DPM1 — 267 ClinVar variants

All ClinVar germline DPM1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 104 flagged for review →

13 Pathogenic · 2 Pathogenic/Likely pathogenic · 6 Likely pathogenic · 14 Conflicting · 9 Benign · 6 Benign/Likely benign · 101 Likely benign · 116 Uncertain significance

Full DPM1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 104

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 3

ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.

Predictors lean, ClinVar uncertain 59

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.

Predictors split 42

The independent predictors disagree with each other — read with care.

All DPM1 variants

Pathogenic 13

  • p.Arg92Gly Multiple submitters congenital disorder of glycosylation type 1E
  • p.Gly111fs Multiple submitters congenital disorder of glycosylation type 1E
  • c.564-1G>T Single submitter congenital disorder of glycosylation type 1E
  • p.Arg191Ter Single submitter congenital disorder of glycosylation type 1E
  • p.Asn57_Tyr58insTer Single submitter congenital disorder of glycosylation type 1E
  • p.Glu137Ter Single submitter congenital disorder of glycosylation type 1E
  • p.Glu18fs Single submitter congenital disorder of glycosylation type 1E
  • p.Ile164fs Single submitter congenital disorder of glycosylation type 1E
  • p.Ile61fs Single submitter congenital disorder of glycosylation type 1E
  • p.Leu176fs Single submitter congenital disorder of glycosylation type 1E
  • p.Leu189Ter Single submitter congenital disorder of glycosylation type 1E
  • c.373-5T>A No assertion criteria congenital disorder of glycosylation type 1E
  • p.Gln210fs No assertion criteria congenital disorder of glycosylation type 1E

Pathogenic/Likely pathogenic 2

  • p.Gly152Val Multiple submitters congenital disorder of glycosylation type 1E
  • p.Met1Leu Multiple submitters congenital disorder of glycosylation type 1E

Likely pathogenic 6

  • p.His124Arg Multiple submitters congenital disorder of glycosylation type 1E
  • c.495-1G>T Single submitter congenital disorder of glycosylation type 1E
  • c.563+1G>A Single submitter congenital disorder of glycosylation type 1E
  • p.Arg92Ter Single submitter
  • p.Glu76fs Single submitter
  • p.Ser248Pro Single submitter congenital disorder of glycosylation type 1E

Conflicting classifications of pathogenicity 14

  • c.161+10C>T Single submitter congenital disorder of glycosylation type 1E
  • c.295+7C>T Single submitter congenital disorder of glycosylation type 1E
  • c.295+8G>A Single submitter congenital disorder of glycosylation type 1E
  • c.494+2T>C Single submitter Inborn genetic diseases
  • p.Ala217Thr Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Arg147Cys Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Arg14Trp Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Arg8Cys Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Glu36Val Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Gly152= Single submitter congenital disorder of glycosylation type 1E
  • p.Leu253= Single submitter congenital disorder of glycosylation type 1E
  • p.Leu96= Single submitter congenital disorder of glycosylation type 1E
  • p.Met1Val Single submitter congenital disorder of glycosylation type 1E
  • p.Tyr190= Single submitter congenital disorder of glycosylation type 1E

Benign 9

Benign/Likely benign 6

  • c.296-12T>C Multiple submitters congenital disorder of glycosylation type 1E
  • c.398+13T>C Multiple submitters congenital disorder of glycosylation type 1E
  • c.679-7_679-6insT Multiple submitters congenital disorder of glycosylation type 1E
  • c.679-7_679-6insTT Multiple submitters congenital disorder of glycosylation type 1E
  • c.679-8del Multiple submitters
  • c.679-8dup Multiple submitters congenital disorder of glycosylation type 1E

