CNTN4 — 294 ClinVar variants
All ClinVar germline CNTN4 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 142 flagged for review →
2 Conflicting · 103 Benign · 38 Likely benign · 151 Uncertain significance
Full CNTN4 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 142
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.
Predictors lean, ClinVar uncertain 118
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- CNTN4 p.Glu765Asp Uncertain significance Multiple submitters
- CNTN4 p.Ala1002Thr Uncertain significance Single submitter
- CNTN4 p.Ala102Val Uncertain significance Single submitter
- CNTN4 p.Ala306Gly Uncertain significance Single submitter
- CNTN4 p.Ala472Thr Uncertain significance Single submitter
- CNTN4 p.Ala602Asp Uncertain significance Single submitter
- CNTN4 p.Ala697Thr Uncertain significance Single submitter
- CNTN4 p.Ala757Thr Uncertain significance Single submitter
- CNTN4 p.Ala876Thr Uncertain significance Single submitter
- CNTN4 p.Ala95Val Uncertain significance Single submitter
- CNTN4 p.Arg135Cys Uncertain significance Single submitter
- CNTN4 p.Arg169His Uncertain significance Single submitter
- CNTN4 p.Arg170Cys Uncertain significance Single submitter
- CNTN4 p.Arg170Leu Uncertain significance Single submitter
- CNTN4 p.Arg307Ser Uncertain significance Single submitter
- CNTN4 p.Arg361Ser Uncertain significance Single submitter
- CNTN4 p.Arg415Thr Uncertain significance Single submitter
- CNTN4 p.Arg445Lys Uncertain significance Single submitter
- CNTN4 p.Arg564Gln Uncertain significance Single submitter
- CNTN4 p.Arg618Ile Uncertain significance Single submitter
- CNTN4 p.Arg635Gly Uncertain significance Single submitter
- CNTN4 p.Arg635Lys Uncertain significance Single submitter
- CNTN4 p.Arg673His Uncertain significance Single submitter
- CNTN4 p.Arg687Ser Uncertain significance Single submitter
-
CNTN4 p.Arg842Thr
Uncertain significance
Single submitter
CNTN4-related disorder
- CNTN4 p.Arg854Gln Uncertain significance Single submitter
- CNTN4 p.Asn202Asp Uncertain significance Single submitter
- CNTN4 p.Asn277Asp Uncertain significance Single submitter
- CNTN4 p.Asn284Ser Uncertain significance Single submitter
- CNTN4 p.Asn466Ser Uncertain significance Single submitter
- CNTN4 p.Asn866Lys Uncertain significance Single submitter
- CNTN4 p.Asp543His Uncertain significance Single submitter
- CNTN4 p.Asp545Asn Uncertain significance Single submitter
- CNTN4 p.Asp547Asn Uncertain significance Single submitter
- CNTN4 p.Asp622Ala Uncertain significance Single submitter
- CNTN4 p.Asp965Asn Uncertain significance Single submitter
- CNTN4 p.Cys429Arg Uncertain significance Single submitter
- CNTN4 p.Gln117Arg Uncertain significance Single submitter
- CNTN4 p.Gln11Lys Uncertain significance Single submitter
- CNTN4 p.Gln287Leu Uncertain significance Single submitter
- CNTN4 p.Glu365Gly Uncertain significance Single submitter
- CNTN4 p.Glu513Asp Uncertain significance Single submitter
- CNTN4 p.Glu51Gln Uncertain significance Single submitter
- CNTN4 p.Glu700Asp Uncertain significance Single submitter
- CNTN4 p.Glu765Gly Uncertain significance Single submitter
- CNTN4 p.Glu827Lys Uncertain significance Single submitter
- CNTN4 p.Gly240Arg Uncertain significance Single submitter
- CNTN4 p.Gly308Ala Uncertain significance Single submitter
- CNTN4 p.Gly423Cys Uncertain significance Single submitter
- CNTN4 p.Gly444Arg Uncertain significance Single submitter
- CNTN4 p.Gly444Glu Uncertain significance Single submitter
- CNTN4 p.Gly460Arg Uncertain significance Single submitter
- CNTN4 p.Gly554Ala Uncertain significance Single submitter
- CNTN4 p.Gly72Ala Uncertain significance Single submitter
- CNTN4 p.Gly906Arg Uncertain significance Single submitter
- CNTN4 p.His525Tyr Uncertain significance Single submitter
