MGAT2 — 164 ClinVar variants
All ClinVar germline MGAT2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 83 flagged for review →
6 Pathogenic · 9 Likely pathogenic · 5 Conflicting · 4 Benign · 4 Benign/Likely benign · 18 Likely benign · 118 Uncertain significance
Full MGAT2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 83
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 1
ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.
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MGAT2 p.Pro77Ser
Conflicting
Single submitter
MGAT2-congenital disorder of glycosylation
Predictors lean, ClinVar uncertain 68
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
-
MGAT2 p.Ala421Val
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
MGAT2 p.Ala78Thr
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
MGAT2 p.Asn146Ser
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
MGAT2 p.Asn186Lys
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
MGAT2 p.Gln182Glu
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
MGAT2 p.Gly49Asp
Uncertain significance
Multiple submitters
MGAT2-congenital disorder of glycosylation
-
MGAT2 p.Gly55Arg
Uncertain significance
Multiple submitters
MGAT2-congenital disorder of glycosylation
-
MGAT2 p.Pro171Thr
Uncertain significance
Multiple submitters
MGAT2-congenital disorder of glycosylation
- MGAT2 p.Ser26Gly Uncertain significance Multiple submitters
-
MGAT2 p.Thr324Ser
Uncertain significance
Multiple submitters
MGAT2-congenital disorder of glycosylation
-
MGAT2 p.Tyr269His
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
MGAT2 p.Val23Ala
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
MGAT2 p.Val245Leu
Uncertain significance
Multiple submitters
MGAT2-congenital disorder of glycosylation
-
MGAT2 p.Ala114Val
Uncertain significance
Single submitter
MGAT2-congenital disorder of glycosylation
-
MGAT2 p.Ala205Gly
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Ala84Ser
Uncertain significance
Single submitter
MGAT2-congenital disorder of glycosylation
-
MGAT2 p.Arg132Thr
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Arg90Trp
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Arg92Leu
Uncertain significance
Single submitter
MGAT2-congenital disorder of glycosylation
-
MGAT2 p.Asn401Ser
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Asn69Ser
Uncertain significance
Single submitter
MGAT2-congenital disorder of glycosylation
-
MGAT2 p.Asp136Asn
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Asp261Tyr
Uncertain significance
Single submitter
MGAT2-congenital disorder of glycosylation
-
MGAT2 p.Asp343His
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Cys170Tyr
Uncertain significance
Single submitter
MGAT2-congenital disorder of glycosylation
-
MGAT2 p.Cys283Tyr
Uncertain significance
Single submitter
MGAT2-congenital disorder of glycosylation
-
MGAT2 p.Cys334Gly
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Gln142Glu
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Gln162Lys
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Gln280His
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Gln31Glu
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Glu117Gln
Uncertain significance
Single submitter
MGAT2-congenital disorder of glycosylation
-
MGAT2 p.Glu83Lys
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Gly253Arg
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Gly430Arg
Uncertain significance
Single submitter
MGAT2-congenital disorder of glycosylation
-
MGAT2 p.Gly432Arg
Uncertain significance
Single submitter
MGAT2-congenital disorder of glycosylation
-
MGAT2 p.His374Tyr
Uncertain significance
Single submitter
MGAT2-congenital disorder of glycosylation
-
MGAT2 p.Ile369Met
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Ile395Val
Uncertain significance
Single submitter
Inborn genetic diseases
- MGAT2 p.Ile413Val Uncertain significance Single submitter
-
MGAT2 p.Leu120Pro
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Leu120Val
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Leu173Met
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Leu256Val
Uncertain significance
Single submitter
MGAT2-congenital disorder of glycosylation
-
MGAT2 p.Leu289His
Uncertain significance
Single submitter
MGAT2-congenital disorder of glycosylation
-
MGAT2 p.Lys109Asn
Uncertain significance
Single submitter
MGAT2-congenital disorder of glycosylation
-
MGAT2 p.Lys226Arg
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Lys306Arg
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Phe272Leu
Uncertain significance
Single submitter
MGAT2-congenital disorder of glycosylation
-
MGAT2 p.Pro284Ser
Uncertain significance
Single submitter
MGAT2-congenital disorder of glycosylation
-
MGAT2 p.Pro40Leu
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Pro58Arg
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Pro58Leu
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Pro77Leu
Uncertain significance
Single submitter
MGAT2-congenital disorder of glycosylation
-
MGAT2 p.Ser191Gly
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Ser290Phe
Uncertain significance
Single submitter
MGAT2-congenital disorder of glycosylation
-
MGAT2 p.Ser392Asn
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Thr230Pro
Uncertain significance
Single submitter
MGAT2-congenital disorder of glycosylation
-
MGAT2 p.Thr335Ala
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Thr412Ala
Uncertain significance
Single submitter
MGAT2-congenital disorder of glycosylation
-
MGAT2 p.Thr412Asn
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Tyr328Cys
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Val107Ile
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Val172Ala
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Val288Ile
Uncertain significance
Single submitter
MGAT2-congenital disorder of glycosylation
-
MGAT2 p.Val420Gly
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Val60Leu
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Val67Phe
Uncertain significance
Single submitter
Inborn genetic diseases
Predictors split 14
The independent predictors disagree with each other — read with care.
