AP2M1 — 300 ClinVar variants
All ClinVar germline AP2M1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 84 flagged for review →
1 Pathogenic · 1 Pathogenic/Likely pathogenic · 3 Conflicting · 23 Benign · 6 Benign/Likely benign · 162 Likely benign · 104 Uncertain significance
Full AP2M1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 84
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 55
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
-
AP2M1 p.Arg199Gln
Uncertain significance
Multiple submitters
intellectual developmental disorder 60 with seizures
-
AP2M1 p.Arg40Trp
Uncertain significance
Multiple submitters
Inborn genetic diseases
- AP2M1 p.Cys246Arg Uncertain significance Multiple submitters
- AP2M1 p.Cys86Tyr Uncertain significance Multiple submitters
-
AP2M1 p.Val58Ile
Uncertain significance
Multiple submitters
complex neurodevelopmental disorder
- AP2M1 p.Ala128Thr Uncertain significance Single submitter
-
AP2M1 p.Ala194Asp
Uncertain significance
Single submitter
Inborn genetic diseases
- AP2M1 p.Ala368Thr Uncertain significance Single submitter
- AP2M1 p.Ala75Thr Uncertain significance Single submitter
- AP2M1 p.Ala90Ser Uncertain significance Single submitter
- AP2M1 p.Ala90Thr Uncertain significance Single submitter
-
AP2M1 p.Arg162Gln
Uncertain significance
Single submitter
Inborn genetic diseases
- AP2M1 p.Arg169Cys Uncertain significance Single submitter
- AP2M1 p.Arg261Cys Uncertain significance Single submitter
-
AP2M1 p.Arg33Trp
Uncertain significance
Single submitter
intellectual developmental disorder 60 with seizures
-
AP2M1 p.Arg357His
Uncertain significance
Single submitter
Inborn genetic diseases
- AP2M1 p.Arg383Gln Uncertain significance Single submitter
- AP2M1 p.Arg423His Uncertain significance Single submitter
- AP2M1 p.Arg44Cys Uncertain significance Single submitter
-
AP2M1 p.Arg60Trp
Uncertain significance
Single submitter
intellectual developmental disorder 60 with seizures
- AP2M1 p.Asp23Ala Uncertain significance Single submitter
- AP2M1 p.Cys251Gly Uncertain significance Single submitter
- AP2M1 p.Gln154Arg Uncertain significance Single submitter
- AP2M1 p.Gln318Pro Uncertain significance Single submitter
- AP2M1 p.Glu211Lys Uncertain significance Single submitter
- AP2M1 p.Glu321Lys Uncertain significance Single submitter
-
AP2M1 p.Glu80Lys
Uncertain significance
Single submitter
neurodevelopmental disorder
- AP2M1 p.Glu98Lys Uncertain significance Single submitter
- AP2M1 p.Gly189Arg Uncertain significance Single submitter
-
AP2M1 p.Gly297Glu
Uncertain significance
Single submitter
Inborn genetic diseases
- AP2M1 p.Gly94Val Uncertain significance Single submitter
- AP2M1 p.Ile101Val Uncertain significance Single submitter
- AP2M1 p.Ile283Val Uncertain significance Single submitter
- AP2M1 p.Ile284Val Uncertain significance Single submitter
- AP2M1 p.Ile307Met Uncertain significance Single submitter
- AP2M1 p.Ile355Asn Uncertain significance Single submitter
- AP2M1 p.Ile96Val Uncertain significance Single submitter
- AP2M1 p.Lys219Gln Uncertain significance Single submitter
- AP2M1 p.Met358Thr Uncertain significance Single submitter
- AP2M1 p.Met77Val Uncertain significance Single submitter
- AP2M1 p.Met85Ile Uncertain significance Single submitter
- AP2M1 p.Met89Arg Uncertain significance Single submitter
- AP2M1 p.Phe32Ser Uncertain significance Single submitter
- AP2M1 p.Pro121Arg Uncertain significance Single submitter
- AP2M1 p.Pro325Thr Uncertain significance Single submitter
- AP2M1 p.Ser97Asn Uncertain significance Single submitter
- AP2M1 p.Thr126Ala Uncertain significance Single submitter
- AP2M1 p.Thr134Ala Uncertain significance Single submitter
- AP2M1 p.Thr330Arg Uncertain significance Single submitter
-
AP2M1 p.Tyr168Cys
Uncertain significance
Single submitter
Inborn genetic diseases
- AP2M1 p.Tyr344Ser Uncertain significance Single submitter
- AP2M1 p.Val19Ile Uncertain significance Single submitter
- AP2M1 p.Val296Ala Uncertain significance Single submitter
-
AP2M1 p.Val306Ile
Uncertain significance
Single submitter
intellectual developmental disorder 60 with seizures
- AP2M1 p.Val47Ile Uncertain significance Single submitter
Predictors split 29
The independent predictors disagree with each other — read with care.
