CNTN6 — 256 ClinVar variants
All ClinVar germline CNTN6 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 163 flagged for review →
1 Pathogenic · 2 Likely pathogenic · 2 Conflicting · 16 Benign · 4 Benign/Likely benign · 44 Likely benign · 187 Uncertain significance
Full CNTN6 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 163
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 134
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- CNTN6 p.Ala1023Pro Uncertain significance Single submitter
- CNTN6 p.Ala1023Thr Uncertain significance Single submitter
- CNTN6 p.Ala156Thr Uncertain significance Single submitter
- CNTN6 p.Ala280Gly Uncertain significance Single submitter
- CNTN6 p.Ala387Thr Uncertain significance Single submitter
- CNTN6 p.Ala387Val Uncertain significance Single submitter
- CNTN6 p.Ala407Thr Uncertain significance Single submitter
- CNTN6 p.Ala52Gly Uncertain significance Single submitter
- CNTN6 p.Ala816Thr Uncertain significance Single submitter
- CNTN6 p.Ala825Thr Uncertain significance Single submitter
- CNTN6 p.Ala871Val Uncertain significance Single submitter
- CNTN6 p.Ala885Gly Uncertain significance Single submitter
- CNTN6 p.Arg232Cys Uncertain significance Single submitter
- CNTN6 p.Arg263Lys Uncertain significance Single submitter
- CNTN6 p.Arg2Ser Uncertain significance Single submitter
- CNTN6 p.Arg363Ile Uncertain significance Single submitter
- CNTN6 p.Arg438Thr Uncertain significance Single submitter
- CNTN6 p.Arg595Lys Uncertain significance Single submitter
- CNTN6 p.Arg674His Uncertain significance Single submitter
- CNTN6 p.Arg741Trp Uncertain significance Single submitter
- CNTN6 p.Arg764Lys Uncertain significance Single submitter
- CNTN6 p.Asn346Lys Uncertain significance Single submitter
- CNTN6 p.Asn538Ser Uncertain significance Single submitter
- CNTN6 p.Asn625Thr Uncertain significance Single submitter
- CNTN6 p.Asn895Ser Uncertain significance Single submitter
- CNTN6 p.Asn945Thr Uncertain significance Single submitter
- CNTN6 p.Asn957Ser Uncertain significance Single submitter
- CNTN6 p.Asp190Asn Uncertain significance Single submitter
- CNTN6 p.Asp258His Uncertain significance Single submitter
- CNTN6 p.Asp40Val Uncertain significance Single submitter
- CNTN6 p.Gln204Glu Uncertain significance Single submitter
- CNTN6 p.Gln216Glu Uncertain significance Single submitter
- CNTN6 p.Gln365Lys Uncertain significance Single submitter
- CNTN6 p.Gln803Lys Uncertain significance Single submitter
- CNTN6 p.Gln812His Uncertain significance Single submitter
- CNTN6 p.Gln93His Uncertain significance Single submitter
- CNTN6 p.Gln947Arg Uncertain significance Single submitter
- CNTN6 p.Glu1006Asp Uncertain significance Single submitter
- CNTN6 p.Glu136Asp Uncertain significance Single submitter
- CNTN6 p.Glu235Ala Uncertain significance Single submitter
- CNTN6 p.Glu290Asp Uncertain significance Single submitter
- CNTN6 p.Glu460Asp Uncertain significance Single submitter
- CNTN6 p.Glu801Asp Uncertain significance Single submitter
- CNTN6 p.Glu924Gly Uncertain significance Single submitter
- CNTN6 p.Glu954Asp Uncertain significance Single submitter
- CNTN6 p.Gly19Asp Uncertain significance Single submitter