Likely benign 101

  • c.162-17A>G Multiple submitters congenital disorder of glycosylation type 1E
  • c.373-33_373-28del Multiple submitters
  • c.495-130A>G Multiple submitters
  • c.495-249C>G Multiple submitters
  • c.679-9_679-8dup Multiple submitters congenital disorder of glycosylation type 1E
  • p.Asn57= Multiple submitters congenital disorder of glycosylation type 1E
  • p.Pro228= Multiple submitters congenital disorder of glycosylation type 1E
  • p.Thr223= Multiple submitters congenital disorder of glycosylation type 1E
  • p.Val6= Multiple submitters congenital disorder of glycosylation type 1E
  • c.161+16_161+21del Single submitter congenital disorder of glycosylation type 1E
  • c.161+18C>T Single submitter congenital disorder of glycosylation type 1E
  • c.161+20_161+22del Single submitter congenital disorder of glycosylation type 1E
  • c.261+8A>G Single submitter congenital disorder of glycosylation type 1E
  • c.262-19C>A Single submitter congenital disorder of glycosylation type 1E
  • c.262-19C>T Single submitter congenital disorder of glycosylation type 1E
  • c.262-9T>C Single submitter congenital disorder of glycosylation type 1E
  • c.295+15C>T Single submitter
  • c.295+18dup Single submitter congenital disorder of glycosylation type 1E
  • c.295+8G>C Single submitter congenital disorder of glycosylation type 1E
  • c.296-10T>C Single submitter congenital disorder of glycosylation type 1E
  • c.296-14A>C Single submitter congenital disorder of glycosylation type 1E
  • c.296-49T>C Single submitter
  • c.296-5T>C Single submitter congenital disorder of glycosylation type 1E
  • c.296-9C>A Single submitter congenital disorder of glycosylation type 1E
  • c.296-9C>G Single submitter congenital disorder of glycosylation type 1E
  • c.372+12G>A Single submitter congenital disorder of glycosylation type 1E
  • c.372+8del Single submitter congenital disorder of glycosylation type 1E
  • c.373-11T>C Single submitter congenital disorder of glycosylation type 1E
  • c.373-17T>C Single submitter congenital disorder of glycosylation type 1E
  • c.398+20T>C Single submitter congenital disorder of glycosylation type 1E
  • c.398+309T>A Single submitter
  • c.399-13A>T Single submitter congenital disorder of glycosylation type 1E
  • c.399-18A>G Single submitter congenital disorder of glycosylation type 1E
  • c.399-250C>T Single submitter
  • c.494+16dup Single submitter congenital disorder of glycosylation type 1E
  • c.494+17del Single submitter congenital disorder of glycosylation type 1E
  • c.494+217G>A Single submitter
  • c.494+7A>G Single submitter congenital disorder of glycosylation type 1E
  • c.494+8C>T Single submitter congenital disorder of glycosylation type 1E
  • c.494+9A>C Single submitter congenital disorder of glycosylation type 1E
  • c.494+9A>G Single submitter congenital disorder of glycosylation type 1E
  • c.495-15T>G Single submitter congenital disorder of glycosylation type 1E
  • c.495-174C>T Single submitter
  • c.495-18G>C Single submitter congenital disorder of glycosylation type 1E
  • c.495-195G>C Single submitter
  • c.495-281dup Single submitter
  • c.563+15T>C Single submitter congenital disorder of glycosylation type 1E
  • c.564-20A>G Single submitter congenital disorder of glycosylation type 1E
  • c.564-24AT[3] Single submitter congenital disorder of glycosylation type 1E
  • c.678+18A>C Single submitter congenital disorder of glycosylation type 1E
  • c.678+8A>G Single submitter congenital disorder of glycosylation type 1E
