MSN — 280 ClinVar variants
All ClinVar germline MSN variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 113 flagged for review →
12 Pathogenic · 7 Likely pathogenic · 10 Conflicting · 24 Benign · 10 Benign/Likely benign · 96 Likely benign · 121 Uncertain significance
Full MSN gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 113
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 6
ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.
-
MSN p.Ala390Ser
Conflicting
Single submitter
Inborn genetic diseases
-
MSN p.Ala524Thr
Conflicting
Single submitter
Inborn genetic diseases
-
MSN p.Arg81His
Conflicting
Single submitter
Inborn genetic diseases
-
MSN p.Gln394Arg
Conflicting
Single submitter
Inborn genetic diseases
-
MSN p.Glu355Lys
Conflicting
Single submitter
Inborn genetic diseases
-
MSN p.Gly149Arg
Conflicting
Single submitter
Inborn genetic diseases
Predictors lean, ClinVar uncertain 83
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- MSN p.Ala122Thr Uncertain significance Multiple submitters
-
MSN p.Arg273Trp
Uncertain significance
Multiple submitters
combined immunodeficiency due to moesin deficiency
-
MSN p.Arg293Cys
Uncertain significance
Multiple submitters
combined immunodeficiency due to moesin deficiency
- MSN p.Arg294Cys Uncertain significance Multiple submitters
-
MSN p.Arg295His
Uncertain significance
Multiple submitters
Inborn genetic diseases
- MSN p.Glu346Asp Uncertain significance Multiple submitters
-
MSN p.Ile340Thr
Uncertain significance
Multiple submitters
Inborn genetic diseases
- MSN p.Ile37Val Uncertain significance Multiple submitters
-
MSN p.Pro272Leu
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
MSN p.Thr369Ser
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
MSN p.Tyr85Cys
Uncertain significance
Multiple submitters
Inborn genetic diseases
- MSN p.Ala282Val Uncertain significance Single submitter
- MSN p.Ala434Val Uncertain significance Single submitter
- MSN p.Ala442Val Uncertain significance Single submitter
- MSN p.Ala540Ser Uncertain significance Single submitter
- MSN p.Ala540Val Uncertain significance Single submitter
- MSN p.Ala546Ser Uncertain significance Single submitter
-
MSN p.Arg320Cys
Uncertain significance
Single submitter
Inborn genetic diseases
- MSN p.Arg330His Uncertain significance Single submitter
- MSN p.Arg342Gln Uncertain significance Single submitter
- MSN p.Arg371Lys Uncertain significance Single submitter
- MSN p.Arg408Gln Uncertain significance Single submitter
- MSN p.Arg435Gln Uncertain significance Single submitter
- MSN p.Arg435Pro Uncertain significance Single submitter
- MSN p.Arg495Gln Uncertain significance Single submitter
-
MSN p.Arg503His
Uncertain significance
Single submitter
Inborn genetic diseases
- MSN p.Arg508Cys Uncertain significance Single submitter
- MSN p.Arg560Cys Uncertain significance Single submitter
- MSN p.Arg563Trp Uncertain significance Single submitter
- MSN p.Arg71Gln Uncertain significance Single submitter
- MSN p.Arg8Cys Uncertain significance Single submitter
- MSN p.Asn112Ser Uncertain significance Single submitter
- MSN p.Asn23Ser Uncertain significance Single submitter
-
MSN p.Asn251Ser
Uncertain significance
Single submitter
Inborn genetic diseases
- MSN p.Asn531Ile Uncertain significance Single submitter
- MSN p.Asn531Ser Uncertain significance Single submitter
-
MSN p.Asp113Glu
Uncertain significance
Single submitter
Inborn genetic diseases
- MSN p.Asp252Gly Uncertain significance Single submitter
-
MSN p.Asp69Asn
Uncertain significance
Single submitter
Inborn genetic diseases
- MSN p.Gln21His Uncertain significance Single submitter