-
MGAT2 p.Gln281Pro
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
MGAT2 p.Pro197His
Uncertain significance
Multiple submitters
MGAT2-congenital disorder of glycosylation
-
MGAT2 p.Pro266Leu
Uncertain significance
Multiple submitters
MGAT2-congenital disorder of glycosylation
-
MGAT2 p.Arg4His
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Asp101Val
Uncertain significance
Single submitter
MGAT2-congenital disorder of glycosylation
-
MGAT2 p.Asp136Val
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Glu438Val
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Gly166Val
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Gly209Trp
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Gly21Arg
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.His270Leu
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Phe155Leu
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Thr335Arg
Uncertain significance
Single submitter
Inborn genetic diseases
-
MGAT2 p.Thr88Arg
Uncertain significance
Single submitter
MGAT2-congenital disorder of glycosylation
All MGAT2 variants
Pathogenic 6
- p.Ala252fs No assertion criteria MGAT2-congenital disorder of glycosylation
- p.Asn318Asp No assertion criteria MGAT2-congenital disorder of glycosylation
- p.Asp267His No assertion criteria MGAT2-congenital disorder of glycosylation
- p.Cys339Ter No assertion criteria MGAT2-congenital disorder of glycosylation
- p.Gln31Ter No assertion criteria MGAT2-congenital disorder of glycosylation
- p.His262Arg No assertion criteria MGAT2-congenital disorder of glycosylation
Likely pathogenic 9
- p.Asp336fs Multiple submitters
- p.Lys237Asn Multiple submitters MGAT2-related disorders
- p.Arg116fs Single submitter
- p.Arg249Ter Single submitter
- p.Asn400fs Single submitter MGAT2-congenital disorder of glycosylation
- p.Gln394_Gly432delinsHis Single submitter
- p.Leu365fs Single submitter MGAT2-congenital disorder of glycosylation
- p.Ser59fs Single submitter MGAT2-congenital disorder of glycosylation
- p.Trp362Ter Single submitter MGAT2-congenital disorder of glycosylation
Conflicting classifications of pathogenicity 5
- p.Gly21= Single submitter MGAT2-congenital disorder of glycosylation
- p.Leu411= Single submitter MGAT2-congenital disorder of glycosylation
- p.Lys33Asn Single submitter Inborn genetic diseases
- p.Pro77Ser Single submitter MGAT2-congenital disorder of glycosylation ⚠
- p.Tyr341= Single submitter MGAT2-congenital disorder of glycosylation
Benign 4
Benign/Likely benign 4
Likely benign 18
- c.*366C>G Multiple submitters MGAT2-congenital disorder of glycosylation
- p.Asn212= Multiple submitters MGAT2-congenital disorder of glycosylation
- p.Gly430= Multiple submitters MGAT2-congenital disorder of glycosylation
- p.Gly51= Multiple submitters MGAT2-congenital disorder of glycosylation
- p.Ser137= Multiple submitters
- c.*11T>C Single submitter
- p.Gln368= Single submitter MGAT2-congenital disorder of glycosylation
- p.Gly63= Single submitter MGAT2-congenital disorder of glycosylation
- p.Leu134= Single submitter MGAT2-congenital disorder of glycosylation
- p.Leu278= Single submitter MGAT2-congenital disorder of glycosylation
- p.Leu365= Single submitter
- p.Pro197= Single submitter
- p.Pro40= Single submitter
- p.Tyr352= Single submitter MGAT2-congenital disorder of glycosylation
- p.Val10= Single submitter
- p.Val175= Single submitter MGAT2-congenital disorder of glycosylation
- p.Val307= Single submitter MGAT2-congenital disorder of glycosylation
- p.Val23= No assertion criteria MGAT2-related disorder
Uncertain significance 118
- p.Ala421Val Multiple submitters Inborn genetic diseases ⚠
- p.Ala78Thr Multiple submitters Inborn genetic diseases ⚠
- p.Asn146Ser Multiple submitters Inborn genetic diseases ⚠
