NECTIN1 — 239 ClinVar variants
All ClinVar germline NECTIN1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 41 flagged for review →
5 Pathogenic · 3 Likely pathogenic · 22 Conflicting · 10 Benign · 1 Benign/Likely benign · 57 Likely benign · 141 Uncertain significance
Full NECTIN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 41
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 5
ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.
-
NECTIN1 p.Arg199Gln
Conflicting
Single submitter
cleft lip/palate-ectodermal dysplasia syndrome
-
NECTIN1 p.Arg210His
Conflicting
Single submitter
cleft lip/palate-ectodermal dysplasia syndrome
-
NECTIN1 p.Arg212His
Conflicting
Single submitter
cleft lip/palate-ectodermal dysplasia syndrome
-
NECTIN1 p.Gly44Ser
Conflicting
Single submitter
cleft lip/palate-ectodermal dysplasia syndrome
-
NECTIN1 p.Gly507Glu
Conflicting
Single submitter
cleft lip/palate-ectodermal dysplasia syndrome
Predictors lean, ClinVar uncertain 27
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
-
NECTIN1 p.Asp491Asn
Uncertain significance
Multiple submitters
cleft lip/palate-ectodermal dysplasia syndrome
-
NECTIN1 p.Gly445Ser
Uncertain significance
Multiple submitters
cleft lip/palate-ectodermal dysplasia syndrome
-
NECTIN1 p.Gly480Ser
Uncertain significance
Multiple submitters
cleft lip/palate-ectodermal dysplasia syndrome
-
NECTIN1 p.Pro340Gln
Uncertain significance
Multiple submitters
Inborn genetic diseases
- NECTIN1 p.Ala10Val Uncertain significance Single submitter
-
NECTIN1 p.Ala349Gly
Uncertain significance
Single submitter
Inborn genetic diseases
- NECTIN1 p.Arg234Cys Uncertain significance Single submitter
- NECTIN1 p.Arg298Gly Uncertain significance Single submitter
- NECTIN1 p.Arg477His Uncertain significance Single submitter
- NECTIN1 p.Arg94His Uncertain significance Single submitter
-
NECTIN1 p.Asp106Asn
Uncertain significance
Single submitter
Inborn genetic diseases
- NECTIN1 p.Asp233Glu Uncertain significance Single submitter
- NECTIN1 p.Asp233Gly Uncertain significance Single submitter
-
NECTIN1 p.Gly455Ser
Uncertain significance
Single submitter
Inborn genetic diseases
- NECTIN1 p.Ile315Leu Uncertain significance Single submitter
- NECTIN1 p.Lys465Gln Uncertain significance Single submitter
- NECTIN1 p.Pro342Ser Uncertain significance Single submitter
-
NECTIN1 p.Thr153Ala
Uncertain significance
Single submitter
Inborn genetic diseases
- NECTIN1 p.Thr354Met Uncertain significance Single submitter
- NECTIN1 p.Thr354Ser Uncertain significance Single submitter
- NECTIN1 p.Tyr481Cys Uncertain significance Single submitter
-
NECTIN1 p.Val228Ile
Uncertain significance
Single submitter
cleft lip/palate-ectodermal dysplasia syndrome
- NECTIN1 p.Val243Met Uncertain significance Single submitter
- NECTIN1 p.Val28Ile Uncertain significance Single submitter
- NECTIN1 p.Val375Leu Uncertain significance Single submitter
- NECTIN1 p.Val375Met Uncertain significance Single submitter
- NECTIN1 p.Val395Met Uncertain significance Single submitter
Predictors split 9
The independent predictors disagree with each other — read with care.