- MSN p.Gln447Arg Uncertain significance Single submitter
- MSN p.Gln447Lys Uncertain significance Single submitter
- MSN p.Gln450Arg Uncertain significance Single submitter
- MSN p.Gln480Pro Uncertain significance Single submitter
-
MSN p.Gln48His
Uncertain significance
Single submitter
Inborn genetic diseases
- MSN p.Glu169Gly Uncertain significance Single submitter
- MSN p.Glu17Ala Uncertain significance Single submitter
-
MSN p.Glu319Gly
Uncertain significance
Single submitter
Inborn genetic diseases
- MSN p.Glu355Gly Uncertain significance Single submitter
- MSN p.Glu364Gly Uncertain significance Single submitter
- MSN p.Glu398Gly Uncertain significance Single submitter
-
MSN p.Glu41Gly
Uncertain significance
Single submitter
Inborn genetic diseases
- MSN p.Glu513Asp Uncertain significance Single submitter
- MSN p.Gly487Arg Uncertain significance Single submitter
- MSN p.Gly487Glu Uncertain significance Single submitter
- MSN p.His176Leu Uncertain significance Single submitter
- MSN p.His314Gln Uncertain significance Single submitter
- MSN p.Ile208Met Uncertain significance Single submitter
-
MSN p.Ile20Val
Uncertain significance
Single submitter
Inborn genetic diseases
- MSN p.Ile227Phe Uncertain significance Single submitter
- MSN p.Leu153Phe Uncertain significance Single submitter
- MSN p.Leu59Gln Uncertain significance Single submitter
- MSN p.Lys165Asn Uncertain significance Single submitter
- MSN p.Lys296Gln Uncertain significance Single submitter
- MSN p.Lys437Asn Uncertain significance Single submitter
- MSN p.Lys79Arg Uncertain significance Single submitter
- MSN p.Met318Ile Uncertain significance Single submitter
-
MSN p.Met322Val
Uncertain significance
Single submitter
Inborn genetic diseases
-
MSN p.Met451Val
Uncertain significance
Single submitter
Inborn genetic diseases
-
MSN p.Met549Val
Uncertain significance
Single submitter
Inborn genetic diseases
- MSN p.Pro154Leu Uncertain significance Single submitter
- MSN p.Pro265Leu Uncertain significance Single submitter
- MSN p.Ser144Pro Uncertain significance Single submitter
- MSN p.Ser144Thr Uncertain significance Single submitter
- MSN p.Ser384Ile Uncertain significance Single submitter
- MSN p.Ser504Ile Uncertain significance Single submitter
- MSN p.Ser527Leu Uncertain significance Single submitter
- MSN p.Thr235Ser Uncertain significance Single submitter
- MSN p.Thr526Ile Uncertain significance Single submitter
-
MSN p.Val130Ile
Uncertain significance
Single submitter
Inborn genetic diseases
- MSN p.Val188Ile Uncertain significance Single submitter
-
MSN p.Ala129Ser
Uncertain significance
No assertion criteria
MSN-related disorder
-
MSN p.Leu47Met
Uncertain significance
No assertion criteria
autism
Predictors split 24
The independent predictors disagree with each other — read with care.
-
MSN p.Arg393His
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
MSN p.Glu367Lys
Uncertain significance
Multiple submitters
MSN-related disorder
-
MSN p.Pro272Ser
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
MSN p.Ser144Cys
Uncertain significance
Multiple submitters
Inborn genetic diseases
- MSN p.Arg180His Uncertain significance Single submitter
-
MSN p.Arg370Cys
Conflicting
Single submitter
Inborn genetic diseases
- MSN p.Arg379Trp Benign Single submitter
-
MSN p.Arg381Cys
Uncertain significance
Single submitter
combined immunodeficiency due to moesin deficiency
- MSN p.Arg381His Uncertain significance Single submitter
- MSN p.Arg408Trp Conflicting Single submitter
- MSN p.Arg460Cys Uncertain significance Single submitter
- MSN p.Arg503Cys Uncertain significance Single submitter
- MSN p.Asp136Asn Likely benign Single submitter
