CNTN3 — 155 ClinVar variants
All ClinVar germline CNTN3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 115 flagged for review →
12 Benign · 1 Benign/Likely benign · 19 Likely benign · 123 Uncertain significance
Full CNTN3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 115
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 lean, ClinVar uncertain 91
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- CNTN3 p.Arg841Gln Uncertain significance Multiple submitters
-
CNTN3 p.Glu168Lys
Uncertain significance
Multiple submitters
CNTN3-related disorder
- CNTN3 p.Ala119Pro Uncertain significance Single submitter
- CNTN3 p.Ala239Thr Uncertain significance Single submitter
- CNTN3 p.Ala407Pro Uncertain significance Single submitter
- CNTN3 p.Ala467Val Uncertain significance Single submitter
- CNTN3 p.Ala892Thr Uncertain significance Single submitter
- CNTN3 p.Ala928Val Uncertain significance Single submitter
- CNTN3 p.Arg1000Thr Uncertain significance Single submitter
- CNTN3 p.Arg171Gln Uncertain significance Single submitter
- CNTN3 p.Arg171Trp Uncertain significance Single submitter
- CNTN3 p.Arg217His Uncertain significance Single submitter
- CNTN3 p.Arg309Gly Uncertain significance Single submitter
- CNTN3 p.Arg636Trp Uncertain significance Single submitter
- CNTN3 p.Arg741Cys Uncertain significance Single submitter
- CNTN3 p.Arg993Gln Uncertain significance Single submitter
- CNTN3 p.Asn468Lys Uncertain significance Single submitter
- CNTN3 p.Asn489Thr Uncertain significance Single submitter
- CNTN3 p.Asn844His Uncertain significance Single submitter
- CNTN3 p.Asn895Ser Uncertain significance Single submitter
- CNTN3 p.Asp461Asn Uncertain significance Single submitter
- CNTN3 p.Asp530Asn Uncertain significance Single submitter
- CNTN3 p.Asp654Asn Uncertain significance Single submitter
- CNTN3 p.Gln117Arg Uncertain significance Single submitter
- CNTN3 p.Gln524His Uncertain significance Single submitter
- CNTN3 p.Gln808Glu Uncertain significance Single submitter
- CNTN3 p.Gln951His Uncertain significance Single submitter
- CNTN3 p.Glu177Asp Uncertain significance Single submitter
- CNTN3 p.Glu361Gln Uncertain significance Single submitter
- CNTN3 p.Glu691Gln Uncertain significance Single submitter
- CNTN3 p.Glu691Lys Uncertain significance Single submitter
- CNTN3 p.Glu696Lys Uncertain significance Single submitter
- CNTN3 p.Glu968Gly Uncertain significance Single submitter
- CNTN3 p.Gly145Ser Uncertain significance Single submitter
- CNTN3 p.Gly582Glu Uncertain significance Single submitter
- CNTN3 p.Gly683Asp Uncertain significance Single submitter
- CNTN3 p.Gly735Glu Uncertain significance Single submitter
- CNTN3 p.Gly847Arg Uncertain significance Single submitter
- CNTN3 p.His149Arg Uncertain significance Single submitter
- CNTN3 p.His834Pro Uncertain significance Single submitter
- CNTN3 p.Ile1006Thr Uncertain significance Single submitter
- CNTN3 p.Ile387Met Uncertain significance Single submitter
- CNTN3 p.Ile387Val Uncertain significance Single submitter
- CNTN3 p.Ile46Val Uncertain significance Single submitter
- CNTN3 p.Ile629Val Uncertain significance Single submitter
- CNTN3 p.Ile826Val Uncertain significance Single submitter
- CNTN3 p.Ile966Val Uncertain significance Single submitter