- CNTN6 p.Gly547Ala Uncertain significance Single submitter
- CNTN6 p.Gly547Val Uncertain significance Single submitter
- CNTN6 p.Gly54Cys Uncertain significance Single submitter
- CNTN6 p.Gly731Arg Uncertain significance Single submitter
-
CNTN6 p.Gly981Ala
Uncertain significance
Single submitter
CNTN6-related disorder
- CNTN6 p.Ile1002Val Uncertain significance Single submitter
- CNTN6 p.Ile1028Thr Uncertain significance Single submitter
- CNTN6 p.Ile14Leu Uncertain significance Single submitter
- CNTN6 p.Ile14Thr Uncertain significance Single submitter
- CNTN6 p.Ile237Val Uncertain significance Single submitter
- CNTN6 p.Ile281Val Uncertain significance Single submitter
- CNTN6 p.Ile331Val Uncertain significance Single submitter
- CNTN6 p.Ile372Val Uncertain significance Single submitter
- CNTN6 p.Ile47Phe Uncertain significance Single submitter
- CNTN6 p.Ile47Val Uncertain significance Single submitter
- CNTN6 p.Ile495Thr Uncertain significance Single submitter
- CNTN6 p.Ile554Thr Uncertain significance Single submitter
- CNTN6 p.Ile593Met Uncertain significance Single submitter
- CNTN6 p.Ile683Thr Uncertain significance Single submitter
- CNTN6 p.Ile794Thr Uncertain significance Single submitter
- CNTN6 p.Ile852Thr Uncertain significance Single submitter
- CNTN6 p.Ile866Leu Uncertain significance Single submitter
- CNTN6 p.Leu22Ile Uncertain significance Single submitter
- CNTN6 p.Leu252Phe Uncertain significance Single submitter
- CNTN6 p.Leu329Val Uncertain significance Single submitter
- CNTN6 p.Leu336Val Uncertain significance Single submitter
- CNTN6 p.Leu464Phe Uncertain significance Single submitter
- CNTN6 p.Leu519Pro Uncertain significance Single submitter
- CNTN6 p.Leu665Phe Uncertain significance Single submitter
- CNTN6 p.Leu941Met Uncertain significance Single submitter
- CNTN6 p.Leu971Phe Uncertain significance Single submitter
- CNTN6 p.Lys545Arg Uncertain significance Single submitter
- CNTN6 p.Lys574Arg Uncertain significance Single submitter
-
CNTN6 p.Lys6Glu
Uncertain significance
Single submitter
CNTN6-related disorder
- CNTN6 p.Lys750Arg Uncertain significance Single submitter
- CNTN6 p.Lys913Gln Uncertain significance Single submitter
- CNTN6 p.Met222Ile Uncertain significance Single submitter
- CNTN6 p.Met375Lys Uncertain significance Single submitter
- CNTN6 p.Met563Leu Uncertain significance Single submitter
- CNTN6 p.Met929Thr Uncertain significance Single submitter
- CNTN6 p.Phe1019Ile Uncertain significance Single submitter
- CNTN6 p.Phe197Tyr Uncertain significance Single submitter
- CNTN6 p.Pro163Arg Uncertain significance Single submitter
- CNTN6 p.Pro163Thr Uncertain significance Single submitter
- CNTN6 p.Pro188Ser Uncertain significance Single submitter
- CNTN6 p.Pro211Thr Uncertain significance Single submitter
- CNTN6 p.Pro347His Uncertain significance Single submitter
- CNTN6 p.Pro360Ala Uncertain significance Single submitter
- CNTN6 p.Pro520Ser Uncertain significance Single submitter
- CNTN6 p.Pro770Ala Uncertain significance Single submitter
- CNTN6 p.Pro893Ala Uncertain significance Single submitter
- CNTN6 p.Pro89His Uncertain significance Single submitter
- CNTN6 p.Pro902Ser Uncertain significance Single submitter
