NHP2 — 217 ClinVar variants
All ClinVar germline NHP2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 85 flagged for review →
3 Pathogenic · 4 Conflicting · 3 Benign · 10 Benign/Likely benign · 79 Likely benign · 118 Uncertain significance
Full NHP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 85
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 lean, ClinVar uncertain 75
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
-
NHP2 p.Ala17Val
Uncertain significance
Multiple submitters
dyskeratosis congenita
-
NHP2 p.Ala39Thr
Uncertain significance
Multiple submitters
dyskeratosis congenita
-
NHP2 p.Arg101Gly
Uncertain significance
Multiple submitters
dyskeratosis congenita
-
NHP2 p.Arg61Gln
Uncertain significance
Multiple submitters
dyskeratosis congenita
-
NHP2 p.Asp140Asn
Uncertain significance
Multiple submitters
dyskeratosis congenita
-
NHP2 p.Asp9Asn
Uncertain significance
Multiple submitters
dyskeratosis congenita
-
NHP2 p.Glu12Gln
Uncertain significance
Multiple submitters
dyskeratosis congenita
-
NHP2 p.Glu145Val
Uncertain significance
Multiple submitters
dyskeratosis congenita
-
NHP2 p.Gly63Arg
Uncertain significance
Multiple submitters
dyskeratosis congenita
-
NHP2 p.Met79Leu
Uncertain significance
Multiple submitters
dyskeratosis congenita
-
NHP2 p.Met97Val
Uncertain significance
Multiple submitters
dyskeratosis congenita
-
NHP2 p.Pro131Thr
Uncertain significance
Multiple submitters
dyskeratosis congenita
-
NHP2 p.Pro37Ser
Uncertain significance
Multiple submitters
dyskeratosis congenita
-
NHP2 p.Thr112Met
Uncertain significance
Multiple submitters
dyskeratosis congenita, autosomal recessive 2
-
NHP2 p.Thr44Ser
Uncertain significance
Multiple submitters
dyskeratosis congenita
-
NHP2 p.Tyr24Asn
Uncertain significance
Multiple submitters
dyskeratosis congenita
-
NHP2 p.Val64Met
Uncertain significance
Multiple submitters
dyskeratosis congenita
-
NHP2 p.Ala138Gly
Uncertain significance
Single submitter
dyskeratosis congenita, autosomal recessive 2
-
NHP2 p.Ala35Val
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Ala39Asp
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Ala54Thr
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Ala6Val
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Arg122Cys
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Arg122His
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Arg122Ser
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Arg61Trp
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Asn72Ser
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Asp100Asn
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Asp7His
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Cys125Arg
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Cys18Tyr
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Cys98Gly
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Gln147His
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Gln147Lys
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Gln59His
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Gln68His
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Glu133Lys
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Glu141Gly
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Glu66Lys
Uncertain significance
Single submitter
dyskeratosis congenita
- NHP2 p.Glu89Lys Uncertain significance Single submitter
-
NHP2 p.Gly10Arg
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Gly119Arg
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Gly20Ala
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Gly74Arg
Uncertain significance
Single submitter
dyskeratosis congenita
- NHP2 p.Ile51Val Uncertain significance Single submitter
-
NHP2 p.Ile78Asn
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Ile88Val
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Leu149Val
Uncertain significance
Single submitter
dyskeratosis congenita, autosomal recessive 2
-
NHP2 p.Leu27Gln
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Leu28Pro
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Leu47Pro
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Lys121Arg
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Lys46Asn
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Lys52Arg
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Lys53Glu
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Lys56Arg
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Lys58Gln
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Lys76Asn
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Met128Thr
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Met79Ile
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Met79Thr
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Pro109Leu
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Pro152His
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Pro152Leu
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Pro87Ser
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Thr124Ile
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Thr23Ala
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Tyr105Cys
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Tyr107Asn
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Tyr107Cys
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Val106Ile
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Val29Gly
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Val55Leu
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Val55Met
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Val67Ile
Uncertain significance
Single submitter
dyskeratosis congenita, autosomal recessive 2
Predictors split 10
The independent predictors disagree with each other — read with care.