- p.Asn186Lys Multiple submitters Inborn genetic diseases ⚠
- p.Gln182Glu Multiple submitters Inborn genetic diseases ⚠
- p.Gln281Pro Multiple submitters Inborn genetic diseases ⚠
- p.Gly49Asp Multiple submitters MGAT2-congenital disorder of glycosylation ⚠
- p.Gly55Arg Multiple submitters MGAT2-congenital disorder of glycosylation ⚠
- p.Ile255Thr Multiple submitters MGAT2-congenital disorder of glycosylation
- p.Pro171Thr Multiple submitters MGAT2-congenital disorder of glycosylation ⚠
- p.Pro197His Multiple submitters MGAT2-congenital disorder of glycosylation ⚠
- p.Pro266Leu Multiple submitters MGAT2-congenital disorder of glycosylation ⚠
- p.Ser26Gly Multiple submitters ⚠
- p.Thr324Ser Multiple submitters MGAT2-congenital disorder of glycosylation ⚠
- p.Tyr269His Multiple submitters Inborn genetic diseases ⚠
- p.Val23Ala Multiple submitters Inborn genetic diseases ⚠
- p.Val245Leu Multiple submitters MGAT2-congenital disorder of glycosylation ⚠
- c.-110G>C Single submitter MGAT2-congenital disorder of glycosylation
- c.-121C>G Single submitter MGAT2-congenital disorder of glycosylation
- c.-125C>G Single submitter MGAT2-congenital disorder of glycosylation
- c.-143G>C Single submitter MGAT2-congenital disorder of glycosylation
- c.-161C>G Single submitter MGAT2-congenital disorder of glycosylation
- c.-190G>A Single submitter MGAT2-congenital disorder of glycosylation
- c.-296C>T Single submitter MGAT2-congenital disorder of glycosylation
- c.-304C>A Single submitter MGAT2-congenital disorder of glycosylation
- c.-338C>T Single submitter MGAT2-congenital disorder of glycosylation
- c.-350C>G Single submitter MGAT2-congenital disorder of glycosylation
- c.-360G>T Single submitter MGAT2-congenital disorder of glycosylation
- c.-425C>T Single submitter MGAT2-congenital disorder of glycosylation
- c.-429G>A Single submitter MGAT2-congenital disorder of glycosylation
- c.*144C>A Single submitter MGAT2-congenital disorder of glycosylation
- c.*189T>G Single submitter MGAT2-congenital disorder of glycosylation
- c.*210C>A Single submitter MGAT2-congenital disorder of glycosylation
- c.*310A>G Single submitter MGAT2-congenital disorder of glycosylation
- c.*372A>T Single submitter MGAT2-congenital disorder of glycosylation
- c.*579C>T Single submitter MGAT2-congenital disorder of glycosylation
- c.*598T>C Single submitter MGAT2-congenital disorder of glycosylation
- c.*666_*669del Single submitter
- c.*722T>C Single submitter MGAT2-congenital disorder of glycosylation
- c.*791G>A Single submitter MGAT2-congenital disorder of glycosylation
- c.*821C>T Single submitter MGAT2-congenital disorder of glycosylation
- c.*825A>G Single submitter MGAT2-congenital disorder of glycosylation
- p.Ala114Val Single submitter MGAT2-congenital disorder of glycosylation ⚠
- p.Ala205Gly Single submitter Inborn genetic diseases ⚠
- p.Ala84Ser Single submitter MGAT2-congenital disorder of glycosylation ⚠
- p.Arg105Ser Single submitter MGAT2-congenital disorder of glycosylation
- p.Arg132Thr Single submitter Inborn genetic diseases ⚠
- p.Arg4His Single submitter Inborn genetic diseases ⚠
- p.Arg90Trp Single submitter Inborn genetic diseases ⚠
- p.Arg92Leu Single submitter MGAT2-congenital disorder of glycosylation ⚠
- p.Asn401Ser Single submitter Inborn genetic diseases ⚠
- p.Asn69Ser Single submitter MGAT2-congenital disorder of glycosylation ⚠
- p.Asp101Val Single submitter MGAT2-congenital disorder of glycosylation ⚠
- p.Asp136Asn Single submitter Inborn genetic diseases ⚠
- p.Asp136Val Single submitter Inborn genetic diseases ⚠
- p.Asp261Tyr Single submitter MGAT2-congenital disorder of glycosylation ⚠
- p.Asp343His Single submitter Inborn genetic diseases ⚠
- p.Cys170Tyr Single submitter MGAT2-congenital disorder of glycosylation ⚠