- CNTN6 p.Ser17Tyr Uncertain significance Single submitter
- CNTN6 p.Ser244Phe Uncertain significance Single submitter
- CNTN6 p.Ser276Thr Uncertain significance Single submitter
- CNTN6 p.Ser278Pro Uncertain significance Single submitter
- CNTN6 p.Ser442Phe Uncertain significance Single submitter
- CNTN6 p.Ser44Pro Uncertain significance Single submitter
- CNTN6 p.Ser463Asn Uncertain significance Single submitter
- CNTN6 p.Ser626Ile Uncertain significance Single submitter
- CNTN6 p.Ser74Thr Uncertain significance Single submitter
- CNTN6 p.Ser797Phe Uncertain significance Single submitter
- CNTN6 p.Thr126Ile Uncertain significance Single submitter
- CNTN6 p.Thr158Ile Uncertain significance Single submitter
- CNTN6 p.Thr370Ile Uncertain significance Single submitter
- CNTN6 p.Thr447Lys Uncertain significance Single submitter
- CNTN6 p.Thr449Ala Uncertain significance Single submitter
- CNTN6 p.Thr582Ile Uncertain significance Single submitter
- CNTN6 p.Thr613Ser Uncertain significance Single submitter
- CNTN6 p.Thr720Met Uncertain significance Single submitter
- CNTN6 p.Thr746Lys Uncertain significance Single submitter
- CNTN6 p.Thr832Ala Uncertain significance Single submitter
- CNTN6 p.Thr832Asn Uncertain significance Single submitter
- CNTN6 p.Thr844Arg Uncertain significance Single submitter
- CNTN6 p.Thr863Ala Uncertain significance Single submitter
- CNTN6 p.Thr884Ser Uncertain significance Single submitter
- CNTN6 p.Trp351Arg Uncertain significance Single submitter
- CNTN6 p.Trp535Arg Uncertain significance Single submitter
- CNTN6 p.Trp912Cys Uncertain significance Single submitter
- CNTN6 p.Tyr384His Uncertain significance Single submitter
- CNTN6 p.Val166Ile Uncertain significance Single submitter
- CNTN6 p.Val273Ile Uncertain significance Single submitter
- CNTN6 p.Val423Leu Uncertain significance Single submitter
- CNTN6 p.Val518Leu Uncertain significance Single submitter
- CNTN6 p.Val676Ala Uncertain significance Single submitter
- CNTN6 p.Val705Leu Uncertain significance Single submitter
-
CNTN6 p.Val215Leu
Uncertain significance
No assertion criteria
CNTN6-related disorder
Predictors split 27
The independent predictors disagree with each other — read with care.
- CNTN6 p.Ala299Ser Uncertain significance Single submitter
- CNTN6 p.Ala52Val Uncertain significance Single submitter
- CNTN6 p.Ala881Pro Uncertain significance Single submitter
- CNTN6 p.Arg25Cys Uncertain significance Single submitter
- CNTN6 p.Arg636Gln Uncertain significance Single submitter
- CNTN6 p.Asn306Lys Uncertain significance Single submitter
- CNTN6 p.Gln99Lys Uncertain significance Single submitter
- CNTN6 p.Gly310Ser Likely benign Single submitter
- CNTN6 p.Gly382Ala Uncertain significance Single submitter
- CNTN6 p.His571Asn Uncertain significance Single submitter
- CNTN6 p.Ile229Met Likely benign Single submitter
- CNTN6 p.Ile395Thr Uncertain significance Single submitter
- CNTN6 p.Met563Lys Uncertain significance Single submitter
- CNTN6 p.Phe485Leu Uncertain significance Single submitter
- CNTN6 p.Phe876Ser Uncertain significance Single submitter
- CNTN6 p.Pro527Leu Uncertain significance Single submitter
- CNTN6 p.Ser130Arg Uncertain significance Single submitter