-
NHP2 p.His132Tyr
Uncertain significance
Multiple submitters
dyskeratosis congenita, autosomal recessive 2
-
NHP2 p.Met97Thr
Uncertain significance
Multiple submitters
dyskeratosis congenita
-
NHP2 p.Arg45Trp
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Asn72Lys
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Glu89Ala
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Lys52Asn
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Pro104Leu
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Pro33Ser
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Thr23Ile
Uncertain significance
Single submitter
dyskeratosis congenita
-
NHP2 p.Val146Leu
Uncertain significance
Single submitter
dyskeratosis congenita
All NHP2 variants
Pathogenic 3
- p.Ter154Arg Single submitter dyskeratosis congenita, autosomal recessive 1
- p.Tyr139His No assertion criteria dyskeratosis congenita, autosomal recessive 2
- p.Val126Met No assertion criteria dyskeratosis congenita, autosomal recessive 2
Conflicting classifications of pathogenicity 4
- c.160+10A>T Single submitter dyskeratosis congenita
- c.160+9G>A Single submitter dyskeratosis congenita
- p.Tyr48Cys Single submitter dyskeratosis congenita
- p.Val90= Single submitter dyskeratosis congenita
Benign 3
- c.231-13dup Single submitter dyskeratosis congenita
- c.231-20_231-19del Single submitter dyskeratosis congenita
- c.337-299A>G Single submitter
Benign/Likely benign 10
- c.160+11C>T Multiple submitters dyskeratosis congenita
- c.160+16G>C Multiple submitters dyskeratosis congenita, autosomal recessive 2
- c.231-17_231-16del Multiple submitters dyskeratosis congenita
- c.336+20del Multiple submitters dyskeratosis congenita
- c.337-14T>C Multiple submitters dyskeratosis congenita, autosomal recessive 1
- c.*11T>A Multiple submitters
- p.Ala117= Multiple submitters dyskeratosis congenita, autosomal recessive 1
- p.Ala118Thr Multiple submitters dyskeratosis congenita
- p.Arg101Gln Multiple submitters dyskeratosis congenita
- p.Pro123= Multiple submitters dyskeratosis congenita
Likely benign 79
- c.160+10A>G Multiple submitters dyskeratosis congenita
- c.160+18G>T Multiple submitters dyskeratosis congenita
- c.230+8C>A Multiple submitters dyskeratosis congenita
- c.336+12G>A Multiple submitters dyskeratosis congenita
- c.337-133G>A Multiple submitters
- c.337-6C>T Multiple submitters dyskeratosis congenita, autosomal recessive 2
- c.-10G>T Multiple submitters
- p.Ala15= Multiple submitters dyskeratosis congenita
- p.Ala35= Multiple submitters dyskeratosis congenita
- p.Ala54= Multiple submitters dyskeratosis congenita
- p.Lys65= Multiple submitters dyskeratosis congenita
- p.Pro11= Multiple submitters dyskeratosis congenita
- p.Pro131= Multiple submitters dyskeratosis congenita
- p.Tyr139= Multiple submitters dyskeratosis congenita
- p.Tyr24= Multiple submitters dyskeratosis congenita
- p.Val126= Multiple submitters dyskeratosis congenita
- c.160+10A>C Single submitter dyskeratosis congenita
- c.160+11C>A Single submitter dyskeratosis congenita
- c.160+11C>G Single submitter dyskeratosis congenita
- c.160+12G>A Single submitter dyskeratosis congenita
- c.160+13G>A Single submitter dyskeratosis congenita