- CNTN3 p.Leu426Val Uncertain significance Single submitter
- CNTN3 p.Lys417Gln Uncertain significance Single submitter
- CNTN3 p.Lys692Gln Uncertain significance Single submitter
- CNTN3 p.Lys854Glu Uncertain significance Single submitter
- CNTN3 p.Met929Leu Uncertain significance Single submitter
- CNTN3 p.Pro188Leu Uncertain significance Single submitter
- CNTN3 p.Pro227His Uncertain significance Single submitter
- CNTN3 p.Pro725Ser Uncertain significance Single submitter
- CNTN3 p.Ser348Phe Uncertain significance Single submitter
- CNTN3 p.Ser425Asn Uncertain significance Single submitter
- CNTN3 p.Ser457Thr Uncertain significance Single submitter
- CNTN3 p.Ser507Tyr Uncertain significance Single submitter
- CNTN3 p.Ser549Phe Uncertain significance Single submitter
- CNTN3 p.Ser884Gly Uncertain significance Single submitter
- CNTN3 p.Thr313Ile Uncertain significance Single submitter
- CNTN3 p.Thr476Asn Uncertain significance Single submitter
- CNTN3 p.Thr476Ser Uncertain significance Single submitter
- CNTN3 p.Thr47Ile Uncertain significance Single submitter
- CNTN3 p.Thr613Ala Uncertain significance Single submitter
- CNTN3 p.Thr758Ser Uncertain significance Single submitter
- CNTN3 p.Thr877Met Uncertain significance Single submitter
- CNTN3 p.Thr977Ala Uncertain significance Single submitter
- CNTN3 p.Thr978Ala Uncertain significance Single submitter
- CNTN3 p.Thr97Ile Uncertain significance Single submitter
- CNTN3 p.Tyr155His Uncertain significance Single submitter
- CNTN3 p.Tyr295His Uncertain significance Single submitter
- CNTN3 p.Tyr631Cys Uncertain significance Single submitter
- CNTN3 p.Tyr942Cys Uncertain significance Single submitter
- CNTN3 p.Val331Met Uncertain significance Single submitter
- CNTN3 p.Val359Leu Uncertain significance Single submitter
- CNTN3 p.Val427Ile Uncertain significance Single submitter
- CNTN3 p.Val450Ala Uncertain significance Single submitter
- CNTN3 p.Val450Met Uncertain significance Single submitter
- CNTN3 p.Val496Ile Uncertain significance Single submitter
- CNTN3 p.Val579Met Uncertain significance Single submitter
- CNTN3 p.Val652Ile Uncertain significance Single submitter
- CNTN3 p.Val662Ala Uncertain significance Single submitter
- CNTN3 p.Val676Gly Uncertain significance Single submitter
- CNTN3 p.Val724Leu Uncertain significance Single submitter
- CNTN3 p.Val769Met Uncertain significance Single submitter
- CNTN3 p.Val804Glu Uncertain significance Single submitter
- CNTN3 p.Val804Leu Uncertain significance Single submitter
- CNTN3 p.Val935Ile Uncertain significance Single submitter
-
CNTN3 p.Ser271Arg
Uncertain significance
No assertion criteria
CNTN3-related disorder
Predictors split 24
The independent predictors disagree with each other — read with care.
- CNTN3 p.His625Arg Benign Multiple submitters
- CNTN3 p.Ser243Leu Benign/Likely benign Multiple submitters
- CNTN3 p.Ala292Thr Likely benign Single submitter
- CNTN3 p.Ala590Gly Uncertain significance Single submitter
- CNTN3 p.Arg565Thr Uncertain significance Single submitter
- CNTN3 p.Arg76His Uncertain significance Single submitter
- CNTN3 p.Asn538Ser Uncertain significance Single submitter
- CNTN3 p.Asn832Asp Uncertain significance Single submitter