  • c.678+9C>G Single submitter congenital disorder of glycosylation type 1E
  • c.678+9C>T Single submitter congenital disorder of glycosylation type 1E
  • c.679-12T>A Single submitter congenital disorder of glycosylation type 1E
  • c.679-12T>G Single submitter congenital disorder of glycosylation type 1E
  • c.679-165T>A Single submitter
  • c.679-16T>C Single submitter congenital disorder of glycosylation type 1E
  • c.679-8T>A Single submitter congenital disorder of glycosylation type 1E
  • c.-33A>C Single submitter
  • c.-38delT Single submitter
  • c.-42A>G Single submitter
  • c.*19T>A Single submitter
  • c.*30A>G Single submitter
  • p.Ala101= Single submitter congenital disorder of glycosylation type 1E
  • p.Ala119= Single submitter congenital disorder of glycosylation type 1E
  • p.Ala2= Single submitter congenital disorder of glycosylation type 1E
  • p.Arg11Pro Single submitter Inborn genetic diseases
  • p.Arg14= Single submitter congenital disorder of glycosylation type 1E
  • p.Arg23= Single submitter congenital disorder of glycosylation type 1E
  • p.Arg234= Single submitter congenital disorder of glycosylation type 1E
  • p.Arg92= Single submitter congenital disorder of glycosylation type 1E
  • p.Asn39= Single submitter congenital disorder of glycosylation type 1E
  • p.Asp158= Single submitter congenital disorder of glycosylation type 1E
  • p.Asp73= Single submitter congenital disorder of glycosylation type 1E
  • p.Gly138= Single submitter congenital disorder of glycosylation type 1E
  • p.Gly153= Single submitter congenital disorder of glycosylation type 1E
  • p.Gly153= Single submitter congenital disorder of glycosylation type 1E
  • p.Gly206= Single submitter congenital disorder of glycosylation type 1E
  • p.Gly242= Single submitter congenital disorder of glycosylation type 1E
  • p.Ile115= Single submitter congenital disorder of glycosylation type 1E
  • p.Ile128= Single submitter congenital disorder of glycosylation type 1E
  • p.Leu189= Single submitter congenital disorder of glycosylation type 1E
  • p.Leu220= Single submitter congenital disorder of glycosylation type 1E
  • p.Leu256= Single submitter congenital disorder of glycosylation type 1E
  • p.Leu4= Single submitter congenital disorder of glycosylation type 1E
  • p.Leu78= Single submitter congenital disorder of glycosylation type 1E
  • p.Leu89= Single submitter congenital disorder of glycosylation type 1E
  • p.Pro22= Single submitter congenital disorder of glycosylation type 1E
  • p.Pro228= Single submitter congenital disorder of glycosylation type 1E
  • p.Pro41= Single submitter congenital disorder of glycosylation type 1E
  • p.Pro91= Single submitter congenital disorder of glycosylation type 1E
  • p.Ser7= Single submitter congenital disorder of glycosylation type 1E
  • p.Thr184= Single submitter congenital disorder of glycosylation type 1E
  • p.Tyr113= Single submitter congenital disorder of glycosylation type 1E
  • p.Tyr207= Single submitter congenital disorder of glycosylation type 1E
  • p.Tyr82= Single submitter congenital disorder of glycosylation type 1E
  • p.Val143= Single submitter congenital disorder of glycosylation type 1E
  • p.Val154= Single submitter congenital disorder of glycosylation type 1E
  • p.Val19= Single submitter congenital disorder of glycosylation type 1E
  • p.Val29= Single submitter congenital disorder of glycosylation type 1E
  • p.Trp157Cys No assertion criteria intellectual disability