- c.160+14C>A Single submitter dyskeratosis congenita
- c.160+16G>A Single submitter dyskeratosis congenita
- c.160+18G>A Single submitter dyskeratosis congenita
- c.160+20G>T Single submitter dyskeratosis congenita
- c.160+7C>A Single submitter dyskeratosis congenita
- c.160+7C>T Single submitter dyskeratosis congenita
- c.160+8G>A Single submitter dyskeratosis congenita
- c.160+9_160+10insGGCGGCC Single submitter dyskeratosis congenita
- c.160+9del Single submitter dyskeratosis congenita
- c.161-15C>G Single submitter dyskeratosis congenita
- c.161-16T>G Single submitter dyskeratosis congenita
- c.161-17C>T Single submitter dyskeratosis congenita
- c.161-4G>A Single submitter dyskeratosis congenita
- c.161-5T>G Single submitter dyskeratosis congenita
- c.161-7G>A Single submitter dyskeratosis congenita
- c.161-8C>T Single submitter dyskeratosis congenita
- c.230+13C>A Single submitter dyskeratosis congenita
- c.230+13C>T Single submitter dyskeratosis congenita
- c.230+15_230+18del Single submitter dyskeratosis congenita
- c.230+16C>T Single submitter dyskeratosis congenita
- c.230+17C>T Single submitter dyskeratosis congenita
- c.230+19C>G Single submitter dyskeratosis congenita
- c.230+81G>A Single submitter
- c.230+9C>A Single submitter dyskeratosis congenita
- c.231-13TC[2] Single submitter dyskeratosis congenita
- c.231-20dup Single submitter dyskeratosis congenita
- c.231-228A>G Single submitter
- c.231-276G>A Single submitter
- c.231-3C>T Single submitter
- c.336+11C>T Single submitter dyskeratosis congenita
- c.336+16C>G Single submitter dyskeratosis congenita
- c.336+18C>T Single submitter dyskeratosis congenita
- c.336+20_336+21del Single submitter dyskeratosis congenita
- c.337-11C>T Single submitter dyskeratosis congenita
- c.337-15C>T Single submitter dyskeratosis congenita
- c.337-18C>T Single submitter dyskeratosis congenita
- c.337-29del Single submitter
- c.*226G>A Single submitter
- p.Ala6= Single submitter dyskeratosis congenita
- p.Arg101= Single submitter dyskeratosis congenita
- p.Arg122= Single submitter dyskeratosis congenita
- p.Arg62= Single submitter dyskeratosis congenita
- p.Asp113= Single submitter dyskeratosis congenita
- p.Asp9= Single submitter dyskeratosis congenita
- p.Glu21= Single submitter dyskeratosis congenita
- p.Glu89= Single submitter dyskeratosis congenita
- p.Gly20= Single submitter dyskeratosis congenita
- p.His132= Single submitter dyskeratosis congenita
- p.Ile108= Single submitter dyskeratosis congenita
- p.Leu149= Single submitter dyskeratosis congenita
- p.Leu38= Single submitter dyskeratosis congenita
- p.Lys5= Single submitter dyskeratosis congenita
- p.Phe70= Single submitter dyskeratosis congenita
- p.Pro152= Single submitter dyskeratosis congenita
- p.Pro8= Single submitter dyskeratosis congenita
- p.Thr44= Single submitter dyskeratosis congenita
- p.Val71= Single submitter dyskeratosis congenita
- c.*4G>A No assertion criteria NHP2-related disorder
Uncertain significance 118
- c.-2C>A Multiple submitters
- p.Ala17Val Multiple submitters dyskeratosis congenita ⚠
- p.Ala39Thr Multiple submitters dyskeratosis congenita ⚠