- MSN p.Gln230Arg Likely benign Single submitter
- MSN p.Gln308Glu Uncertain significance Single submitter
- MSN p.Gln410Pro Uncertain significance Single submitter
- MSN p.Glu364Lys Uncertain significance Single submitter
- MSN p.Glu444Gly Uncertain significance Single submitter
-
MSN p.Glu91Lys
Uncertain significance
Single submitter
Inborn genetic diseases
- MSN p.His161Tyr Uncertain significance Single submitter
- MSN p.Met182Val Likely benign Single submitter
-
MSN p.Met285Val
Uncertain significance
Single submitter
Inborn genetic diseases
- MSN p.Met421Thr Uncertain significance Single submitter
- MSN p.Val268Ile Benign Single submitter
All MSN variants
Pathogenic 12
- p.Arg171Trp Multiple submitters combined immunodeficiency due to moesin deficiency
- p.Ala372fs Single submitter
- p.Arg427Ter Single submitter
- p.Arg435Ter Single submitter
- p.Gln196fs Single submitter
- p.Gln196Ter Single submitter
- p.Gln450Ter Single submitter
- p.Glu17Ter Single submitter
- p.Glu395fs Single submitter
- p.Ser491fs Single submitter
- p.Trp168Ter Single submitter
- p.Lys352fs No assertion criteria combined immunodeficiency due to moesin deficiency
Likely pathogenic 7
- c.1251+1G>A Single submitter
- c.13-1G>A Single submitter
- p.Arg553Ter Single submitter combined immunodeficiency due to moesin deficiency
- p.Asn138fs Single submitter MSN-related disorder
- p.Asp534Ala Single submitter combined immunodeficiency due to moesin deficiency
- p.Glu547fs Single submitter
- p.Ser527Ter Single submitter MSN-related disorder
Conflicting classifications of pathogenicity 10
- p.Ala390Ser Single submitter Inborn genetic diseases ⚠
- p.Ala524Thr Single submitter Inborn genetic diseases ⚠
- p.Arg370Cys Single submitter Inborn genetic diseases ⚠
- p.Arg408Trp Single submitter ⚠
- p.Arg81His Single submitter Inborn genetic diseases ⚠
- p.Gln394Arg Single submitter Inborn genetic diseases ⚠
- p.Glu355Lys Single submitter Inborn genetic diseases ⚠
- p.Glu41= Single submitter
- p.Gly149Arg Single submitter Inborn genetic diseases ⚠
- p.Val518Leu Single submitter Inborn genetic diseases
Benign 24
- c.1570-14A>G Multiple submitters
- p.His176= Multiple submitters
- c.1091-11T>C Single submitter
- c.1344+14C>T Single submitter
- c.1345-3C>T Single submitter
- c.192+15C>A Single submitter
- c.192+17C>T Single submitter
- c.193-10C>T Single submitter
- c.468-19T>A Single submitter
- c.796-3C>T Single submitter
- p.Arg100His Single submitter
- p.Arg379Trp Single submitter ⚠
- p.Arg427Gln Single submitter
- p.Arg81Cys Single submitter
- p.Asn138Ser Single submitter
- p.Asp409= Single submitter
- p.Asp542= Single submitter
- p.Glu401= Single submitter
- p.Lys557= Single submitter
- p.Thr469= Single submitter
- p.Thr539= Single submitter
- p.Val268Ile Single submitter ⚠
- p.Val472= Single submitter
- p.Val70Leu Single submitter
Benign/Likely benign 10
- c.1252-4G>A Multiple submitters
- c.1345-8C>T Multiple submitters
- c.96+7C>T Multiple submitters
- c.960-14A>G Multiple submitters
- p.Ala382= Multiple submitters
- p.Arg371= Multiple submitters
- p.Lys278= Multiple submitters
- p.Pro118= Multiple submitters
- p.Ser527= Multiple submitters
- p.Val256= Multiple submitters
Likely benign 96
- c.551+10C>T Multiple submitters
- c.96+8G>A Multiple submitters
- p.Asp572= Multiple submitters
- p.Gly213= Multiple submitters
- p.Leu365= Multiple submitters
- p.Lys143= Multiple submitters
- p.Ser90= Multiple submitters
- p.Thr57= Multiple submitters
- c.1091-13C>T Single submitter
- c.1091-18C>G Single submitter
- c.1091-8C>T Single submitter
- c.12+10G>A Single submitter
- c.12+11del Single submitter
- c.12+17_12+18insC Single submitter