- p.Cys283Tyr Single submitter MGAT2-congenital disorder of glycosylation ⚠
- p.Cys334Gly Single submitter Inborn genetic diseases ⚠
- p.Cys339fs Single submitter MGAT2-congenital disorder of glycosylation
- p.Gln142Glu Single submitter Inborn genetic diseases ⚠
- p.Gln162Lys Single submitter Inborn genetic diseases ⚠
- p.Gln280His Single submitter Inborn genetic diseases ⚠
- p.Gln31Glu Single submitter Inborn genetic diseases ⚠
- p.Glu117Gln Single submitter MGAT2-congenital disorder of glycosylation ⚠
- p.Glu35= Single submitter MGAT2-congenital disorder of glycosylation
- p.Glu438Val Single submitter Inborn genetic diseases ⚠
- p.Glu83Lys Single submitter Inborn genetic diseases ⚠
- p.Gly166Val Single submitter Inborn genetic diseases ⚠
- p.Gly209Trp Single submitter Inborn genetic diseases ⚠
- p.Gly21Arg Single submitter Inborn genetic diseases ⚠
- p.Gly253Arg Single submitter Inborn genetic diseases ⚠
- p.Gly430Arg Single submitter MGAT2-congenital disorder of glycosylation ⚠
- p.Gly432Arg Single submitter MGAT2-congenital disorder of glycosylation ⚠
- p.His262_Tyr263insTer Single submitter
- p.His270Leu Single submitter Inborn genetic diseases ⚠
- p.His374Tyr Single submitter MGAT2-congenital disorder of glycosylation ⚠
- p.Ile150= Single submitter MGAT2-congenital disorder of glycosylation
- p.Ile369Met Single submitter Inborn genetic diseases ⚠
- p.Ile395Val Single submitter Inborn genetic diseases ⚠
- p.Ile413Val Single submitter ⚠
- p.Ile5Met Single submitter MGAT2-congenital disorder of glycosylation
- p.Leu118= Single submitter MGAT2-congenital disorder of glycosylation
- p.Leu120Pro Single submitter Inborn genetic diseases ⚠
- p.Leu120Val Single submitter Inborn genetic diseases ⚠
- p.Leu173Met Single submitter Inborn genetic diseases ⚠
- p.Leu256Val Single submitter MGAT2-congenital disorder of glycosylation ⚠
- p.Leu289His Single submitter MGAT2-congenital disorder of glycosylation ⚠
- p.Lys109Asn Single submitter MGAT2-congenital disorder of glycosylation ⚠
- p.Lys226Arg Single submitter Inborn genetic diseases ⚠
- p.Lys306Arg Single submitter Inborn genetic diseases ⚠
- p.Phe155Leu Single submitter Inborn genetic diseases ⚠
- p.Phe22= Single submitter MGAT2-congenital disorder of glycosylation
- p.Phe272Leu Single submitter MGAT2-congenital disorder of glycosylation ⚠
- p.Pro284Ser Single submitter MGAT2-congenital disorder of glycosylation ⚠
- p.Pro40Leu Single submitter Inborn genetic diseases ⚠
- p.Pro58Arg Single submitter Inborn genetic diseases ⚠
- p.Pro58Leu Single submitter Inborn genetic diseases ⚠
- p.Pro77Leu Single submitter MGAT2-congenital disorder of glycosylation ⚠
- p.Ser191Gly Single submitter Inborn genetic diseases ⚠
- p.Ser290Phe Single submitter MGAT2-congenital disorder of glycosylation ⚠
- p.Ser392Asn Single submitter Inborn genetic diseases ⚠
- p.Thr230Pro Single submitter MGAT2-congenital disorder of glycosylation ⚠
- p.Thr335Ala Single submitter Inborn genetic diseases ⚠
- p.Thr335Arg Single submitter Inborn genetic diseases ⚠
- p.Thr412Ala Single submitter MGAT2-congenital disorder of glycosylation ⚠
- p.Thr412Asn Single submitter Inborn genetic diseases ⚠
- p.Thr412fs Single submitter MGAT2-congenital disorder of glycosylation
- p.Thr88Arg Single submitter MGAT2-congenital disorder of glycosylation ⚠
- p.Tyr328Cys Single submitter Inborn genetic diseases ⚠
- p.Val107Ile Single submitter Inborn genetic diseases ⚠
- p.Val16= Single submitter MGAT2-congenital disorder of glycosylation
- p.Val172Ala Single submitter Inborn genetic diseases ⚠
- p.Val288Ile Single submitter MGAT2-congenital disorder of glycosylation ⚠
- p.Val420Gly Single submitter Inborn genetic diseases ⚠
- p.Val60Leu Single submitter Inborn genetic diseases ⚠
- p.Val67Phe Single submitter Inborn genetic diseases ⚠