CNTNAP3 — 213 ClinVar variants

All ClinVar germline CNTNAP3 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 189 flagged for review →

1 Conflicting · 1 Benign · 16 Likely benign · 195 Uncertain significance

Full CNTNAP3 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 189

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 1

ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.

CNTNAP3 p.Glu775Lys Conflicting Single submitter

Predictors lean, ClinVar uncertain 151

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification. · showing the 150 best-reviewed of 151

Predictors split 37

The independent predictors disagree with each other — read with care.

All CNTNAP3 variants

Conflicting classifications of pathogenicity 1

p.Glu775Lys Single submitter ⚠

Benign 1

p.Pro318= Single submitter

Likely benign 16

p.Ala902= Single submitter
p.Arg1050Gln Single submitter
p.Arg1050Gly Single submitter
p.Arg205Lys Single submitter
p.Arg326His Single submitter
p.Arg413Gln Single submitter
p.Arg689Leu Single submitter
p.Glu1112Ala Single submitter
p.Ile204Val Single submitter
p.Met1010Ile Single submitter
p.Phe1004= Single submitter
p.Pro435= Single submitter
p.Ser1122Asn Single submitter
p.Thr282Met Single submitter
p.Tyr659= Single submitter
p.Val207Ile Single submitter

Uncertain significance 195

p.Ala1002Thr Single submitter ⚠
p.Ala1090Thr Single submitter ⚠
p.Ala1099Ser Single submitter ⚠
p.Ala1150Pro Single submitter ⚠
p.Ala1152Val Single submitter ⚠
p.Ala1159Val Single submitter ⚠
p.Ala1160Glu Single submitter ⚠
p.Ala1177Pro Single submitter
p.Ala1198Val Single submitter ⚠
p.Ala1205Thr Single submitter ⚠
p.Ala1208Glu Single submitter ⚠
p.Ala1208Val Single submitter ⚠
p.Ala523Glu Single submitter ⚠
p.Ala629Val Single submitter ⚠
p.Ala640Pro Single submitter ⚠
p.Ala640Thr Single submitter ⚠
p.Ala663Thr Single submitter ⚠
p.Ala987Val Single submitter ⚠
p.Arg1033Gly Single submitter ⚠
p.Arg1039Thr Single submitter ⚠
p.Arg1184His Single submitter ⚠
p.Arg1214Gln Single submitter ⚠
p.Arg1267Ser Single submitter ⚠
p.Arg1275Cys Single submitter ⚠
p.Arg1275Pro Single submitter ⚠
p.Arg322Gln Single submitter ⚠
p.Arg322Trp Single submitter ⚠
p.Arg399Gly Single submitter ⚠
p.Arg413Pro Single submitter ⚠
p.Arg414Cys Single submitter ⚠
p.Arg414Ser Single submitter ⚠
p.Arg598Gln Single submitter ⚠
p.Arg644Gly Single submitter ⚠
p.Arg675Cys Single submitter ⚠
p.Arg683His Single submitter ⚠
p.Arg693Gly Single submitter ⚠
p.Arg743Gln Single submitter ⚠
p.Arg743Trp Single submitter ⚠
p.Arg909Cys Single submitter ⚠
p.Arg909His Single submitter ⚠
p.Arg926Thr Single submitter ⚠
p.Arg970Cys Single submitter ⚠
p.Arg970His Single submitter ⚠
p.Arg979Cys Single submitter ⚠
p.Arg979Leu Single submitter ⚠
p.Asn1073Asp Single submitter ⚠
p.Asn1097Ser Single submitter ⚠
p.Asn1136Ser Single submitter ⚠
p.Asn1278Asp Single submitter ⚠
p.Asn246Asp Single submitter ⚠
p.Asn359Ser Single submitter ⚠
p.Asn386His Single submitter ⚠
p.Asn386Lys Single submitter ⚠
p.Asn729Ser Single submitter ⚠
p.Asn798Ser Single submitter ⚠
p.Asn833Lys Single submitter ⚠
p.Asn874Ser Single submitter ⚠
p.Asn998Ser Single submitter ⚠
p.Asp1034Ala Single submitter ⚠
p.Asp206Tyr Single submitter
p.Asp289Gly Single submitter ⚠
p.Asp342Tyr Single submitter ⚠
p.Asp450Asn Single submitter ⚠
p.Asp543Gly Single submitter ⚠
p.Asp567Asn Single submitter ⚠
p.Asp694Glu Single submitter ⚠
p.Asp855Asn Single submitter ⚠
p.Cys931Trp Single submitter ⚠
p.Cys984Ser Single submitter ⚠
p.Gln1015Arg Single submitter ⚠
p.Gln18Glu Single submitter ⚠
p.Gln476Glu Single submitter ⚠
p.Gln531Glu Single submitter ⚠
p.Gln875Glu Single submitter ⚠
p.Gln891Lys Single submitter ⚠
p.Gln891Pro Single submitter ⚠