- p.Arg101Gly Multiple submitters dyskeratosis congenita ⚠
- p.Arg61Gln Multiple submitters dyskeratosis congenita ⚠
- p.Asp140Asn Multiple submitters dyskeratosis congenita ⚠
- p.Asp9Asn Multiple submitters dyskeratosis congenita ⚠
- p.Glu12Gln Multiple submitters dyskeratosis congenita ⚠
- p.Glu145Val Multiple submitters dyskeratosis congenita ⚠
- p.Gly63Arg Multiple submitters dyskeratosis congenita ⚠
- p.His132Tyr Multiple submitters dyskeratosis congenita, autosomal recessive 2 ⚠
- p.Met79Leu Multiple submitters dyskeratosis congenita ⚠
- p.Met97fs Multiple submitters dyskeratosis congenita, autosomal recessive 2
- p.Met97Thr Multiple submitters dyskeratosis congenita ⚠
- p.Met97Val Multiple submitters dyskeratosis congenita ⚠
- p.Pro131Thr Multiple submitters dyskeratosis congenita ⚠
- p.Pro37Ser Multiple submitters dyskeratosis congenita ⚠
- p.Ser110Thr Multiple submitters dyskeratosis congenita
- p.Thr112Met Multiple submitters dyskeratosis congenita, autosomal recessive 2 ⚠
- p.Thr44Ser Multiple submitters dyskeratosis congenita ⚠
- p.Tyr24Asn Multiple submitters dyskeratosis congenita ⚠
- p.Val64Met Multiple submitters dyskeratosis congenita ⚠
- c.160+4A>C Single submitter dyskeratosis congenita
- c.160+4A>G Single submitter dyskeratosis congenita
- c.160+5G>C Single submitter dyskeratosis congenita
- c.161-2A>T Single submitter dyskeratosis congenita
- c.230+4dup Single submitter dyskeratosis congenita
- c.231-9T>C Single submitter dyskeratosis congenita
- c.336+2T>C Single submitter dyskeratosis congenita
- c.337-3T>C Single submitter dyskeratosis congenita
- c.-11C>T Single submitter
- c.*8C>T Single submitter
- p.Ala138Gly Single submitter dyskeratosis congenita, autosomal recessive 2 ⚠
- p.Ala35Val Single submitter dyskeratosis congenita ⚠
- p.Ala39Asp Single submitter dyskeratosis congenita ⚠
- p.Ala54Thr Single submitter dyskeratosis congenita ⚠
- p.Ala6Val Single submitter dyskeratosis congenita ⚠
- p.Arg122Cys Single submitter dyskeratosis congenita ⚠
- p.Arg122His Single submitter dyskeratosis congenita ⚠
- p.Arg122Ser Single submitter dyskeratosis congenita ⚠
- p.Arg41fs Single submitter dyskeratosis congenita
- p.Arg42del Single submitter dyskeratosis congenita
- p.Arg45Trp Single submitter dyskeratosis congenita ⚠
- p.Arg61Trp Single submitter dyskeratosis congenita ⚠
- p.Asn72Lys Single submitter dyskeratosis congenita ⚠
- p.Asn72Ser Single submitter dyskeratosis congenita ⚠
- p.Asp100Asn Single submitter dyskeratosis congenita ⚠
- p.Asp7His Single submitter dyskeratosis congenita ⚠
- p.Cys125Arg Single submitter dyskeratosis congenita ⚠
- p.Cys18Tyr Single submitter dyskeratosis congenita ⚠
- p.Cys98Gly Single submitter dyskeratosis congenita ⚠
- p.Gln147His Single submitter dyskeratosis congenita ⚠
- p.Gln147Lys Single submitter dyskeratosis congenita ⚠
- p.Gln147Ter Single submitter dyskeratosis congenita
- p.Gln36fs Single submitter dyskeratosis congenita
- p.Gln59His Single submitter dyskeratosis congenita ⚠
- p.Gln68His Single submitter dyskeratosis congenita ⚠
- p.Glu133Lys Single submitter dyskeratosis congenita ⚠
- p.Glu134del Single submitter dyskeratosis congenita
- p.Glu141Gly Single submitter dyskeratosis congenita ⚠