-
AP2M1 p.Ala28Thr
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
AP2M1 p.Arg169His
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
AP2M1 p.Ser97Gly
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
AP2M1 p.Val352Met
Uncertain significance
Multiple submitters
Inborn genetic diseases
- AP2M1 p.Ala28Val Uncertain significance Single submitter
-
AP2M1 p.Ala67Thr
Conflicting
Single submitter
Inborn genetic diseases
- AP2M1 p.Ala75Ser Uncertain significance Single submitter
-
AP2M1 p.Arg40Gln
Uncertain significance
Single submitter
Inborn genetic diseases
- AP2M1 p.Arg44His Uncertain significance Single submitter
- AP2M1 p.Asn35Ser Uncertain significance Single submitter
- AP2M1 p.Asp415Asn Uncertain significance Single submitter
- AP2M1 p.Gln365Arg Uncertain significance Single submitter
-
AP2M1 p.Glu147Gly
Uncertain significance
Single submitter
Inborn genetic diseases
- AP2M1 p.Glu273Asp Uncertain significance Single submitter
-
AP2M1 p.Glu363Gln
Uncertain significance
Single submitter
intellectual developmental disorder 60 with seizures
-
AP2M1 p.Gly25Arg
Uncertain significance
Single submitter
intellectual developmental disorder 60 with seizures
-
AP2M1 p.His416Arg
Uncertain significance
Single submitter
Inborn genetic diseases
- AP2M1 p.Ile159Thr Uncertain significance Single submitter
-
AP2M1 p.Ile386Val
Uncertain significance
Single submitter
Inborn genetic diseases
-
AP2M1 p.Lys304Thr
Uncertain significance
Single submitter
intellectual developmental disorder 60 with seizures
- AP2M1 p.Met338Arg Uncertain significance Single submitter
-
AP2M1 p.Met77Thr
Uncertain significance
Single submitter
Inborn genetic diseases
- AP2M1 p.Phe118Tyr Uncertain significance Single submitter
- AP2M1 p.Phe132Ile Uncertain significance Single submitter
- AP2M1 p.Ser153Arg Uncertain significance Single submitter
-
AP2M1 p.Ser180Cys
Uncertain significance
Single submitter
intellectual developmental disorder 60 with seizures
- AP2M1 p.Thr134Met Likely benign Single submitter
-
AP2M1 p.Tyr83Cys
Uncertain significance
Single submitter
Inborn genetic diseases
- AP2M1 p.Val303Ile Benign Single submitter
All AP2M1 variants
Pathogenic 1
- p.Tyr120Asn Single submitter
Pathogenic/Likely pathogenic 1
- p.Arg170Trp Multiple submitters intellectual developmental disorder 60 with seizures
Conflicting classifications of pathogenicity 3
- c.423+4C>A Single submitter
- c.429+3A>G Single submitter
- p.Ala67Thr Single submitter Inborn genetic diseases ⚠
Benign 23
- c.1173+73T>C Multiple submitters intellectual developmental disorder 60 with seizures
- c.565+17G>A Multiple submitters intellectual developmental disorder 60 with seizures
- c.75-4T>C Multiple submitters intellectual developmental disorder 60 with seizures
- p.Ala395= Multiple submitters intellectual developmental disorder 60 with seizures
- p.Asp87= Multiple submitters
- p.Ile320= Multiple submitters intellectual developmental disorder 60 with seizures
- c.1173+180G>A Single submitter
- c.1173+24G>C Single submitter
- c.340+11C>T Single submitter
- c.340+56G>A Single submitter intellectual developmental disorder 60 with seizures
- c.423+4C>T Single submitter
- c.707+56G>T Single submitter intellectual developmental disorder 60 with seizures