- CNTN3 p.Asn832Ser Uncertain significance Single submitter
- CNTN3 p.Asp169Glu Uncertain significance Single submitter
- CNTN3 p.Asp94Glu Uncertain significance Single submitter
- CNTN3 p.Gln176Arg Uncertain significance Single submitter
- CNTN3 p.Glu482Gly Uncertain significance Single submitter
- CNTN3 p.Gly382Arg Uncertain significance Single submitter
- CNTN3 p.Gly40Cys Uncertain significance Single submitter
- CNTN3 p.Gly733Ser Uncertain significance Single submitter
- CNTN3 p.Leu121Val Uncertain significance Single submitter
- CNTN3 p.Leu814Pro Uncertain significance Single submitter
- CNTN3 p.Met415Thr Uncertain significance Single submitter
- CNTN3 p.Phe544Ser Uncertain significance Single submitter
- CNTN3 p.Pro527Leu Uncertain significance Single submitter
- CNTN3 p.Val166Ala Uncertain significance Single submitter
- CNTN3 p.Val281Met Uncertain significance Single submitter
-
CNTN3 p.Lys246Glu
Benign
No assertion criteria
CNTN3-related disorder
All CNTN3 variants
Benign 12
- c.359-5A>C Multiple submitters
- c.56-10A>T Multiple submitters
- c.947-7A>G Multiple submitters
- p.Gln947= Multiple submitters
- p.His625Arg Multiple submitters ⚠
- p.Ser588= Multiple submitters
- p.Thr657Met Multiple submitters
- p.Thr901Met Multiple submitters
- p.Ala811= No assertion criteria CNTN3-related disorder
- p.Asn708Ser No assertion criteria CNTN3-related disorder
- p.Lys246Glu No assertion criteria CNTN3-related disorder ⚠
- p.Val1019Ile No assertion criteria CNTN3-related disorder
Benign/Likely benign 1
- p.Ser243Leu Multiple submitters ⚠
Likely benign 19
- c.1213+9G>A Single submitter
- c.2167-5T>C Single submitter
- p.Ala292Thr Single submitter ⚠
- p.His75Asp Single submitter
- p.His75Tyr Single submitter
- p.Leu458Phe Single submitter
- p.Ser243= Single submitter
- p.Thr657= Single submitter
- p.Val1026Ala Single submitter
- p.Val646Ile Single submitter
- c.1945+7C>T No assertion criteria CNTN3-related disorder
- p.Ala488Thr No assertion criteria CNTN3-related disorder
- p.Glu187= No assertion criteria CNTN3-related disorder
- p.Lys848= No assertion criteria CNTN3-related disorder
- p.Pro285= No assertion criteria CNTN3-related disorder
- p.Ser516= No assertion criteria CNTN3-related disorder
- p.Thr936Lys No assertion criteria CNTN3-related disorder
- p.Tyr477= No assertion criteria CNTN3-related disorder
- p.Val604Met No assertion criteria CNTN3-related disorder
Uncertain significance 123
- c.1669-4A>G Multiple submitters
- p.Arg841Gln Multiple submitters ⚠
- p.Glu168Lys Multiple submitters CNTN3-related disorder ⚠
- c.1669-2A>C Single submitter
- p.Ala119Pro Single submitter ⚠
- p.Ala239Thr Single submitter ⚠
- p.Ala407Pro Single submitter ⚠
- p.Ala467Val Single submitter ⚠
- p.Ala590Gly Single submitter ⚠
- p.Ala892Thr Single submitter ⚠
- p.Ala928Val Single submitter ⚠
- p.Arg1000Thr Single submitter ⚠
- p.Arg171Gln Single submitter ⚠
- p.Arg171Trp Single submitter ⚠
- p.Arg217His Single submitter ⚠
- p.Arg309Gly Single submitter ⚠
- p.Arg311Ser Single submitter
- p.Arg565Thr Single submitter ⚠
- p.Arg636Trp Single submitter ⚠
- p.Arg714Trp Single submitter
- p.Arg741Cys Single submitter ⚠
- p.Arg741His Single submitter
- p.Arg76His Single submitter ⚠
- p.Arg993Gln Single submitter ⚠
- p.Asn468Lys Single submitter ⚠