-
CNTN6 p.Ser611Arg
Uncertain significance
Single submitter
CNTN6-related disorder
- CNTN6 p.Ser745Leu Likely benign Single submitter
- CNTN6 p.Ser813Ile Uncertain significance Single submitter
- CNTN6 p.Thr500Ile Uncertain significance Single submitter
- CNTN6 p.Tyr477Phe Uncertain significance Single submitter
- CNTN6 p.Val231Leu Uncertain significance Single submitter
- CNTN6 p.Val579Leu Uncertain significance Single submitter
- CNTN6 p.Val821Phe Uncertain significance Single submitter
- CNTN6 p.Val857Ala Uncertain significance Single submitter
-
CNTN6 p.Met819Ile
Likely benign
No assertion criteria
CNTN6-related disorder
All CNTN6 variants
Pathogenic 1
- p.Tyr315fs Single submitter
Likely pathogenic 2
- c.1492+1G>T Single submitter autism spectrum disorder
- p.Ser189Ter Single submitter Autistic behavior
Conflicting classifications of pathogenicity 2
- p.Arg232His Single submitter ⚠
- p.Ser453Asn Single submitter ⚠
Benign 16
- c.1213+8G>A Multiple submitters
- p.Ala440Ser Multiple submitters
- p.Arg135Ter Multiple submitters
- p.Gly96= Multiple submitters
- p.Ile1024Leu Multiple submitters
- p.Leu181= Multiple submitters
- p.Leu464= Multiple submitters
- p.Phe150Ser Multiple submitters
- p.Val753= Multiple submitters
- c.1668+8A>T Single submitter
- c.761+6GTTTTT[2] Single submitter
- p.Glu400Gln Single submitter
- p.Lys546Arg Single submitter
- p.Val8= Single submitter
- p.Gly888= No assertion criteria CNTN6-related disorder
- p.Thr720= No assertion criteria CNTN6-related disorder
Benign/Likely benign 4
- p.Gly1001= Multiple submitters
- p.Ile529Leu Multiple submitters
- p.Lys113= Multiple submitters
- p.Ser984= Multiple submitters
Likely benign 44
- p.Arg303Gln Multiple submitters
- c.1214-12T>A Single submitter
- c.1214-14G>A Single submitter
- c.1364+15A>G Single submitter
- c.1364+25dup Single submitter
- c.1786+20A>G Single submitter
- c.183-9del Single submitter
- c.183-9dup Single submitter
- c.2402-13_2402-10del Single submitter
- c.2518-15G>A Single submitter
- c.359-14C>T Single submitter
- c.455-17T>C Single submitter
- p.Ala590= Single submitter
- p.Ala620Pro Single submitter
- p.Ala827Val Single submitter
- p.Arg217Cys Single submitter
- p.Asn730= Single submitter
- p.Gly310Ser Single submitter ⚠
- p.Gly486= Single submitter
- p.Gly735= Single submitter
- p.Ile198Val Single submitter
- p.Ile229Met Single submitter ⚠
- p.Ile874Val Single submitter
- p.Leu264= Single submitter
- p.Lys489= Single submitter
- p.Lys993= Single submitter
- p.Pro148Arg Single submitter
- p.Pro700= Single submitter
- p.Ser745Leu Single submitter ⚠
- p.Ser891= Single submitter
- p.Thr128Ile Single submitter
- p.Thr447= Single submitter
- p.Thr793Ser Single submitter
- p.Thr873= Single submitter
- p.Tyr60= Single submitter
- p.Val504= Single submitter
- p.Val532= Single submitter
- p.Val840= Single submitter
- p.Gln729= No assertion criteria CNTN6-related disorder
- p.Leu841= No assertion criteria CNTN6-related disorder
- p.Leu869= No assertion criteria CNTN6-related disorder
- p.Met819Ile No assertion criteria CNTN6-related disorder ⚠
- p.Ser57= No assertion criteria CNTN6-related disorder
- p.Ser986Thr No assertion criteria CNTN6-related disorder
