CNP — 69 ClinVar variants
All ClinVar germline CNP variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 57 flagged for review →
5 Pathogenic · 1 Benign · 10 Likely benign · 53 Uncertain significance
Full CNP gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 57
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 2
ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.
-
CNP p.Lys20Arg
Pathogenic
No assertion criteria
myopia 2, autosomal dominant
-
CNP p.Lys20Thr
Pathogenic
No assertion criteria
myopia 2, autosomal dominant
Predictors lean, ClinVar uncertain 31
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- CNP p.Ala218Val Uncertain significance Single submitter
- CNP p.Ala269Val Uncertain significance Single submitter
-
CNP p.Ala281Val
Uncertain significance
Single submitter
leukodystrophy, hypomyelinating, 20
- CNP p.Ala92Thr Uncertain significance Single submitter
- CNP p.Arg114Gln Uncertain significance Single submitter
- CNP p.Arg128Gln Uncertain significance Single submitter
- CNP p.Arg203His Uncertain significance Single submitter
- CNP p.Arg325Gln Uncertain significance Single submitter
- CNP p.Arg328His Uncertain significance Single submitter
- CNP p.Arg360Gln Uncertain significance Single submitter
- CNP p.Arg379Cys Uncertain significance Single submitter
- CNP p.Asn215Lys Uncertain significance Single submitter
- CNP p.Gln305Glu Uncertain significance Single submitter
- CNP p.Gln407Glu Uncertain significance Single submitter
- CNP p.Glu222Lys Uncertain significance Single submitter
- CNP p.Glu231Lys Uncertain significance Single submitter
- CNP p.Glu366Ala Uncertain significance Single submitter
- CNP p.Gly214Ala Uncertain significance Single submitter
- CNP p.Gly357Arg Uncertain significance Single submitter
- CNP p.Gly408Val Uncertain significance Single submitter
- CNP p.His216Gln Uncertain significance Single submitter
- CNP p.Ile351Met Uncertain significance Single submitter
- CNP p.Leu289Phe Uncertain significance Single submitter
- CNP p.Leu346Phe Uncertain significance Single submitter
- CNP p.Pro311Leu Uncertain significance Single submitter
- CNP p.Ser303Asn Uncertain significance Single submitter
- CNP p.Ser9Gly Uncertain significance Single submitter
- CNP p.Trp310Cys Uncertain significance Single submitter
-
CNP p.Tyr373Cys
Uncertain significance
Single submitter
achondroplasia
- CNP p.Val249Met Uncertain significance Single submitter
-
CNP p.Val339Ile
Uncertain significance
Single submitter
myopia 2, autosomal dominant
Predictors split 24
The independent predictors disagree with each other — read with care.
-
CNP p.Arg353Trp
Uncertain significance
Multiple submitters
Marfanoid habitus and intellectual disability
- CNP p.Arg203Cys Uncertain significance Single submitter
- CNP p.Arg299Gln Uncertain significance Single submitter
- CNP p.Arg369Trp Uncertain significance Single submitter
- CNP p.Arg93Gln Uncertain significance Single submitter
- CNP p.Asp338Glu Uncertain significance Single submitter
- CNP p.Gln354His Uncertain significance Single submitter
- CNP p.Glu212Asp Uncertain significance Single submitter
- CNP p.Glu267Asp Likely benign Single submitter
- CNP p.Glu304Gln Uncertain significance Single submitter
- CNP p.Glu304Lys Uncertain significance Single submitter
- CNP p.Gly358Asp Uncertain significance Single submitter
- CNP p.Gly376Ala Uncertain significance Single submitter
