathogenicity 1
- p.Pro512Leu Single submitter cerebellar ataxia ⚠
Benign 1
- c.1122+19G>A Multiple submitters
Likely benign 21
- c.1554+15T>G Single submitter
- c.1705+14T>C Single submitter
- c.1900+13_1900+16del Single submitter
- c.2001+8A>T Single submitter
- c.217-4A>G Single submitter
- c.280-12T>C Single submitter
- c.826+16A>T Single submitter
- c.966+6A>C Single submitter
- p.Ala333Thr Single submitter
- p.Arg132= Single submitter
- p.Arg239His Single submitter
- p.Gln312Arg Single submitter
- p.Leu362Phe Single submitter autism spectrum disorder ⚠
- p.Pro2= Single submitter
- p.Pro451= Single submitter
- p.Pro683Ala Single submitter
- p.Ser12Arg Single submitter
- p.Ser15Phe Single submitter ⚠
- p.Ser179= Single submitter
- p.Thr443Ile Single submitter
- p.Val225= Single submitter
Uncertain significance 120
- p.Arg132Cys Multiple submitters ⚠
- p.Gln206Arg Multiple submitters ⚠
- p.Pro424Leu Multiple submitters ⚠
- p.Pro528Thr Multiple submitters ⚠
- c.1123-7C>G Single submitter
- c.1554+2T>C Single submitter neurodegeneration, childhood-onset, with cerebellar ataxia and cognitive decline
- c.1706-2A>C Single submitter
- c.280-11T>C Single submitter
- c.280-1G>A Single submitter
- c.826+16A>G Single submitter neurodevelopmental disorder with language impairment, autism, and attention deficit-hyperactivity disorder
- p.Ala109Ser Single submitter ⚠
- p.Ala210Val Single submitter ⚠
- p.Ala265Thr Single submitter ⚠
- p.Ala267Ser Single submitter ⚠
- p.Ala333Ser Single submitter ⚠
- p.Ala38Thr Single submitter ⚠
- p.Ala38Val Single submitter ⚠
- p.Ala469Thr Single submitter ⚠
- p.Ala469Val Single submitter ⚠
- p.Ala486Ser Single submitter ⚠
- p.Ala486Thr Single submitter ⚠
- p.Ala486Val Single submitter ⚠
- p.Ala48Thr Single submitter ⚠
- p.Ala543Pro Single submitter ⚠
- p.Arg202= Single submitter
- p.Arg239Cys Single submitter ⚠
- p.Arg297Thr Single submitter ⚠
- p.Arg458Pro Single submitter ⚠
- p.Arg599Cys Single submitter ⚠
- p.Arg612Gly Single submitter ⚠
- p.Arg640His Single submitter ⚠
- p.Arg660Gln Single submitter ⚠
- p.Asn204Ile Single submitter ⚠
- p.Asn204Ser Single submitter ⚠
- p.Asn325Ser Single submitter ⚠
- p.Asn521Ser Single submitter ⚠
- p.Asn594Asp Single submitter ⚠
- p.Asn630Ser Single submitter ⚠
- p.Asn645Ser Single submitter ⚠
- p.Asp216Val Single submitter ⚠
- p.Asp270Tyr Single submitter ⚠
- p.Asp351Val Single submitter ⚠
- p.Asp465Glu Single submitter ⚠
- p.Asp77Gly Single submitter ⚠
- p.Gln113Ter Single submitter
- p.Gln286Pro Single submitter ⚠
- p.Gln298Ter Single submitter neurodevelopmental disorder with language impairment, autism, and attention deficit-hyperactivity disorder
- p.Gln329Glu Single submitter ⚠
- p.Gln330Arg Single submitter ⚠
- p.Gln393Lys Single submitter ⚠
- p.Gln40Leu Single submitter ⚠
- p.Gln494Arg Single submitter ⚠
- p.Gln567His Single submitter ⚠
- p.Gln653fs Single submitter
- p.Gln79Arg Single submitter ⚠
- p.Glu101fs Single submitter
- p.Glu196Ala Single submitter ⚠
- p.Glu281Lys Single submitter ⚠
- p.Glu311= Single submitter
- p.Glu315Val Single submitter ⚠
- p.Glu381Gln Single submitter ⚠
- p.Glu440Leu Single submitter
- p.Gly11Asp Single submitter ⚠
- p.Gly16Arg Single submitter ⚠
- p.Gly220Val Single submitter ⚠
- p.Gly25Val Single submitter ⚠
- p.Gly650Ser Single submitter ⚠
- p.His209Arg Single submitter ⚠
- p.His250Arg Single submitter ⚠
- p.His412Leu Single submitter ⚠
- p.His41Tyr Single submitter ⚠
- p.His502Gln Single submitter
- p.His581Arg Single submitter ⚠
- p.Ile57Phe Single submitter ⚠
- p.Ile57Thr Single submitter ⚠
- p.Leu183Phe Single submitter ⚠
- p.Leu185Trp Single submitter ⚠
- p.Leu186Val Single submitter ⚠
- p.Leu501Ser Single submitter ⚠
- p.Leu58Phe Single submitter ⚠
- p.Lys231Glu Single submitter neurodevelopmental disorder with language impairment, autism, and attention deficit-hyperactivity disorder ⚠
- p.Met117fs Single submitter
- p.Met403Ile Single submitter ⚠
- p.Met522Thr Single submitter ⚠
- p.Met622Ile Single submitter ⚠
- p.Phe189Leu Single submitter ⚠
- p.Phe299Leu Single submitter ⚠
- p.Phe372Ile Single submitter ⚠
- p.Phe656Cys Single submitter ⚠
- p.Pro279Ala Single submitter ⚠
- p.Pro346Leu Single submitter ⚠
- p.Pro352Ala Single submitter ⚠
- p.Pro410Ala Single submitter ⚠
- p.Pro659Ala Single submitter ⚠
- p.Pro683Thr Single submitter ⚠
- p.Ser10Asn Single submitter ⚠
- p.Ser115Gly Single submitter ⚠
- p.Ser179Pro Single submitter ⚠
- p.Ser26Gly Single submitter ⚠
- p.Ser335fs Single submitter
- p.Ser481Ala Single submitter ⚠
- p.Ser503Asn Single submitter ⚠
- p.Ser504Gly Single submitter ⚠
- p.Ser615Ala Single submitter ⚠
- p.Ser644Thr Single submitter ⚠
- p.Thr126Ala Single submitter ⚠
- p.Thr317Ala Single submitter ⚠
- p.Thr317Ile Single submitter ⚠
- p.Thr320Met Single submitter ⚠
- p.Thr478Ala Single submitter CAPRIN1-related disorder ⚠
- p.Thr518Met Single submitter
- p.Thr568Arg Single submitter ⚠
- p.Thr572Ile Single submitter ⚠
- p.Tyr207Cys Single submitter ⚠
- p.Tyr283Cys Single submitter ⚠
- p.Tyr605Ter Single submitter CAPRIN1-associated disorder
- p.Val149Gly Single submitter ⚠
- p.Val225Ala Single submitter ⚠
- p.Val324Leu Single submitter ⚠
- p.Val175Leu No assertion criteria CAPRIN1-related disorder ⚠