- c.12+18G>C Single submitter
- c.1251+14G>A Single submitter
- c.1252-8A>T Single submitter
- c.13-10C>A Single submitter
- c.1344+11G>A Single submitter
- c.1344+17A>C Single submitter
- c.1344+20G>A Single submitter
- c.1344+7C>G Single submitter
- c.1344+7C>T Single submitter
- c.1569+16C>T Single submitter
- c.1569+18A>T Single submitter
- c.1569+8A>C Single submitter
- c.1570-7C>A Single submitter
- c.193-14C>T Single submitter
- c.193-20A>C Single submitter
- c.468-14C>T Single submitter
- c.468-20A>G Single submitter
- c.468-4C>G Single submitter
- c.552-10T>C Single submitter
- c.699-18T>C Single submitter
- c.795+10T>A Single submitter
- c.795+14C>T Single submitter
- c.795+16C>T Single submitter
- c.796-15C>T Single submitter
- c.796-6C>T Single submitter
- c.96+8G>C Single submitter
- c.960-4C>T Single submitter
- c.97-14G>T Single submitter
- p.Ala148= Single submitter
- p.Ala148Val Single submitter
- p.Ala19= Single submitter
- p.Ala282= Single submitter
- p.Ala418= Single submitter
- p.Ala488= Single submitter
- p.Ala82= Single submitter
- p.Arg408= Single submitter
- p.Arg560= Single submitter
- p.Arg8His Single submitter
- p.Asn325= Single submitter
- p.Asn515= Single submitter
- p.Asp114= Single submitter
- p.Asp136Asn Single submitter ⚠
- p.Asp261= Single submitter
- p.Asp298= Single submitter
- p.Asp31= Single submitter
- p.Asp493= Single submitter
- p.Gln196= Single submitter
- p.Gln230Arg Single submitter ⚠
- p.Gln317= Single submitter
- p.Gln446= Single submitter
- p.Glu397= Single submitter
- p.Glu415= Single submitter
- p.Glu513= Single submitter
- p.Gly219= Single submitter
- p.Gly26= Single submitter
- p.His179= Single submitter
- p.Ile20= Single submitter
- p.Ile354= Single submitter
- p.Leu111= Single submitter
- p.Leu125= Single submitter
- p.Leu163= Single submitter
- p.Leu290= Single submitter
- p.Leu323= Single submitter
- p.Leu373= Single submitter
- p.Leu419= Single submitter
- p.Leu529= Single submitter
- p.Lys514= Single submitter
- p.Met182Val Single submitter ⚠
- p.Phe267= Single submitter
- p.Pro154= Single submitter
- p.Pro86= Single submitter
- p.Thr121= Single submitter
- p.Thr235= Single submitter
- p.Thr24= Single submitter
- p.Thr25= Single submitter
- p.Thr299= Single submitter
- p.Thr558= Single submitter
- p.Val106= Single submitter
- p.Val188= Single submitter
- p.Val203= Single submitter
- p.Val302= Single submitter
- p.Glu535Ter No assertion criteria EBV-positive nodal T- and NK-cell lymphoma
Uncertain significance 121
- p.Ala122Thr Multiple submitters ⚠
- p.Arg273Trp Multiple submitters combined immunodeficiency due to moesin deficiency ⚠
- p.Arg293Cys Multiple submitters combined immunodeficiency due to moesin deficiency ⚠
- p.Arg294Cys Multiple submitters ⚠
- p.Arg295His Multiple submitters Inborn genetic diseases ⚠
- p.Arg393His Multiple submitters Inborn genetic diseases ⚠
- p.Glu346Asp Multiple submitters ⚠
- p.Glu367Lys Multiple submitters MSN-related disorder ⚠
- p.Ile340Thr Multiple submitters Inborn genetic diseases ⚠
- p.Ile37Val Multiple submitters ⚠
- p.Met292Leu Multiple submitters
- p.Pro272Leu Multiple submitters Inborn genetic diseases ⚠
- p.Pro272Ser Multiple submitters Inborn genetic diseases ⚠
- p.Ser144Cys Multiple submitters Inborn genetic diseases ⚠
- p.Thr369Ser Multiple submitters Inborn genetic diseases ⚠
- p.Tyr85Cys Multiple submitters Inborn genetic diseases ⚠
- c.13-5C>A Single submitter
- c.1570-3C>T Single submitter
- c.468-18C>T Single submitter
- c.551+5G>A Single submitter
- c.698+4T>A Single submitter
- c.698+5A>G Single submitter
- c.959+4G>T Single submitter
- p.480QDE[1] Single submitter
- p.Ala264fs Single submitter