- CNTN4 p.His548Asn Uncertain significance Single submitter
- CNTN4 p.His59Asn Uncertain significance Single submitter
- CNTN4 p.Ile213Lys Uncertain significance Single submitter
- CNTN4 p.Ile267Val Uncertain significance Single submitter
- CNTN4 p.Ile402Val Uncertain significance Single submitter
- CNTN4 p.Ile427Val Uncertain significance Single submitter
- CNTN4 p.Ile478Val Uncertain significance Single submitter
- CNTN4 p.Ile682Thr Uncertain significance Single submitter
- CNTN4 p.Ile746Ser Uncertain significance Single submitter
- CNTN4 p.Ile746Val Uncertain significance Single submitter
- CNTN4 p.Ile864Val Uncertain significance Single submitter
- CNTN4 p.Ile86Phe Uncertain significance Single submitter
- CNTN4 p.Ile909Thr Uncertain significance Single submitter
- CNTN4 p.Ile969Val Uncertain significance Single submitter
- CNTN4 p.Ile987Val Uncertain significance Single submitter
- CNTN4 p.Leu17Val Uncertain significance Single submitter
- CNTN4 p.Leu280Phe Uncertain significance Single submitter
- CNTN4 p.Leu39Val Uncertain significance Single submitter
- CNTN4 p.Leu960Phe Uncertain significance Single submitter
- CNTN4 p.Lys442Arg Uncertain significance Single submitter
- CNTN4 p.Lys776Glu Uncertain significance Single submitter
- CNTN4 p.Lys846Asn Uncertain significance Single submitter
- CNTN4 p.Lys916Arg Uncertain significance Single submitter
- CNTN4 p.Met748Val Uncertain significance Single submitter
- CNTN4 p.Phe171Val Uncertain significance Single submitter
- CNTN4 p.Phe28Leu Uncertain significance Single submitter
- CNTN4 p.Phe773Val Uncertain significance Single submitter
- CNTN4 p.Phe975Val Uncertain significance Single submitter
- CNTN4 p.Pro148Thr Uncertain significance Single submitter
- CNTN4 p.Pro266Ser Uncertain significance Single submitter
- CNTN4 p.Pro504Ser Uncertain significance Single submitter
- CNTN4 p.Pro518Leu Uncertain significance Single submitter
- CNTN4 p.Pro58Thr Uncertain significance Single submitter
- CNTN4 p.Ser1014Gly Uncertain significance Single submitter
- CNTN4 p.Ser526Leu Uncertain significance Single submitter
- CNTN4 p.Ser707Gly Uncertain significance Single submitter
- CNTN4 p.Ser78Asn Uncertain significance Single submitter
- CNTN4 p.Ser78Gly Uncertain significance Single submitter
- CNTN4 p.Ser913Ala Uncertain significance Single submitter
- CNTN4 p.Thr455Ile Uncertain significance Single submitter
- CNTN4 p.Thr489Ser Uncertain significance Single submitter
- CNTN4 p.Thr522Met Uncertain significance Single submitter
- CNTN4 p.Thr865Met Uncertain significance Single submitter
- CNTN4 p.Trp318Cys Uncertain significance Single submitter
- CNTN4 p.Tyr165His Uncertain significance Single submitter
- CNTN4 p.Tyr630His Uncertain significance Single submitter
- CNTN4 p.Tyr940Phe Uncertain significance Single submitter
- CNTN4 p.Val110Leu Uncertain significance Single submitter
- CNTN4 p.Val172Ile Uncertain significance Single submitter
- CNTN4 p.Val205Ile Uncertain significance Single submitter
- CNTN4 p.Val254Ile Uncertain significance Single submitter
- CNTN4 p.Val327Leu Uncertain significance Single submitter
- CNTN4 p.Val333Ala Uncertain significance Single submitter
- CNTN4 p.Val416Leu Uncertain significance Single submitter
- CNTN4 p.Val426Leu Uncertain significance Single submitter
- CNTN4 p.Val467Ile Uncertain significance Single submitter
- CNTN4 p.Val511Ala Uncertain significance Single submitter
- CNTN4 p.Val52Leu Uncertain significance Single submitter
- CNTN4 p.Val767Met Uncertain significance Single submitter
- CNTN4 p.Val924Met Uncertain significance Single submitter
- CNTN4 p.Val933Gly Uncertain significance Single submitter
- CNTN4 p.Thr417Asn Uncertain significance No assertion criteria
Predictors split 22
The independent predictors disagree with each other — read with care.