p.Gln911Arg Single submitter ⚠
p.Gln915Pro Single submitter ⚠
p.Glu1064Asp Single submitter
p.Glu1234Asp Single submitter ⚠
p.Glu278Lys Single submitter ⚠
p.Glu561Lys Single submitter ⚠
p.Glu589Lys Single submitter ⚠
p.Glu745Ala Single submitter ⚠
p.Glu945Ala Single submitter ⚠
p.Glu946Lys Single submitter ⚠
p.Glu999Gly Single submitter
p.Gly1074Val Single submitter ⚠
p.Gly1101Ala Single submitter ⚠
p.Gly1223Val Single submitter ⚠
p.Gly1248Arg Single submitter ⚠
p.Gly314Glu Single submitter
p.Gly388Ala Single submitter ⚠
p.Gly493Asp Single submitter
p.Gly500Arg Single submitter ⚠
p.Gly509Glu Single submitter ⚠
p.Gly532Glu Single submitter ⚠
p.Gly546Ser Single submitter ⚠
p.Gly575Asp Single submitter ⚠
p.Gly685Trp Single submitter ⚠
p.Gly787Arg Single submitter ⚠
p.Gly828Arg Single submitter ⚠
p.Gly835Arg Single submitter ⚠
p.Gly966Glu Single submitter ⚠
p.Gly972Ala Single submitter ⚠
p.His1017Tyr Single submitter ⚠
p.His1085Pro Single submitter ⚠
p.His228Tyr Single submitter ⚠
p.His464Asn Single submitter ⚠
p.His907Gln Single submitter ⚠
p.Ile1142Val Single submitter ⚠
p.Ile256Met Single submitter ⚠
p.Ile256Val Single submitter ⚠
p.Ile527Phe Single submitter ⚠
p.Ile542Arg Single submitter ⚠
p.Ile607Thr Single submitter ⚠
p.Ile731Thr Single submitter ⚠
p.Leu1020Ser Single submitter ⚠
p.Leu1027Phe Single submitter ⚠
p.Leu1037Ser Single submitter ⚠
p.Leu1129Phe Single submitter
p.Leu1141Phe Single submitter ⚠
p.Leu1220Val Single submitter ⚠
p.Leu266Pro Single submitter ⚠
p.Leu540Val Single submitter ⚠
p.Leu726Ser Single submitter ⚠
p.Leu784Phe Single submitter ⚠
p.Leu834Met Single submitter ⚠
p.Lys199Asn Single submitter ⚠
p.Lys290Arg Single submitter ⚠
p.Lys348Glu Single submitter ⚠
p.Lys349Arg Single submitter ⚠
p.Lys429Arg Single submitter ⚠
p.Met1200Arg Single submitter ⚠
p.Met1200Leu Single submitter ⚠
p.Met215Ile Single submitter ⚠
p.Met899Leu Single submitter ⚠
p.Phe1173Leu Single submitter ⚠
p.Phe212Leu Single submitter ⚠
p.Phe819Cys Single submitter ⚠
p.Phe830Ile Single submitter ⚠
p.Pro1088Arg Single submitter ⚠
p.Pro1199Ser Single submitter ⚠
p.Pro1212Arg Single submitter ⚠
p.Pro1212Leu Single submitter ⚠
p.Pro258Leu Single submitter ⚠
p.Pro318Ala Single submitter ⚠
p.Pro435Thr Single submitter ⚠
p.Pro439Ser Single submitter ⚠
p.Pro553Leu Single submitter ⚠
p.Pro638Leu Single submitter ⚠
p.Pro651Gln Single submitter ⚠
p.Pro717Thr Single submitter ⚠
p.Pro807Leu Single submitter ⚠
p.Pro903Ser Single submitter ⚠
p.Ser1021Thr Single submitter ⚠
p.Ser1029Pro Single submitter ⚠
p.Ser1209Cys Single submitter ⚠
p.Ser301Ala Single submitter ⚠
p.Ser416Ala Single submitter ⚠
p.Ser418Thr Single submitter ⚠
p.Ser570Cys Single submitter ⚠
p.Ser914Arg Single submitter ⚠
p.Ser963Arg Single submitter ⚠
p.Thr1006Ala Single submitter ⚠
p.Thr292Ile Single submitter ⚠
p.Thr579Ala Single submitter ⚠
p.Thr696Ser Single submitter ⚠
p.Thr723Ser Single submitter ⚠
p.Thr864Met Single submitter ⚠
p.Thr949Ser Single submitter ⚠
p.Thr951Met Single submitter ⚠
p.Trp701Cys Single submitter ⚠
p.Tyr1012Phe Single submitter ⚠
p.Tyr735Phe Single submitter ⚠
p.Val1028Ile Single submitter ⚠
p.Val1035Ala Single submitter ⚠
p.Val1138Ile Single submitter ⚠
p.Val1197Leu Single submitter ⚠
p.Val11Leu Single submitter ⚠
p.Val1250Met Single submitter ⚠
p.Val275Ile Single submitter ⚠
p.Val284Ile Single submitter ⚠
p.Val288Leu Single submitter ⚠
p.Val288Met Single submitter ⚠
p.Val343Asp Single submitter ⚠
p.Val370Ala Single submitter ⚠
p.Val392Ala Single submitter ⚠
p.Val392Met Single submitter ⚠
p.Val420Ile Single submitter ⚠
p.Val468Met Single submitter ⚠
p.Val469Ala Single submitter ⚠
p.Val479Met Single submitter ⚠
p.Val817Met Single submitter ⚠
p.Val940Leu Single submitter ⚠