- c.708-3C>T Single submitter
- c.75-19A>G Single submitter
- c.827+12G>A Single submitter
- c.963+10G>A Single submitter
- c.963+3G>A Single submitter
- p.Asn27= Single submitter
- p.Phe132= Single submitter
- p.Thr299Ser Single submitter
- p.Val191= Single submitter
- p.Val303Ile Single submitter ⚠
- c.74+513T>C No assertion criteria AP2M1-related disorder
Benign/Likely benign 6
Likely benign 162
- c.75-5C>T Multiple submitters
- p.Glu408= Multiple submitters
- p.Leu285= Multiple submitters
- p.Lys341= Multiple submitters
- p.Ser347= Multiple submitters
- p.Ser414= Multiple submitters
- c.1061+10T>C Single submitter
- c.1061+11C>A Single submitter
- c.1061+13T>A Single submitter
- c.1062-11T>C Single submitter
- c.1062-15T>C Single submitter
- c.1062-16G>A Single submitter
- c.1062-4C>G Single submitter
- c.1173+12G>C Single submitter
- c.1173+17G>A Single submitter
- c.1173+87G>C Single submitter
- c.1173+9G>C Single submitter
- c.1174-10C>T Single submitter
- c.340+12G>A Single submitter
- c.340+9G>A Single submitter
- c.341-14C>T Single submitter
- c.341-16T>C Single submitter
- c.341-18G>T Single submitter
- c.341-8T>G Single submitter
- c.341-9T>C Single submitter
- c.423+12G>T Single submitter
- c.423+13T>C Single submitter
- c.423+17G>T Single submitter
- c.423+20T>C Single submitter
- c.424-10C>T Single submitter
- c.424-12T>C Single submitter
- c.424-18T>C Single submitter
- c.424-20G>A Single submitter
- c.424-20G>T Single submitter
- c.424-6C>T Single submitter
- c.429+13C>A Single submitter
- c.429+13C>G Single submitter
- c.429+8C>T Single submitter
- c.430-14C>T Single submitter
- c.430-6A>C Single submitter
- c.430-7C>G Single submitter
- c.430-7del Single submitter
- c.565+16C>A Single submitter
- c.565+16C>T Single submitter
- c.565+19C>G Single submitter
- c.565+9C>T Single submitter
- c.566-10C>T Single submitter
- c.566-13G>T Single submitter
- c.566-15C>T Single submitter
- c.566-4C>T Single submitter
- c.707+10G>A Single submitter
- c.707+16G>C Single submitter
- c.707+16G>T Single submitter
- c.707+19C>T Single submitter
- c.708-4G>T Single submitter
- c.708-8G>A Single submitter
- c.708-8G>C Single submitter
- c.74+11_74+17del Single submitter
- c.74+14C>T Single submitter
- c.74+15G>A Single submitter
- c.74+485G>T Single submitter
- c.74+509T>C Single submitter
- c.74+7C>T Single submitter
- c.74+8_74+9insT Single submitter
- c.75-18T>C Single submitter
- c.75-20T>G Single submitter
- c.75-5C>G Single submitter
- c.75-643G>A Single submitter
- c.75-6C>T Single submitter
- c.75-7C>A Single submitter
- c.75-7C>T Single submitter
- c.75-9T>C Single submitter
- c.827+7T>C Single submitter
- c.827+9G>A Single submitter
- c.828-11C>T Single submitter
- c.828-19T>C Single submitter
- c.963+14G>T Single submitter
- c.963+17C>G Single submitter
- c.963+17C>T Single submitter
- c.963+18_963+20del Single submitter
- c.963+18A>G Single submitter
- c.963+20G>A Single submitter
- c.963+8C>G Single submitter
- c.963+9_963+10del Single submitter
- c.964-13G>A Single submitter
- c.964-17A>G Single submitter
- c.964-8A>C Single submitter
- c.964-8A>G Single submitter
- c.-3G>A Single submitter
- p.Ala128= Single submitter
- p.Ala242= Single submitter
