NECTIN4 — 81 ClinVar variants
All ClinVar germline NECTIN4 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 26 flagged for review →
10 Pathogenic · 2 Likely pathogenic · 1 Conflicting · 11 Benign · 2 Benign/Likely benign · 32 Likely benign · 23 Uncertain significance
Full NECTIN4 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 26
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 vs ClinVar 1
ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.
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NECTIN4 p.Arg284Gln
Pathogenic
No assertion criteria
ectodermal dysplasia-syndactyly syndrome 1
Predictors lean, ClinVar uncertain 17
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- NECTIN4 p.Asn489Asp Uncertain significance Multiple submitters
- NECTIN4 p.Glu8Lys Uncertain significance Multiple submitters
-
NECTIN4 p.Met436Val
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
NECTIN4 p.Pro463Ala
Uncertain significance
Multiple submitters
ectodermal dysplasia-syndactyly syndrome 1
-
NECTIN4 p.Thr497Met
Uncertain significance
Multiple submitters
ectodermal dysplasia-syndactyly syndrome 1
- NECTIN4 p.Arg324Thr Uncertain significance Single submitter
- NECTIN4 p.Cys270Tyr Uncertain significance Single submitter
- NECTIN4 p.Glu414Lys Uncertain significance Single submitter
-
NECTIN4 p.Glu78Gln
Uncertain significance
Single submitter
Inborn genetic diseases
- NECTIN4 p.Gly311Ser Uncertain significance Single submitter
- NECTIN4 p.Gly490Val Uncertain significance Single submitter
- NECTIN4 p.Lys85Asn Uncertain significance Single submitter
- NECTIN4 p.Pro104Arg Uncertain significance Single submitter
- NECTIN4 p.Ser192Phe Uncertain significance Single submitter
-
NECTIN4 p.Tyr125Ser
Uncertain significance
Single submitter
ectodermal dysplasia-syndactyly syndrome 1
- NECTIN4 p.Val295Met Uncertain significance Single submitter
-
NECTIN4 p.Arg506Gln
Uncertain significance
No assertion criteria
NECTIN4-related disorder
Predictors split 8
The independent predictors disagree with each other — read with care.
- NECTIN4 p.Phe53Leu Benign Multiple submitters
- NECTIN4 p.Pro104Thr Benign Multiple submitters
- NECTIN4 p.Arg377Cys Uncertain significance Single submitter
-
NECTIN4 p.Arg443Cys
Conflicting
Single submitter
ectodermal dysplasia-syndactyly syndrome 1
-
NECTIN4 p.Arg493Pro
Uncertain significance
Single submitter
ectodermal dysplasia-syndactyly syndrome 1
-
NECTIN4 p.Arg506Trp
Likely pathogenic
Single submitter
ectodermal dysplasia-syndactyly syndrome 1
-
NECTIN4 p.Ile501Val
Uncertain significance
Single submitter
Inborn genetic diseases
- NECTIN4 p.Thr205Ile Uncertain significance Single submitter
All NECTIN4 variants
Pathogenic 10
- p.Arg294Ter Single submitter ectodermal dysplasia-syndactyly syndrome 1
- p.Arg373Ter Single submitter
- p.Gln77Ter Single submitter ectodermal dysplasia-syndactyly syndrome 1
- p.Leu82fs Single submitter
- p.Arg284Gln No assertion criteria ectodermal dysplasia-syndactyly syndrome 1 ⚠
- p.Gln61Ter No assertion criteria ectodermal dysplasia-syndactyly syndrome 1
- p.Pro212Arg No assertion criteria ectodermal dysplasia-syndactyly syndrome 1
- p.Pro304fs No assertion criteria ectodermal dysplasia-syndactyly syndrome 1
- p.Thr185Met No assertion criteria ectodermal dysplasia-syndactyly syndrome 1
- p.Val242Met No assertion criteria ectodermal dysplasia-syndactyly syndrome 1
Likely pathogenic 2
- c.1233+1G>A Single submitter
- p.Arg506Trp Single submitter ectodermal dysplasia-syndactyly syndrome 1 ⚠
Conflicting classifications of pathogenicity 1
- p.Arg443Cys Single submitter ectodermal dysplasia-syndactyly syndrome 1 ⚠
Benign 11
- c.1000+18A>G Multiple submitters
- p.Leu146Met Multiple submitters
- p.Phe53Leu Multiple submitters ⚠
- p.Pro104Thr Multiple submitters ⚠
- c.1001-16G>A Single submitter
- p.Arg294Gln Single submitter
- p.Gly56= Single submitter
- p.Pro412= Single submitter
- p.Thr205= Single submitter
- p.Thr449= Single submitter
- p.Val451= Single submitter
Likely benign 32
- p.Cys127= Multiple submitters
- p.Pro107Leu Multiple submitters
- p.Pro228= Multiple submitters
- p.Ser310= Multiple submitters
- c.1157+13C>A Single submitter
- c.1234-17G>A Single submitter
- c.1308+8C>T Single submitter
- c.439+7G>A Single submitter
- c.731-13C>T Single submitter
- p.Ala203= Single submitter
- p.Ala31= Single submitter
- p.Ala420= Single submitter
- p.Ala7= Single submitter
- p.Arg142= Single submitter
- p.Arg144= Single submitter
- p.Asp184= Single submitter
- p.Glu421= Single submitter
- p.Glu95= Single submitter
- p.Gly422= Single submitter
- p.Gly500= Single submitter
- p.His423= Single submitter
- p.His89= Single submitter
- p.Ile356= Single submitter
- p.Lys49= Single submitter
- p.Pro149= Single submitter
- p.Thr222= Single submitter
- p.Thr393= Single submitter
- p.Thr447= Single submitter
- p.Thr497= Single submitter
- p.Tyr313= Single submitter
- p.Val328= Single submitter
- p.Val40= Single submitter
Uncertain significance 23
- p.Asn489Asp Multiple submitters ⚠
- p.Glu8Lys Multiple submitters ⚠
- p.Met436Val Multiple submitters Inborn genetic diseases ⚠
- p.Pro463Ala Multiple submitters ectodermal dysplasia-syndactyly syndrome 1 ⚠
- p.Thr497Met Multiple submitters ectodermal dysplasia-syndactyly syndrome 1 ⚠
- p.Arg200Ser Single submitter
- p.Arg324Thr Single submitter ⚠
- p.Arg377Cys Single submitter ⚠
- p.Arg493Pro Single submitter ectodermal dysplasia-syndactyly syndrome 1 ⚠
- p.Cys270Tyr Single submitter ⚠
- p.Glu414Lys Single submitter ⚠
- p.Glu78Gln Single submitter Inborn genetic diseases ⚠
- p.Gly311Ser Single submitter ⚠
- p.Gly490Val Single submitter ⚠
- p.Ile501Val Single submitter Inborn genetic diseases ⚠
- p.Leu333= Single submitter
- p.Lys85Asn Single submitter ⚠
- p.Pro104Arg Single submitter ⚠
- p.Ser192Phe Single submitter ⚠
- p.Thr205Ile Single submitter ⚠
- p.Tyr125Ser Single submitter ectodermal dysplasia-syndactyly syndrome 1 ⚠
- p.Val295Met Single submitter ⚠
- p.Arg506Gln No assertion criteria NECTIN4-related disorder ⚠