Uncertain significance 187
- c.1669-6C>T Single submitter
- c.2518-1G>A Single submitter
- c.946+2T>C Single submitter CNTN6-related disorder
- c.946+5G>A Single submitter CNTN6-related disorder
- p.Ala1023Pro Single submitter ⚠
- p.Ala1023Thr Single submitter ⚠
- p.Ala156Thr Single submitter ⚠
- p.Ala280Gly Single submitter ⚠
- p.Ala299Ser Single submitter ⚠
- p.Ala387Thr Single submitter ⚠
- p.Ala387Val Single submitter ⚠
- p.Ala407Thr Single submitter ⚠
- p.Ala52Gly Single submitter ⚠
- p.Ala52Val Single submitter ⚠
- p.Ala816Thr Single submitter ⚠
- p.Ala825Thr Single submitter ⚠
- p.Ala871Val Single submitter ⚠
- p.Ala881Pro Single submitter ⚠
- p.Ala885fs Single submitter CNTN6-related disorder
- p.Ala885Gly Single submitter ⚠
- p.Arg217Gly Single submitter
- p.Arg232Cys Single submitter ⚠
- p.Arg25Cys Single submitter ⚠
- p.Arg263Lys Single submitter ⚠
- p.Arg2Ser Single submitter ⚠
- p.Arg363Ile Single submitter ⚠
- p.Arg438Thr Single submitter ⚠
- p.Arg595Lys Single submitter ⚠
- p.Arg636Gln Single submitter ⚠
- p.Arg674His Single submitter ⚠
- p.Arg714Leu Single submitter
- p.Arg741Gln Single submitter
- p.Arg741Trp Single submitter ⚠
- p.Arg764Lys Single submitter ⚠
- p.Asn193Lys Single submitter
- p.Asn306Lys Single submitter ⚠
- p.Asn346Lys Single submitter ⚠
- p.Asn538Ser Single submitter ⚠
- p.Asn625Thr Single submitter ⚠
- p.Asn895Ser Single submitter ⚠
- p.Asn945Thr Single submitter ⚠
- p.Asn957Ser Single submitter ⚠
- p.Asp190Asn Single submitter ⚠
- p.Asp258His Single submitter ⚠
- p.Asp40Val Single submitter ⚠
- p.Asp800Val Single submitter
- p.Gln204Glu Single submitter ⚠
- p.Gln216Glu Single submitter ⚠
- p.Gln30Leu Single submitter
- p.Gln365Lys Single submitter ⚠
- p.Gln803Lys Single submitter ⚠
- p.Gln812His Single submitter ⚠
- p.Gln93His Single submitter ⚠
- p.Gln947Arg Single submitter ⚠
- p.Gln99Lys Single submitter ⚠
- p.Glu1006Asp Single submitter ⚠
- p.Glu136Asp Single submitter ⚠
- p.Glu187Gly Single submitter CNTN6-related disorder
- p.Glu235Ala Single submitter ⚠
- p.Glu290Asp Single submitter ⚠
- p.Glu460Asp Single submitter ⚠
- p.Glu801Asp Single submitter ⚠
- p.Glu924Gly Single submitter ⚠
- p.Glu954Asp Single submitter ⚠
- p.Glu961Ala Single submitter
- p.Gly19Asp Single submitter ⚠
- p.Gly382Ala Single submitter ⚠
- p.Gly547Ala Single submitter ⚠
- p.Gly547Val Single submitter ⚠
- p.Gly54Cys Single submitter ⚠
- p.Gly731Arg Single submitter ⚠
- p.Gly980Ser Single submitter
- p.Gly981Ala Single submitter CNTN6-related disorder ⚠
- p.His571Asn Single submitter ⚠
- p.Ile1002Val Single submitter ⚠
- p.Ile1028Thr Single submitter ⚠
- p.Ile14Leu Single submitter ⚠
- p.Ile14Thr Single submitter ⚠
- p.Ile237Val Single submitter ⚠
- p.Ile281Val Single submitter ⚠
- p.Ile331Val Single submitter ⚠
- p.Ile372Val Single submitter ⚠
- p.Ile395Thr Single submitter ⚠
- p.Ile466Val Single submitter
- p.Ile47Phe Single submitter ⚠
- p.Ile47Val Single submitter ⚠
- p.Ile495Thr Single submitter ⚠
- p.Ile554Thr Single submitter ⚠
- p.Ile593Met Single submitter ⚠
- p.Ile681Thr Single submitter
- p.Ile683Thr Single submitter ⚠
- p.Ile794Thr Single submitter ⚠
- p.Ile852Thr Single submitter ⚠