- CNTN4 p.Asp817Val Likely benign Multiple submitters
- CNTN4 p.Ala433Val Uncertain significance Single submitter
- CNTN4 p.Ala755Asp Uncertain significance Single submitter
- CNTN4 p.Arg551Ser Uncertain significance Single submitter
- CNTN4 p.Arg687Cys Uncertain significance Single submitter
- CNTN4 p.Arg76His Uncertain significance Single submitter
- CNTN4 p.Asn160Ser Uncertain significance Single submitter
- CNTN4 p.Asn396Lys Uncertain significance Single submitter
- CNTN4 p.Asp167Asn Uncertain significance Single submitter
- CNTN4 p.Asp263Asn Uncertain significance Single submitter
- CNTN4 p.Glu387Asp Uncertain significance Single submitter
- CNTN4 p.Glu798Asp Uncertain significance Single submitter
- CNTN4 p.Gly710Arg Uncertain significance Single submitter
- CNTN4 p.Ile279Ser Uncertain significance Single submitter
- CNTN4 p.Phe964Leu Uncertain significance Single submitter
- CNTN4 p.Pro599Leu Uncertain significance Single submitter
-
CNTN4 p.Pro626Leu
Uncertain significance
Single submitter
CNTN4-related disorder
- CNTN4 p.Ser983Asn Uncertain significance Single submitter
- CNTN4 p.Thr193Ala Uncertain significance Single submitter
- CNTN4 p.Trp910Arg Uncertain significance Single submitter
- CNTN4 p.Val333Phe Uncertain significance Single submitter
-
CNTN4 p.Thr476Ile
Uncertain significance
No assertion criteria
CNTN4-related disorder
All CNTN4 variants
Conflicting classifications of pathogenicity 2
- p.Thr176Ala Single submitter ⚠
- p.Thr612Ser Single submitter ⚠
Benign 103
- c.1486+67C>A Multiple submitters
- c.1487-86A>T Multiple submitters
- c.1663-158A>G Multiple submitters
- c.1663-174G>A Multiple submitters
- c.1663-178C>T Multiple submitters
- c.1663-212C>T Multiple submitters
- c.1663-75C>G Multiple submitters
- c.1784-32G>C Multiple submitters
- c.1784-57C>T Multiple submitters
- c.1784-98G>A Multiple submitters
- c.1942+41A>G Multiple submitters
- c.1943-23C>T Multiple submitters
- c.1943-49T>C Multiple submitters
- c.2092+115T>G Multiple submitters
- c.2092+319A>G Multiple submitters
- c.2093-108C>T Multiple submitters
- c.2093-6G>C Multiple submitters
- c.2093-90C>T Multiple submitters
- c.2164-177C>T Multiple submitters
- c.2164-205A>G Multiple submitters
- c.2398+181G>A Multiple submitters
- c.2398+48T>A Multiple submitters
- c.2398+4T>C Multiple submitters
- c.2398+70G>T Multiple submitters
- c.2511+41A>G Multiple submitters
- c.2512-8C>T Multiple submitters
- c.2698+157C>T Multiple submitters
- c.2812-50G>C Multiple submitters
- c.2812-87G>A Multiple submitters
- c.358+27A>C Multiple submitters
- c.56-277A>G Multiple submitters
- c.56-73T>C Multiple submitters
- c.652+61A>G Multiple submitters
- c.653-143G>A Multiple submitters
- c.653-203T>G Multiple submitters
- c.653-33T>G Multiple submitters
- c.755+13T>G Multiple submitters
- c.755+55A>G Multiple submitters