- p.Ala28= Single submitter
- p.Ala66= Single submitter
- p.Arg199Trp Single submitter
- p.Arg261= Single submitter
- p.Arg323= Single submitter
- p.Asn310= Single submitter
- p.Asn35= Single submitter
- p.Asn376= Single submitter
- p.Asn72= Single submitter
- p.Asn74= Single submitter
- p.Asp117= Single submitter
- p.Asp23= Single submitter
- p.Asp30= Single submitter
- p.Asp417= Single submitter
- p.Cys435= Single submitter
- p.Gln135= Single submitter
- p.Gln148= Single submitter
- p.Gln188= Single submitter
- p.Gln318= Single submitter
- p.Gln365= Single submitter
- p.Glu302= Single submitter
- p.Glu432= Single submitter
- p.Gly12= Single submitter
- p.Gly360= Single submitter
- p.His10= Single submitter
- p.His142= Single submitter
- p.His195= Single submitter
- p.Ile159Met Single submitter
- p.Ile16= Single submitter
- p.Ile24= Single submitter
- p.Ile324= Single submitter
- p.Ile351= Single submitter
- p.Leu116= Single submitter
- p.Leu129= Single submitter
- p.Leu183= Single submitter
- p.Leu192= Single submitter
- p.Leu301= Single submitter
- p.Leu315= Single submitter
- p.Lys227= Single submitter
- p.Lys235= Single submitter
- p.Phe118= Single submitter
- p.Phe81= Single submitter
- p.Pro267= Single submitter
- p.Pro268= Single submitter
- p.Pro286= Single submitter
- p.Pro291= Single submitter
- p.Pro384= Single submitter
- p.Pro385= Single submitter
- p.Pro409= Single submitter
- p.Pro46= Single submitter
- p.Ser124= Single submitter
- p.Ser17Phe Single submitter
- p.Ser186= Single submitter
- p.Ser193= Single submitter
- p.Ser197= Single submitter
- p.Ser331= Single submitter
- p.Ser364= Single submitter
- p.Ser367= Single submitter
- p.Ser397= Single submitter
- p.Thr134= Single submitter
- p.Thr134Met Single submitter ⚠
- p.Thr279= Single submitter
- p.Thr330= Single submitter
- p.Thr48= Single submitter
- p.Tyr344= Single submitter
- p.Val293= Single submitter
- p.Val322= Single submitter
- p.Val406= Single submitter
- p.Val43= Single submitter
- p.Val88= Single submitter
- p.Val177Leu No assertion criteria intellectual developmental disorder 60 with seizures
Uncertain significance 104
- p.Ala28Thr Multiple submitters Inborn genetic diseases ⚠
- p.Arg169His Multiple submitters Inborn genetic diseases ⚠
- p.Arg199Gln Multiple submitters intellectual developmental disorder 60 with seizures ⚠
- p.Arg40Trp Multiple submitters Inborn genetic diseases ⚠
- p.Cys246Arg Multiple submitters ⚠
- p.Cys86Tyr Multiple submitters ⚠
- p.Ser97Gly Multiple submitters Inborn genetic diseases ⚠
- p.Val352Met Multiple submitters Inborn genetic diseases ⚠
- p.Val58Ile Multiple submitters complex neurodevelopmental disorder ⚠
- c.340+73G>C Single submitter
- c.424-9G>A Single submitter
- c.429+6C>G Single submitter
- c.429+6C>T Single submitter
- c.565+5G>C Single submitter
- c.565+6G>T Single submitter
- c.58_74+7del Single submitter
- c.707+11C>T Single submitter
- c.707+14_707+15delinsCT Single submitter
- c.707+5C>T Single submitter
- c.74+6T>C Single submitter
- c.963+5G>A Single submitter
- c.963+6G>A Single submitter
- c.963+8C>T Single submitter
- c.964-3T>C Single submitter
- p.Ala128Thr Single submitter ⚠
- p.Ala194Asp Single submitter Inborn genetic diseases ⚠