Uncertain significance 116

  • c.*12T>C Multiple submitters congenital disorder of glycosylation type 1E
  • p.Ala109Val Multiple submitters congenital disorder of glycosylation type 1E ⚠
  • p.Arg12Met Multiple submitters Inborn genetic diseases ⚠
  • p.Arg191Gln Multiple submitters Inborn genetic diseases ⚠
  • p.Arg20Leu Multiple submitters Inborn genetic diseases ⚠
  • p.Arg216Gln Multiple submitters Inborn genetic diseases ⚠
  • p.Arg234His Multiple submitters congenital disorder of glycosylation type 1E ⚠
  • p.Asn169Ser Multiple submitters congenital disorder of glycosylation type 1E ⚠
  • p.Cys202Tyr Multiple submitters Inborn genetic diseases ⚠
  • p.Glu193Asp Multiple submitters Inborn genetic diseases ⚠
  • p.Glu79Gln Multiple submitters Inborn genetic diseases ⚠
  • p.Gly138Asp Multiple submitters congenital disorder of glycosylation type 1E ⚠
  • p.Ile128Val Multiple submitters Inborn genetic diseases ⚠
  • p.Ile229Val Multiple submitters congenital disorder of glycosylation type 1E ⚠
  • p.Ile56Val Multiple submitters Inborn genetic diseases ⚠
  • p.Ile61Thr Multiple submitters congenital disorder of glycosylation type 1E ⚠
  • p.Pro129Ser Multiple submitters Inborn genetic diseases ⚠
  • p.Pro129Thr Multiple submitters congenital disorder of glycosylation type 1E ⚠
  • p.Ser13Cys Multiple submitters Inborn genetic diseases ⚠
  • p.Ser21Asn Multiple submitters congenital disorder of glycosylation type 1E ⚠
  • p.Ser7Asn Multiple submitters congenital disorder of glycosylation type 1E ⚠
  • p.Ser7Gly Multiple submitters congenital disorder of glycosylation type 1E ⚠
  • p.Thr172Ser Multiple submitters congenital disorder of glycosylation type 1E ⚠
  • p.Thr255Ala Multiple submitters Inborn genetic diseases ⚠
  • p.Thr260Ile Multiple submitters Inborn genetic diseases ⚠
  • p.Tyr236His Multiple submitters Inborn genetic diseases ⚠
  • p.Val208Ile Multiple submitters congenital disorder of glycosylation type 1E ⚠
  • c.162-3del Single submitter congenital disorder of glycosylation type 1E
  • c.295+6T>C Single submitter congenital disorder of glycosylation type 1E
  • c.678+15C>G Single submitter congenital disorder of glycosylation type 1E
  • c.678+1G>C Single submitter congenital disorder of glycosylation type 1E
  • c.678+4T>G Single submitter congenital disorder of glycosylation type 1E
  • c.678+6C>A Single submitter congenital disorder of glycosylation type 1E
  • c.*117A>G Single submitter congenital disorder of glycosylation type 1E
  • c.*159A>G Single submitter congenital disorder of glycosylation type 1E
  • c.*191A>G Single submitter congenital disorder of glycosylation type 1E
  • c.*248T>A Single submitter congenital disorder of glycosylation type 1E
  • p.Ala119Thr Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Ala2Pro Single submitter Inborn genetic diseases ⚠
  • p.Ala2Val Single submitter Inborn genetic diseases ⚠
  • p.Arg133= Single submitter congenital disorder of glycosylation type 1E
  • p.Arg147His Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Arg15Gly Single submitter Inborn genetic diseases ⚠
  • p.Arg161Ile Single submitter Inborn genetic diseases ⚠
  • p.Arg166Cys Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Arg166His Single submitter Inborn genetic diseases ⚠
  • p.Arg216Trp Single submitter Inborn genetic diseases ⚠
  • p.Arg37Cys Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Arg92Gln Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Asp120His Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Asp158Ala Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Asp158Glu Single submitter Inborn genetic diseases ⚠
  • p.Asp182Ala Single submitter Inborn genetic diseases ⚠
  • p.Asp233Gly Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Asp85Gly Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Gln219Arg Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Gln24Arg Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Gln77Glu Single submitter ⚠
  • p.Glu137Lys Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Glu212Gln Single submitter ⚠
  • p.Glu5Gln Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Gly150Arg Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Gly206Ala Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Gly206Val Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Gly225= Single submitter congenital disorder of glycosylation type 1E
  • p.Gly252Arg Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Gly66Arg Single submitter Inborn genetic diseases ⚠
  • p.His123Arg Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Ile114Asn Single submitter Inborn genetic diseases ⚠
  • p.Ile114Val Single submitter Inborn genetic diseases ⚠
  • p.Ile116del Single submitter congenital disorder of glycosylation type 1E
  • p.Ile174Ser Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Ile214Thr Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Ile224Asn Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Ile43Val Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Ile56Met Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Ile60Phe Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Ile87= Single submitter congenital disorder of glycosylation type 1E
  • p.Ile87Val Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Leu159Phe Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Leu253Val Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Leu4Phe Single submitter Inborn genetic diseases ⚠
  • p.Leu4Trp Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Lys126Glu Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Lys136Glu Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Lys160Ile Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Lys162del Single submitter
  • p.Lys197Thr Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Lys205Glu Single submitter ⚠
  • p.Met117Ile Single submitter Inborn genetic diseases ⚠
  • p.Met211Thr Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Met213Val Single submitter Inborn genetic diseases ⚠
  • p.Phe231Ser Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Phe51del Single submitter congenital disorder of glycosylation type 1E
  • p.Phe51Ser Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Pro10Ala Single submitter Inborn genetic diseases ⚠
  • p.Pro10Arg Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Pro10His Single submitter Inborn genetic diseases ⚠
  • p.Pro10Thr Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Pro178Arg Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Pro178Leu Single submitter Inborn genetic diseases ⚠
  • p.Pro32Leu Single submitter Inborn genetic diseases ⚠
  • p.Pro32Ser Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Pro41Arg Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Pro68Ala Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Ser230Ala Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Ser28Leu Single submitter Inborn genetic diseases ⚠
  • p.Thr100Ala Single submitter Inborn genetic diseases ⚠
  • p.Thr71Ile Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Tyr113Asn Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Tyr207Cys Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Tyr58Cys Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Tyr58Phe Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Val154Ile Single submitter congenital disorder of glycosylation type 1E ⚠
  • p.Val194Ala Single submitter Inborn genetic diseases ⚠
  • p.Val19Met Single submitter ⚠