- c.755+84T>C Multiple submitters
- c.755+99A>G Multiple submitters
- c.756-52A>G Multiple submitters
- c.940+4942G>A Multiple submitters
- c.940+5034T>C Multiple submitters
- c.-88-99A>G Multiple submitters
- c.*137G>C Multiple submitters
- p.Ala587Ser Multiple submitters
- p.Arg731= Multiple submitters
- p.Asn623= Multiple submitters
- p.Asp70= Multiple submitters
- p.Asp756= Multiple submitters
- p.Glu354Lys Multiple submitters
- p.Gly177= Multiple submitters
- p.Gly221Asp Multiple submitters
- p.Leu15Phe Multiple submitters
- p.Leu517= Multiple submitters
- p.Pro518= Multiple submitters
- p.Pro637= Multiple submitters
- p.Ser105= Multiple submitters
- p.Tyr735= Multiple submitters
- c.1078-184G>A Single submitter
- c.1208-127A>G Single submitter
- c.1208-280C>A Single submitter
- c.1358+16336C>G Single submitter
- c.1358+16364A>T Single submitter
- c.1358+16485A>G Single submitter
- c.1359-225C>T Single submitter
- c.1486+3470A>G Single submitter
- c.1486+3680G>C Single submitter
- c.1486+3806C>T Single submitter
- c.1662+166C>G Single submitter
- c.1662+187C>T Single submitter
- c.1783+253G>A Single submitter
- c.182+134A>T Single submitter
- c.182+141G>A Single submitter
- c.183-3052G>T Single submitter
- c.1943-260A>G Single submitter
- c.2093-165G>A Single submitter
- c.2511+165T>C Single submitter
- c.2511+173C>T Single submitter
- c.2512-218A>T Single submitter
- c.2512-221T>G Single submitter
- c.2980+300dup Single submitter
- c.358+151A>G Single submitter
- c.359-26772G>A Single submitter
- c.359-26773G>A Single submitter
- c.454+22624G>A Single submitter
- c.455-101A>G Single submitter
- c.55+21045C>T Single submitter
- c.55+71072A>G Single submitter
- c.55+71115A>G Single submitter
- c.56-43692A>C Single submitter
- c.755+199G>A Single submitter
- c.756-311_756-303del Single submitter
- c.940+5012C>A Single submitter
- c.-88-28361A>G Single submitter
- c.-88-28724G>T Single submitter
- c.-88-322G>A Single submitter
- c.-88-78328G>A Single submitter
- c.-88-78540C>A Single submitter
- p.Ala486= Single submitter
- p.Gln567His Single submitter
- p.Thr956= Single submitter
- p.Tyr155= Single submitter
Likely benign 38
- p.Asp817Val Multiple submitters ⚠
- p.Gly302= Multiple submitters
- p.Lys186Gln Multiple submitters
- p.Pro619= Multiple submitters
- p.Pro699= Multiple submitters
- c.2811+12C>A Single submitter
- c.2811+18T>C Single submitter
- c.2981-8C>T Single submitter
- c.56-13C>G Single submitter
- p.Ala339= Single submitter
- p.Arg136Gln Single submitter
- p.Arg499Lys Single submitter
- p.Asn123= Single submitter
- p.Asn466= Single submitter
- p.Asn49Ser Single submitter
- p.Asn678= Single submitter
- p.Asn929= Single submitter
- p.Asp122Glu Single submitter
- p.Asp606= Single submitter
- p.Cys477= Single submitter
- p.Gln859= Single submitter
- p.Gly353= Single submitter