- p.Glu21fs Single submitter dyskeratosis congenita
- p.Glu66fs Single submitter dyskeratosis congenita
- p.Glu66Lys Single submitter dyskeratosis congenita ⚠
- p.Glu89Ala Single submitter dyskeratosis congenita ⚠
- p.Glu89fs Single submitter dyskeratosis congenita
- p.Glu89Lys Single submitter ⚠
- p.Gly10Arg Single submitter dyskeratosis congenita ⚠
- p.Gly119Arg Single submitter dyskeratosis congenita ⚠
- p.Gly119Ser Single submitter dyskeratosis congenita
- p.Gly20Ala Single submitter dyskeratosis congenita ⚠
- p.Gly74Arg Single submitter dyskeratosis congenita ⚠
- p.Gly77= Single submitter dyskeratosis congenita
- p.His132fs Single submitter dyskeratosis congenita
- p.Ile51Met Single submitter
- p.Ile51Val Single submitter ⚠
- p.Ile78Asn Single submitter dyskeratosis congenita ⚠
- p.Ile88Val Single submitter dyskeratosis congenita ⚠
- p.Leu149Val Single submitter dyskeratosis congenita, autosomal recessive 2 ⚠
- p.Leu27Gln Single submitter dyskeratosis congenita ⚠
- p.Leu28Pro Single submitter dyskeratosis congenita ⚠
- p.Leu47_Tyr48insTer Single submitter dyskeratosis congenita
- p.Leu47Pro Single submitter dyskeratosis congenita ⚠
- p.Lys121Arg Single submitter dyskeratosis congenita ⚠
- p.Lys46Asn Single submitter dyskeratosis congenita ⚠
- p.Lys52Arg Single submitter dyskeratosis congenita ⚠
- p.Lys52Asn Single submitter dyskeratosis congenita ⚠
- p.Lys53Glu Single submitter dyskeratosis congenita ⚠
- p.Lys56Arg Single submitter dyskeratosis congenita ⚠
- p.Lys58Gln Single submitter dyskeratosis congenita ⚠
- p.Lys76Asn Single submitter dyskeratosis congenita ⚠
- p.Met128Thr Single submitter dyskeratosis congenita ⚠
- p.Met1Arg Single submitter dyskeratosis congenita
- p.Met79Ile Single submitter dyskeratosis congenita ⚠
- p.Met79Thr Single submitter dyskeratosis congenita ⚠
- p.Pro104Leu Single submitter dyskeratosis congenita ⚠
- p.Pro109Leu Single submitter dyskeratosis congenita ⚠
- p.Pro150His Single submitter dyskeratosis congenita
- p.Pro152His Single submitter dyskeratosis congenita ⚠
- p.Pro152Leu Single submitter dyskeratosis congenita ⚠
- p.Pro33Ser Single submitter dyskeratosis congenita ⚠
- p.Pro87Ser Single submitter dyskeratosis congenita ⚠
- p.Ter154ArgextTer? Single submitter dyskeratosis congenita
- p.Ter154Gly Single submitter dyskeratosis congenita
- p.Thr112= Single submitter dyskeratosis congenita
- p.Thr124fs Single submitter dyskeratosis congenita
- p.Thr124Ile Single submitter dyskeratosis congenita ⚠
- p.Thr23Ala Single submitter dyskeratosis congenita ⚠
- p.Thr23Ile Single submitter dyskeratosis congenita ⚠
- p.Tyr105Cys Single submitter dyskeratosis congenita ⚠
- p.Tyr107Asn Single submitter dyskeratosis congenita ⚠
- p.Tyr107Cys Single submitter dyskeratosis congenita ⚠
- p.Tyr107fs Single submitter dyskeratosis congenita
- p.Val106Ile Single submitter dyskeratosis congenita ⚠
- p.Val146Leu Single submitter dyskeratosis congenita ⚠
- p.Val29Gly Single submitter dyskeratosis congenita ⚠
- p.Val55Leu Single submitter dyskeratosis congenita ⚠
- p.Val55Met Single submitter dyskeratosis congenita ⚠
- p.Val67Ile Single submitter dyskeratosis congenita, autosomal recessive 2 ⚠