- p.Asn489Thr Single submitter ⚠
- p.Asn538Ser Single submitter ⚠
- p.Asn832Asp Single submitter ⚠
- p.Asn832Ser Single submitter ⚠
- p.Asn844His Single submitter ⚠
- p.Asn895Ser Single submitter ⚠
- p.Asp169Glu Single submitter ⚠
- p.Asp461Asn Single submitter ⚠
- p.Asp510Val Single submitter
- p.Asp530Asn Single submitter ⚠
- p.Asp654Asn Single submitter ⚠
- p.Asp94Glu Single submitter ⚠
- p.Gln117Arg Single submitter ⚠
- p.Gln176Arg Single submitter ⚠
- p.Gln524His Single submitter ⚠
- p.Gln808Glu Single submitter ⚠
- p.Gln951His Single submitter ⚠
- p.Glu177Asp Single submitter ⚠
- p.Glu361Gln Single submitter ⚠
- p.Glu482Gly Single submitter ⚠
- p.Glu691Gln Single submitter ⚠
- p.Glu691Lys Single submitter ⚠
- p.Glu696Lys Single submitter ⚠
- p.Glu961Gly Single submitter
- p.Glu968Gly Single submitter ⚠
- p.Gly145Ser Single submitter ⚠
- p.Gly242Asp Single submitter
- p.Gly382Arg Single submitter ⚠
- p.Gly40Cys Single submitter ⚠
- p.Gly582Glu Single submitter ⚠
- p.Gly621Ser Single submitter
- p.Gly683Asp Single submitter ⚠
- p.Gly733Ser Single submitter ⚠
- p.Gly735Glu Single submitter ⚠
- p.Gly847Arg Single submitter ⚠
- p.His149Arg Single submitter ⚠
- p.His834Pro Single submitter ⚠
- p.Ile1006Thr Single submitter ⚠
- p.Ile387Met Single submitter ⚠
- p.Ile387Val Single submitter ⚠
- p.Ile46Val Single submitter ⚠
- p.Ile629Val Single submitter ⚠
- p.Ile826Val Single submitter ⚠
- p.Ile966Val Single submitter ⚠
- p.Leu121Val Single submitter ⚠
- p.Leu426Val Single submitter ⚠
- p.Leu814Pro Single submitter ⚠
- p.Lys417Gln Single submitter ⚠
- p.Lys692Gln Single submitter ⚠
- p.Lys854Glu Single submitter ⚠
- p.Met415Thr Single submitter ⚠
- p.Met929Leu Single submitter ⚠
- p.Phe544Ser Single submitter ⚠
- p.Pro188Leu Single submitter ⚠
- p.Pro227His Single submitter ⚠
- p.Pro527Leu Single submitter ⚠
- p.Pro725Ser Single submitter ⚠
- p.Ser348Phe Single submitter ⚠
- p.Ser425Asn Single submitter ⚠
- p.Ser457Thr Single submitter ⚠
- p.Ser507Tyr Single submitter ⚠
- p.Ser549Phe Single submitter ⚠
- p.Ser884Gly Single submitter ⚠
- p.Thr212Pro Single submitter
- p.Thr313Ile Single submitter ⚠
- p.Thr476Asn Single submitter ⚠
- p.Thr476Ser Single submitter ⚠
- p.Thr47Ile Single submitter ⚠
- p.Thr613Ala Single submitter ⚠
- p.Thr695Ala Single submitter
- p.Thr758Ser Single submitter ⚠
- p.Thr877Met Single submitter ⚠
- p.Thr977Ala Single submitter ⚠
- p.Thr978Ala Single submitter ⚠
- p.Thr97Ile Single submitter ⚠
- p.Tyr155His Single submitter ⚠
- p.Tyr295His Single submitter ⚠
- p.Tyr631Cys Single submitter ⚠
- p.Tyr942Cys Single submitter ⚠
- p.Val166Ala Single submitter ⚠
- p.Val207Met Single submitter
- p.Val281Met Single submitter ⚠
- p.Val331Met Single submitter ⚠
- p.Val359Leu Single submitter ⚠
- p.Val427Ile Single submitter ⚠
- p.Val450Ala Single submitter ⚠
- p.Val450Met Single submitter ⚠
- p.Val496Ile Single submitter ⚠
- p.Val579Met Single submitter ⚠
- p.Val652Ile Single submitter ⚠
- p.Val662Ala Single submitter ⚠
- p.Val676Gly Single submitter ⚠
- p.Val724Leu Single submitter ⚠
- p.Val769Met Single submitter ⚠
- p.Val804Glu Single submitter ⚠
- p.Val804Leu Single submitter ⚠
- p.Val935Ile Single submitter ⚠
- p.Ser271Arg No assertion criteria CNTN3-related disorder ⚠