- p.Ala282Val Single submitter ⚠
- p.Ala361Val Single submitter Inborn genetic diseases
- p.Ala434Val Single submitter ⚠
- p.Ala442Val Single submitter ⚠
- p.Ala540Ser Single submitter ⚠
- p.Ala540Val Single submitter ⚠
- p.Ala546Ser Single submitter ⚠
- p.Arg180His Single submitter ⚠
- p.Arg320Cys Single submitter Inborn genetic diseases ⚠
- p.Arg330His Single submitter ⚠
- p.Arg342Gln Single submitter ⚠
- p.Arg371Lys Single submitter ⚠
- p.Arg381Cys Single submitter combined immunodeficiency due to moesin deficiency ⚠
- p.Arg381His Single submitter ⚠
- p.Arg393_Glu401del Single submitter
- p.Arg408Gln Single submitter ⚠
- p.Arg435Gln Single submitter ⚠
- p.Arg435Pro Single submitter ⚠
- p.Arg460Cys Single submitter ⚠
- p.Arg495Gln Single submitter ⚠
- p.Arg503Cys Single submitter ⚠
- p.Arg503His Single submitter Inborn genetic diseases ⚠
- p.Arg508Cys Single submitter ⚠
- p.Arg560Cys Single submitter ⚠
- p.Arg563Trp Single submitter ⚠
- p.Arg71Gln Single submitter ⚠
- p.Arg8Cys Single submitter ⚠
- p.Asn112Ser Single submitter ⚠
- p.Asn23Ser Single submitter ⚠
- p.Asn251Ser Single submitter Inborn genetic diseases ⚠
- p.Asn531Ile Single submitter ⚠
- p.Asn531Ser Single submitter ⚠
- p.Asp113Glu Single submitter Inborn genetic diseases ⚠
- p.Asp252Gly Single submitter ⚠
- p.Asp69Asn Single submitter Inborn genetic diseases ⚠
- p.Gln21His Single submitter ⚠
- p.Gln308Glu Single submitter ⚠
- p.Gln410Pro Single submitter ⚠
- p.Gln447Arg Single submitter ⚠
- p.Gln447Lys Single submitter ⚠
- p.Gln450Arg Single submitter ⚠
- p.Gln480Pro Single submitter ⚠
- p.Gln48His Single submitter Inborn genetic diseases ⚠
- p.Glu169Gly Single submitter ⚠
- p.Glu17Ala Single submitter ⚠
- p.Glu311Asp Single submitter Inborn genetic diseases
- p.Glu319Gly Single submitter Inborn genetic diseases ⚠
- p.Glu355Gly Single submitter ⚠
- p.Glu364Gly Single submitter ⚠
- p.Glu364Lys Single submitter ⚠
- p.Glu398Gly Single submitter ⚠
- p.Glu41Gly Single submitter Inborn genetic diseases ⚠
- p.Glu444Gly Single submitter ⚠
- p.Glu485_Asn486insGlnAspGlu Single submitter
- p.Glu513Asp Single submitter ⚠
- p.Glu91Lys Single submitter Inborn genetic diseases ⚠
- p.Gly109Asp Single submitter
- p.Gly487Arg Single submitter ⚠
- p.Gly487Glu Single submitter ⚠
- p.His161Tyr Single submitter ⚠
- p.His176Leu Single submitter ⚠
- p.His314Gln Single submitter ⚠
- p.Ile208Met Single submitter ⚠
- p.Ile20Val Single submitter Inborn genetic diseases ⚠
- p.Ile227Phe Single submitter ⚠
- p.Leu153Phe Single submitter ⚠
- p.Leu347Val Single submitter
- p.Leu39Ter Single submitter
- p.Leu59Gln Single submitter ⚠
- p.Lys151Asn Single submitter
- p.Lys162Asn Single submitter
- p.Lys165Asn Single submitter ⚠
- p.Lys296Gln Single submitter ⚠
- p.Lys344Ter Single submitter
- p.Lys437Asn Single submitter ⚠
- p.Lys79Arg Single submitter ⚠
- p.Met285Val Single submitter Inborn genetic diseases ⚠
- p.Met318Ile Single submitter ⚠
- p.Met322Val Single submitter Inborn genetic diseases ⚠
- p.Met421Thr Single submitter ⚠
- p.Met451Val Single submitter Inborn genetic diseases ⚠
- p.Met549Val Single submitter Inborn genetic diseases ⚠
- p.Pro154Leu Single submitter ⚠
- p.Pro265= Single submitter
- p.Pro265Leu Single submitter ⚠
- p.Ser144Pro Single submitter ⚠
- p.Ser144Thr Single submitter ⚠
- p.Ser384Ile Single submitter ⚠
- p.Ser504Ile Single submitter ⚠
- p.Ser527Leu Single submitter ⚠
- p.Thr235Ser Single submitter ⚠
- p.Thr526Ile Single submitter ⚠
- p.Val130Ile Single submitter Inborn genetic diseases ⚠
- p.Val188Ile Single submitter ⚠
- p.Ala129Ser No assertion criteria MSN-related disorder ⚠
- p.Leu47Met No assertion criteria autism ⚠