- p.His326= Single submitter
- p.Ile181= Single submitter
- p.Leu214= Single submitter
- p.Leu939= Single submitter
- p.Lys348Arg Single submitter
- p.Lys973= Single submitter
- p.Phe964= Single submitter
- p.Pro236= Single submitter
- p.Ser526= Single submitter
- p.Ser616= Single submitter
- p.Thr199= Single submitter
- p.Thr417= Single submitter
- p.Val871Ala Single submitter
- p.Gln11= No assertion criteria CNTN4-related disorder
- p.Lys265= No assertion criteria CNTN4-related disorder
- p.Pro905= No assertion criteria CNTN4-related disorder
Uncertain significance 151
- p.Glu765Asp Multiple submitters ⚠
- c.2698+1G>A Single submitter
- c.-88-87028G>A Single submitter CNTN4-associated neurodevelopmental disorder
- p.Ala1002Thr Single submitter ⚠
- p.Ala102Val Single submitter ⚠
- p.Ala306Gly Single submitter ⚠
- p.Ala433Val Single submitter ⚠
- p.Ala472Thr Single submitter ⚠
- p.Ala602Asp Single submitter ⚠
- p.Ala613Thr Single submitter
- p.Ala659Val Single submitter
- p.Ala697Thr Single submitter ⚠
- p.Ala755Asp Single submitter ⚠
- p.Ala757Thr Single submitter ⚠
- p.Ala876Thr Single submitter ⚠
- p.Ala95Val Single submitter ⚠
- p.Arg135Cys Single submitter ⚠
- p.Arg169His Single submitter ⚠
- p.Arg170Cys Single submitter ⚠
- p.Arg170Leu Single submitter ⚠
- p.Arg307Ser Single submitter ⚠
- p.Arg361Ser Single submitter ⚠
- p.Arg415Thr Single submitter ⚠
- p.Arg445Lys Single submitter ⚠
- p.Arg551Ser Single submitter ⚠
- p.Arg564Gln Single submitter ⚠
- p.Arg618Ile Single submitter ⚠
- p.Arg635Gly Single submitter ⚠
- p.Arg635Lys Single submitter ⚠
- p.Arg673His Single submitter ⚠
- p.Arg687Cys Single submitter ⚠
- p.Arg687Ser Single submitter ⚠
- p.Arg76His Single submitter ⚠
- p.Arg842Thr Single submitter CNTN4-related disorder ⚠
- p.Arg854Gln Single submitter ⚠
- p.Asn160Ser Single submitter ⚠
- p.Asn178Asp Single submitter
- p.Asn202Asp Single submitter ⚠
- p.Asn277Asp Single submitter ⚠
- p.Asn284Ser Single submitter ⚠
- p.Asn396Lys Single submitter ⚠
- p.Asn466Ser Single submitter ⚠
- p.Asn866Lys Single submitter ⚠
- p.Asp167Asn Single submitter ⚠
- p.Asp263Asn Single submitter ⚠
- p.Asp543His Single submitter ⚠
- p.Asp545Asn Single submitter ⚠
- p.Asp547Asn Single submitter ⚠
- p.Asp590Tyr Single submitter
- p.Asp622Ala Single submitter ⚠
- p.Asp622Asn Single submitter
- p.Asp756Tyr Single submitter
- p.Asp965Asn Single submitter ⚠
- p.Cys429Arg Single submitter ⚠
- p.Gln117Arg Single submitter ⚠
- p.Gln11Lys Single submitter ⚠
- p.Gln287Leu Single submitter ⚠
- p.Glu365Gly Single submitter ⚠
- p.Glu387Asp Single submitter ⚠
- p.Glu513Asp Single submitter ⚠
- p.Glu51Gln Single submitter ⚠
- p.Glu700Asp Single submitter ⚠
- p.Glu765Gly Single submitter ⚠
- p.Glu798Asp Single submitter ⚠
- p.Glu827Lys Single submitter ⚠
- p.Gly240Arg Single submitter ⚠