- CNP p.Lys175Glu Uncertain significance Single submitter
- CNP p.Lys204Asn Uncertain significance Single submitter
- CNP p.Lys20Glu Uncertain significance Single submitter
- CNP p.Lys20Met Uncertain significance Single submitter
- CNP p.Lys235Asn Likely benign Single submitter
- CNP p.Pro263Leu Uncertain significance Single submitter
- CNP p.Ser303Arg Uncertain significance Single submitter
- CNP p.Ser303Gly Uncertain significance Single submitter
- CNP p.Thr283Met Uncertain significance Single submitter
- CNP p.Thr406Met Uncertain significance Single submitter
-
CNP p.Ser82Leu
Pathogenic
No assertion criteria
leukodystrophy, hypomyelinating, 20
All CNP variants
Pathogenic 5
- c.-67C>T No assertion criteria myopia 2, autosomal dominant
- p.Gly345Asp No assertion criteria myopia 2, autosomal dominant
- p.Lys20Arg No assertion criteria myopia 2, autosomal dominant ⚠
- p.Lys20Thr No assertion criteria myopia 2, autosomal dominant ⚠
- p.Ser82Leu No assertion criteria leukodystrophy, hypomyelinating, 20 ⚠
Benign 1
- p.Gly365= Multiple submitters
Likely benign 10
- c.676+12G>A Single submitter
- p.Asn377Ser Single submitter
- p.Glu267Asp Single submitter ⚠
- p.His126= Single submitter
- p.Leu131= Single submitter
- p.Lys235Asn Single submitter ⚠
- p.Met236Ile Single submitter
- p.Ser279Cys Single submitter
- p.Tyr278= Single submitter
- p.Pro187= No assertion criteria CNP-related disorder
Uncertain significance 53
- p.Arg353Trp Multiple submitters Marfanoid habitus and intellectual disability ⚠
- p.Ala218Val Single submitter ⚠
- p.Ala269Val Single submitter ⚠
- p.Ala281Val Single submitter leukodystrophy, hypomyelinating, 20 ⚠
- p.Ala92Thr Single submitter ⚠
- p.Arg114Gln Single submitter ⚠
- p.Arg128Gln Single submitter ⚠
- p.Arg203Cys Single submitter ⚠
- p.Arg203His Single submitter ⚠
- p.Arg299Gln Single submitter ⚠
- p.Arg325Gln Single submitter ⚠
- p.Arg328His Single submitter ⚠
- p.Arg360Gln Single submitter ⚠
- p.Arg369Trp Single submitter ⚠
- p.Arg379Cys Single submitter ⚠
- p.Arg93Gln Single submitter ⚠
- p.Asn215Lys Single submitter ⚠
- p.Asp338Glu Single submitter ⚠
- p.Gln305Glu Single submitter ⚠
- p.Gln306His Single submitter leukodystrophy, hypomyelinating, 20
- p.Gln354His Single submitter ⚠
- p.Gln407Glu Single submitter ⚠
- p.Glu212Asp Single submitter ⚠
- p.Glu222Lys Single submitter ⚠
- p.Glu231Lys Single submitter ⚠
- p.Glu304Gln Single submitter ⚠
- p.Glu304Lys Single submitter ⚠
- p.Glu366Ala Single submitter ⚠
- p.Gly214Ala Single submitter ⚠
- p.Gly357Arg Single submitter ⚠
- p.Gly358Asp Single submitter ⚠
- p.Gly376Ala Single submitter ⚠
- p.Gly408Val Single submitter ⚠
- p.His216Gln Single submitter ⚠
- p.Ile351Met Single submitter ⚠
- p.Leu289Phe Single submitter ⚠
- p.Leu346Phe Single submitter ⚠
- p.Lys175Glu Single submitter ⚠
- p.Lys204Asn Single submitter ⚠
- p.Lys20Glu Single submitter ⚠
- p.Lys20Met Single submitter ⚠
- p.Pro263Leu Single submitter ⚠
- p.Pro311Leu Single submitter ⚠
- p.Ser303Arg Single submitter ⚠
- p.Ser303Asn Single submitter ⚠
- p.Ser303Gly Single submitter ⚠
- p.Ser9Gly Single submitter ⚠
- p.Thr283Met Single submitter ⚠
- p.Thr406Met Single submitter ⚠
- p.Trp310Cys Single submitter ⚠
- p.Tyr373Cys Single submitter achondroplasia ⚠
- p.Val249Met Single submitter ⚠
- p.Val339Ile Single submitter myopia 2, autosomal dominant ⚠