-
NECTIN1 p.Arg110Cys
Uncertain significance
Multiple submitters
cleft lip/palate-ectodermal dysplasia syndrome
- NECTIN1 p.Glu330Lys Benign/Likely benign Multiple submitters
-
NECTIN1 p.Met143Ile
Uncertain significance
Multiple submitters
cleft lip/palate-ectodermal dysplasia syndrome
- NECTIN1 p.Arg110His Uncertain significance Single submitter
-
NECTIN1 p.Arg96His
Uncertain significance
Single submitter
Inborn genetic diseases
- NECTIN1 p.Leu100Pro Uncertain significance Single submitter
- NECTIN1 p.Phe336Leu Likely benign Single submitter
- NECTIN1 p.Val360Gly Uncertain significance Single submitter
-
NECTIN1 p.Val360Met
Uncertain significance
Single submitter
cleft lip/palate-ectodermal dysplasia syndrome
All NECTIN1 variants
Pathogenic 5
- p.Glu186fs Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- p.Glu95Ter Single submitter
- p.Arg134Ter No assertion criteria cleft lip/palate-ectodermal dysplasia syndrome
- p.Thr324fs No assertion criteria cleft lip/palate-ectodermal dysplasia syndrome
- p.Trp185Ter No assertion criteria cleft lip/palate-ectodermal dysplasia syndrome
Likely pathogenic 3
- p.Gln76Ter Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- p.Trp515Ter Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- p.Arg158Ter No assertion criteria cleft lip/palate-ectodermal dysplasia syndrome
Conflicting classifications of pathogenicity 22
- c.431-4G>A Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.431-5C>T Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.79+4A>G Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.851+1G>A Single submitter
- c.*2751G>A Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- p.Arg199Gln Single submitter cleft lip/palate-ectodermal dysplasia syndrome ⚠
- p.Arg210His Single submitter cleft lip/palate-ectodermal dysplasia syndrome ⚠
- p.Arg212His Single submitter cleft lip/palate-ectodermal dysplasia syndrome ⚠
- p.Asn398= Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- p.Glu125= Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- p.Gly449= Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- p.Gly44Ser Single submitter cleft lip/palate-ectodermal dysplasia syndrome ⚠
- p.Gly507Glu Single submitter cleft lip/palate-ectodermal dysplasia syndrome ⚠
- p.His394= Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- p.Leu189= Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- p.Lys160= Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- p.Ser59= Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- p.Ser88= Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- p.Thr141= Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- p.Thr187= Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- p.Thr206= Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- p.Tyr516= Single submitter cleft lip/palate-ectodermal dysplasia syndrome
Benign 10
- c.*25972C>T Multiple submitters
- c.*2857A>C Multiple submitters cleft lip/palate-ectodermal dysplasia syndrome
- c.*3301T>C Multiple submitters cleft lip/palate-ectodermal dysplasia syndrome
- p.Glu444dup Multiple submitters cleft lip/palate-ectodermal dysplasia syndrome
- c.*537C>T Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*727T>C Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- p.Ala155= Single submitter
- p.Glu443_Glu444dup Single submitter
- p.Glu444del Single submitter
- c.1003+557G>T No assertion criteria NECTIN1-related disorder
Benign/Likely benign 1
- p.Glu330Lys Multiple submitters ⚠
Likely benign 57
- c.*1610G>C Multiple submitters cleft lip/palate-ectodermal dysplasia syndrome
- c.*5C>G Multiple submitters cleft lip/palate-ectodermal dysplasia syndrome
- p.Gly120= Multiple submitters
- c.1004-15C>G Single submitter
- c.1004-19A>C Single submitter
- c.430+5G>A Single submitter
- c.852-10C>T Single submitter
- c.*1391C>T Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*2103C>T Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*2481A>G Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*25967C>T Single submitter
- c.*2702T>C Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*2884G>A Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*3013G>A Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*3173G>A Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- p.Ala127= Single submitter
- p.Ala295= Single submitter
- p.Ala349= Single submitter
- p.Arg382= Single submitter
- p.Arg466= Single submitter
- p.Arg94= Single submitter
- p.Asn242= Single submitter
- p.Asn36= Single submitter
- p.Asn505= Single submitter
- p.Asn55= Single submitter
- p.Asp37= Single submitter
- p.Asp386Asn Single submitter
- p.Asp420= Single submitter
- p.Asp423= Single submitter
- p.Asp506= Single submitter
- p.Cys124= Single submitter
- p.Glu194= Single submitter
- p.Gly27= Single submitter
- p.Gly416= Single submitter
- p.Gly445= Single submitter
- p.Ile227= Single submitter
- p.Ile251= Single submitter
- p.Ile322= Single submitter
- p.Leu138= Single submitter
- p.Leu378= Single submitter
- p.Leu413= Single submitter
- p.Phe23= Single submitter
- p.Phe336Leu Single submitter ⚠
- p.Phe53= Single submitter
- p.Pro351= Single submitter
- p.Pro492= Single submitter
- p.Pro56= Single submitter
- p.Thr299= Single submitter
- p.Tyr490= Single submitter
- p.Tyr81= Single submitter
- c.1003+534G>A No assertion criteria NECTIN1-related disorder
- c.79+9G>A No assertion criteria NECTIN1-related disorder
- p.Ala351= No assertion criteria NECTIN1-related disorder
- p.Asp46= No assertion criteria NECTIN1-related disorder
- p.Gln409= No assertion criteria NECTIN1-related disorder
- p.Pro340= No assertion criteria NECTIN1-related disorder
- p.Thr21= No assertion criteria NECTIN1-related disorder
Uncertain significance 141
- c.*1139G>A Multiple submitters cleft lip/palate-ectodermal dysplasia syndrome
- c.*1179C>G Multiple submitters cleft lip/palate-ectodermal dysplasia syndrome
- c.*1595C>A Multiple submitters cleft lip/palate-ectodermal dysplasia syndrome
- c.*185T>C Multiple submitters cleft lip/palate-ectodermal dysplasia syndrome
- c.*2416A>G Multiple submitters cleft lip/palate-ectodermal dysplasia syndrome
- c.*3440G>A Multiple submitters cleft lip/palate-ectodermal dysplasia syndrome
- c.*3705G>A Multiple submitters cleft lip/palate-ectodermal dysplasia syndrome
- c.*607C>A Multiple submitters cleft lip/palate-ectodermal dysplasia syndrome
- c.*72C>G Multiple submitters cleft lip/palate-ectodermal dysplasia syndrome
- c.*736C>T Multiple submitters cleft lip/palate-ectodermal dysplasia syndrome
- c.*84C>T Multiple submitters cleft lip/palate-ectodermal dysplasia syndrome
- c.*961G>A Multiple submitters cleft lip/palate-ectodermal dysplasia syndrome
- p.Arg110Cys Multiple submitters cleft lip/palate-ectodermal dysplasia syndrome ⚠
- p.Asp491Asn Multiple submitters cleft lip/palate-ectodermal dysplasia syndrome ⚠
- p.Gly445Ser Multiple submitters cleft lip/palate-ectodermal dysplasia syndrome ⚠
- p.Gly480Ser Multiple submitters cleft lip/palate-ectodermal dysplasia syndrome ⚠