- p.Gly308Ala Single submitter ⚠
- p.Gly423Cys Single submitter ⚠
- p.Gly444Arg Single submitter ⚠
- p.Gly444Glu Single submitter ⚠
- p.Gly460Arg Single submitter ⚠
- p.Gly554Ala Single submitter ⚠
- p.Gly709Asp Single submitter
- p.Gly710Arg Single submitter ⚠
- p.Gly72Ala Single submitter ⚠
- p.Gly906Arg Single submitter ⚠
- p.His525Tyr Single submitter ⚠
- p.His548Asn Single submitter ⚠
- p.His59Asn Single submitter ⚠
- p.Ile213Lys Single submitter ⚠
- p.Ile267Val Single submitter ⚠
- p.Ile279Ser Single submitter ⚠
- p.Ile402Val Single submitter ⚠
- p.Ile427Val Single submitter ⚠
- p.Ile478Val Single submitter ⚠
- p.Ile682Thr Single submitter ⚠
- p.Ile746Ser Single submitter ⚠
- p.Ile746Val Single submitter ⚠
- p.Ile864Val Single submitter ⚠
- p.Ile86Phe Single submitter ⚠
- p.Ile909Thr Single submitter ⚠
- p.Ile969Val Single submitter ⚠
- p.Ile987Val Single submitter ⚠
- p.Leu17Val Single submitter ⚠
- p.Leu280Phe Single submitter ⚠
- p.Leu39Val Single submitter ⚠
- p.Leu960Phe Single submitter ⚠
- p.Lys442Arg Single submitter ⚠
- p.Lys442Met Single submitter
- p.Lys776Glu Single submitter ⚠
- p.Lys846Asn Single submitter ⚠
- p.Lys916Arg Single submitter ⚠
- p.Met748Val Single submitter ⚠
- p.Phe171Val Single submitter ⚠
- p.Phe28Leu Single submitter ⚠
- p.Phe773Val Single submitter ⚠
- p.Phe964Leu Single submitter ⚠
- p.Phe975Val Single submitter ⚠
- p.Pro148Thr Single submitter ⚠
- p.Pro266Ser Single submitter ⚠
- p.Pro504Ser Single submitter ⚠
- p.Pro518Leu Single submitter ⚠
- p.Pro58Thr Single submitter ⚠
- p.Pro599Leu Single submitter ⚠
- p.Pro619Leu Single submitter
- p.Pro626Leu Single submitter CNTN4-related disorder ⚠
- p.Ser1014Gly Single submitter ⚠
- p.Ser526Leu Single submitter ⚠
- p.Ser707Gly Single submitter ⚠
- p.Ser78Asn Single submitter ⚠
- p.Ser78Gly Single submitter ⚠
- p.Ser913Ala Single submitter ⚠
- p.Ser983Asn Single submitter ⚠
- p.Thr193Ala Single submitter ⚠
- p.Thr455Ile Single submitter ⚠
- p.Thr489Ser Single submitter ⚠
- p.Thr498Pro Single submitter
- p.Thr522Met Single submitter ⚠
- p.Thr865Met Single submitter ⚠
- p.Trp318Cys Single submitter ⚠
- p.Trp910Arg Single submitter ⚠
- p.Tyr165His Single submitter ⚠
- p.Tyr630His Single submitter ⚠
- p.Tyr940Phe Single submitter ⚠
- p.Val110Leu Single submitter ⚠
- p.Val172Ile Single submitter ⚠
- p.Val205Ile Single submitter ⚠
- p.Val254Ile Single submitter ⚠
- p.Val327Leu Single submitter ⚠
- p.Val333Ala Single submitter ⚠
- p.Val333Phe Single submitter ⚠
- p.Val416Leu Single submitter ⚠
- p.Val426Leu Single submitter ⚠
- p.Val467Ile Single submitter ⚠
- p.Val511Ala Single submitter ⚠
- p.Val52Leu Single submitter ⚠
- p.Val767Met Single submitter ⚠
- p.Val924Met Single submitter ⚠
- p.Val933Gly Single submitter ⚠
- p.Thr417Asn No assertion criteria ⚠
- p.Thr476Ile No assertion criteria CNTN4-related disorder ⚠