- p.Ala28Val Single submitter ⚠
- p.Ala368Thr Single submitter ⚠
- p.Ala75Ser Single submitter ⚠
- p.Ala75Thr Single submitter ⚠
- p.Ala90Ser Single submitter ⚠
- p.Ala90Thr Single submitter ⚠
- p.Arg162Gln Single submitter Inborn genetic diseases ⚠
- p.Arg163Ter Single submitter
- p.Arg169Cys Single submitter ⚠
- p.Arg261Cys Single submitter ⚠
- p.Arg33Trp Single submitter intellectual developmental disorder 60 with seizures ⚠
- p.Arg357His Single submitter Inborn genetic diseases ⚠
- p.Arg383Gln Single submitter ⚠
- p.Arg383Ter Single submitter
- p.Arg40Gln Single submitter Inborn genetic diseases ⚠
- p.Arg423His Single submitter ⚠
- p.Arg44Cys Single submitter ⚠
- p.Arg44His Single submitter ⚠
- p.Arg60Trp Single submitter intellectual developmental disorder 60 with seizures ⚠
- p.Asn35Ser Single submitter ⚠
- p.Asn9fs Single submitter
- p.Asp23Ala Single submitter ⚠
- p.Asp415Asn Single submitter ⚠
- p.Cys251Gly Single submitter ⚠
- p.Gln154Arg Single submitter ⚠
- p.Gln318Pro Single submitter ⚠
- p.Gln365Arg Single submitter ⚠
- p.Glu147Gly Single submitter Inborn genetic diseases ⚠
- p.Glu211Lys Single submitter ⚠
- p.Glu273Asp Single submitter ⚠
- p.Glu321Lys Single submitter ⚠
- p.Glu363Gln Single submitter intellectual developmental disorder 60 with seizures ⚠
- p.Glu80Lys Single submitter neurodevelopmental disorder ⚠
- p.Glu98Lys Single submitter ⚠
- p.Gly189Arg Single submitter ⚠
- p.Gly25Arg Single submitter intellectual developmental disorder 60 with seizures ⚠
- p.Gly297Glu Single submitter Inborn genetic diseases ⚠
- p.Gly94Val Single submitter ⚠
- p.His416Arg Single submitter Inborn genetic diseases ⚠
- p.Ile101Val Single submitter ⚠
- p.Ile159Thr Single submitter ⚠
- p.Ile283Val Single submitter ⚠
- p.Ile284Val Single submitter ⚠
- p.Ile307Met Single submitter ⚠
- p.Ile355Asn Single submitter ⚠
- p.Ile386Val Single submitter Inborn genetic diseases ⚠
- p.Ile96Val Single submitter ⚠
- p.Leu372Glu Single submitter
- p.Lys219Gln Single submitter ⚠
- p.Lys304Thr Single submitter intellectual developmental disorder 60 with seizures ⚠
- p.Met338Arg Single submitter ⚠
- p.Met358Thr Single submitter ⚠
- p.Met77Thr Single submitter Inborn genetic diseases ⚠
- p.Met77Val Single submitter ⚠
- p.Met85Ile Single submitter ⚠
- p.Met89Arg Single submitter ⚠
- p.Phe118Tyr Single submitter ⚠
- p.Phe132Ile Single submitter ⚠
- p.Phe265fs Single submitter
- p.Phe32Ser Single submitter ⚠
- p.Pro121Arg Single submitter ⚠
- p.Pro325Thr Single submitter ⚠
- p.Ser153Arg Single submitter ⚠
- p.Ser180Cys Single submitter intellectual developmental disorder 60 with seizures ⚠
- p.Ser236= Single submitter
- p.Ser97Asn Single submitter ⚠
- p.Thr126Ala Single submitter ⚠
- p.Thr134Ala Single submitter ⚠
- p.Thr330Arg Single submitter ⚠
- p.Tyr168Cys Single submitter Inborn genetic diseases ⚠
- p.Tyr344Ser Single submitter ⚠
- p.Tyr83Cys Single submitter Inborn genetic diseases ⚠
- p.Val19fs Single submitter
- p.Val19Ile Single submitter ⚠
- p.Val296Ala Single submitter ⚠
- p.Val306Ile Single submitter intellectual developmental disorder 60 with seizures ⚠
- p.Val47Ile Single submitter ⚠
- p.Arg21Ter No assertion criteria intellectual developmental disorder 60 with seizures