- p.Ile866Leu Single submitter ⚠
- p.Leu22Ile Single submitter ⚠
- p.Leu252Phe Single submitter ⚠
- p.Leu329Val Single submitter ⚠
- p.Leu336Val Single submitter ⚠
- p.Leu464Phe Single submitter ⚠
- p.Leu519Pro Single submitter ⚠
- p.Leu665Phe Single submitter ⚠
- p.Leu941Met Single submitter ⚠
- p.Leu962Phe Single submitter
- p.Leu971Phe Single submitter ⚠
- p.Lys272Asn Single submitter
- p.Lys432Ile Single submitter
- p.Lys545Arg Single submitter ⚠
- p.Lys574Arg Single submitter ⚠
- p.Lys6Glu Single submitter CNTN6-related disorder ⚠
- p.Lys750Arg Single submitter ⚠
- p.Lys913Gln Single submitter ⚠
- p.Met222Ile Single submitter ⚠
- p.Met375Lys Single submitter ⚠
- p.Met563Leu Single submitter ⚠
- p.Met563Lys Single submitter ⚠
- p.Met929Thr Single submitter ⚠
- p.Phe1019Ile Single submitter ⚠
- p.Phe197Tyr Single submitter ⚠
- p.Phe485Leu Single submitter ⚠
- p.Phe876Ser Single submitter ⚠
- p.Pro163Arg Single submitter ⚠
- p.Pro163Thr Single submitter ⚠
- p.Pro188Ser Single submitter ⚠
- p.Pro211Thr Single submitter ⚠
- p.Pro347His Single submitter ⚠
- p.Pro360Ala Single submitter ⚠
- p.Pro520Ser Single submitter ⚠
- p.Pro527Leu Single submitter ⚠
- p.Pro700Ala Single submitter
- p.Pro770Ala Single submitter ⚠
- p.Pro893Ala Single submitter ⚠
- p.Pro89His Single submitter ⚠
- p.Pro902Ser Single submitter ⚠
- p.Ser130Arg Single submitter ⚠
- p.Ser130Ile Single submitter
- p.Ser17Tyr Single submitter ⚠
- p.Ser243Ter Single submitter CNTN6-related disorder
- p.Ser244Phe Single submitter ⚠
- p.Ser276Thr Single submitter ⚠
- p.Ser278Pro Single submitter ⚠
- p.Ser442Phe Single submitter ⚠
- p.Ser44Pro Single submitter ⚠
- p.Ser463Asn Single submitter ⚠
- p.Ser611Arg Single submitter CNTN6-related disorder ⚠
- p.Ser626Ile Single submitter ⚠
- p.Ser74Thr Single submitter ⚠
- p.Ser797Phe Single submitter ⚠
- p.Ser813Ile Single submitter ⚠
- p.Ser917Cys Single submitter
- p.Thr126Ile Single submitter ⚠
- p.Thr158Ile Single submitter ⚠
- p.Thr370Ile Single submitter ⚠
- p.Thr447Lys Single submitter ⚠
- p.Thr449Ala Single submitter ⚠
- p.Thr500Ile Single submitter ⚠
- p.Thr582Ile Single submitter ⚠
- p.Thr613Ile Single submitter
- p.Thr613Ser Single submitter ⚠
- p.Thr720Met Single submitter ⚠
- p.Thr746Lys Single submitter ⚠
- p.Thr832Ala Single submitter ⚠
- p.Thr832Asn Single submitter ⚠
- p.Thr844Arg Single submitter ⚠
- p.Thr863Ala Single submitter ⚠
- p.Thr884Ile Single submitter
- p.Thr884Ser Single submitter ⚠
- p.Trp337Leu Single submitter
- p.Trp351Arg Single submitter ⚠
- p.Trp535Arg Single submitter ⚠
- p.Trp912Cys Single submitter ⚠
- p.Tyr384His Single submitter ⚠
- p.Tyr392Asn Single submitter
- p.Tyr477Phe Single submitter ⚠
- p.Val166Ile Single submitter ⚠
- p.Val231Leu Single submitter ⚠
- p.Val245Leu Single submitter
- p.Val273Ile Single submitter ⚠
- p.Val423Leu Single submitter ⚠
- p.Val518Leu Single submitter ⚠
- p.Val579Leu Single submitter ⚠
- p.Val676Ala Single submitter ⚠
- p.Val705Leu Single submitter ⚠
- p.Val821Phe Single submitter ⚠
- p.Val857Ala Single submitter ⚠
- c.2402-6T>G No assertion criteria CNTN6-related disorder
- p.Tyr75Ter No assertion criteria CNTN6-related disorder
- p.Val215Leu No assertion criteria CNTN6-related disorder ⚠