- p.Met143Ile Multiple submitters cleft lip/palate-ectodermal dysplasia syndrome ⚠
- p.Pro340Gln Multiple submitters Inborn genetic diseases ⚠
- p.Trp14Cys Multiple submitters cleft lip/palate-ectodermal dysplasia syndrome
- c.-102C>A Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.-146A>C Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.-151A>C Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.-50C>G Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*1087G>A Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*1108G>C Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*1120T>A Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*1126C>T Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*1129A>T Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*1132G>A Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*1168C>T Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*1184G>T Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*1241T>A Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*1266C>T Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*1330G>C Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*1337T>C Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*1368G>A Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*1382T>C Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*1422G>A Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*152C>A Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*1554G>A Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*1555C>T Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*1654C>G Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*165G>T Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*1666C>T Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*1760C>G Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*201G>A Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*2355C>T Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*2374C>T Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*2397A>C Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*2398G>T Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*2413A>G Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*2439G>A Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*2509G>A Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*2551T>G Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*2692C>G Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*269C>T Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*2733T>C Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*2750C>T Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*2847C>T Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*2852T>G Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*2882G>A Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*2902A>C Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*2969A>T Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*296T>C Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*3032T>C Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*3087C>G Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*3136G>A Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*315T>C Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*3174C>A Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*3185C>T Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*3194C>T Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*3294G>T Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*3351G>A Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*3365G>A Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*3405A>C Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*3425G>A Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*3426C>T Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*3488C>T Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*348C>T Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*352C>T Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*3545C>G Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*3567G>A Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*3629C>G Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*3634T>C Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*3636G>A Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*3647G>T Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*3714A>T Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*438C>T Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*46T>C Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*481C>T Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*51G>C Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*521G>C Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*532T>C Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*53A>C Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*554G>A Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*780G>T Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*795C>A Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*853C>G Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*883T>G Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*886C>T Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- c.*917G>T Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- p.Ala10Val Single submitter ⚠
- p.Ala347fs Single submitter
- p.Ala349Gly Single submitter Inborn genetic diseases ⚠
- p.Ala474= Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- p.Arg110His Single submitter ⚠
- p.Arg212Ser Single submitter
- p.Arg234Cys Single submitter ⚠
- p.Arg298Gly Single submitter ⚠
- p.Arg477His Single submitter ⚠
- p.Arg94His Single submitter ⚠
- p.Arg96His Single submitter Inborn genetic diseases ⚠
- p.Asn148= Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- p.Asp106Asn Single submitter Inborn genetic diseases ⚠
- p.Asp233Glu Single submitter ⚠
- p.Asp233Gly Single submitter ⚠
- p.Glu443_Glu444del Single submitter
- p.Glu444_Gly445insGluGluGluGluGlu Single submitter
- p.Glu452Lys Single submitter Inborn genetic diseases
- p.Gly455Ser Single submitter Inborn genetic diseases ⚠
- p.Ile315Leu Single submitter ⚠
- p.Leu100Pro Single submitter ⚠
- p.Leu168= Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- p.Leu300= Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- p.Lys465Gln Single submitter ⚠
- p.Met1Ile Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- p.Pro342Ser Single submitter ⚠
- p.Pro395Thr Single submitter
- p.Thr153Ala Single submitter Inborn genetic diseases ⚠
- p.Thr354Met Single submitter ⚠
- p.Thr354Ser Single submitter ⚠
- p.Tyr460= Single submitter cleft lip/palate-ectodermal dysplasia syndrome
- p.Tyr481Cys Single submitter ⚠
- p.Val228Ile Single submitter cleft lip/palate-ectodermal dysplasia syndrome ⚠
- p.Val243Met Single submitter ⚠
- p.Val28Ile Single submitter ⚠
- p.Val360Gly Single submitter ⚠
- p.Val360Met Single submitter cleft lip/palate-ectodermal dysplasia syndrome ⚠
- p.Val375Leu Single submitter ⚠
- p.Val375Met Single submitter ⚠
- p.Val395Met Single submitter ⚠