AP1S2 — 92 ClinVar variants
All ClinVar germline AP1S2 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 22 flagged for review →
17 Pathogenic · 1 Pathogenic/Likely pathogenic · 6 Likely pathogenic · 1 Conflicting · 12 Benign · 3 Benign/Likely benign · 24 Likely benign · 28 Uncertain significance
Full AP1S2 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions⚑ Evidence disagreements 22
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 6
ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification.
- AP1S2 p.Cys67Arg Uncertain significance Single submitter
- AP1S2 p.Cys68Tyr Uncertain significance Single submitter
-
AP1S2 p.Gln36Arg
Uncertain significance
Single submitter
Inborn genetic diseases
- AP1S2 p.Gly95Ser Uncertain significance Single submitter
- AP1S2 p.Leu15Arg Uncertain significance Single submitter
- AP1S2 p.Val87Met Uncertain significance Single submitter
Predictors split 16
The independent predictors disagree with each other — read with care.
- AP1S2 p.Asn129Thr Uncertain significance Multiple submitters
-
AP1S2 p.Gly158Arg
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
AP1S2 p.Ile134Thr
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
AP1S2 p.Ile82Val
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
AP1S2 p.Leu54Val
Uncertain significance
Multiple submitters
Inborn genetic diseases
-
AP1S2 p.Val38Ile
Benign/Likely benign
Multiple submitters
Inborn genetic diseases
- AP1S2 p.Ala40Val Uncertain significance Single submitter
- AP1S2 p.Asn129Ile Uncertain significance Single submitter
-
AP1S2 p.Glu135Ala
Uncertain significance
Single submitter
intellectual disability
- AP1S2 p.Glu155Val Uncertain significance Single submitter
- AP1S2 p.Glu50Gln Uncertain significance Single submitter
- AP1S2 p.Gly158Glu Uncertain significance Single submitter
- AP1S2 p.Ile134Val Uncertain significance Single submitter
- AP1S2 p.Ile157Thr Uncertain significance Single submitter
- AP1S2 p.Leu139Arg Uncertain significance Single submitter
-
AP1S2 p.Thr125Pro
Uncertain significance
Single submitter
Inborn genetic diseases
All AP1S2 variants
Pathogenic 17
- p.Arg52Ter Multiple submitters syndromic X-linked intellectual disability 5
- p.Gln123Ter Multiple submitters syndromic X-linked intellectual disability 5
- c.1-3C>A Single submitter syndromic X-linked intellectual disability 5
- c.288+1G>A Single submitter syndromic X-linked intellectual disability 5
- c.289-2A>G Single submitter
- c.426+1G>T Single submitter syndromic X-linked intellectual disability 5
- p.Arg14Ter Single submitter syndromic X-linked intellectual disability 5
- p.Arg60fs Single submitter
- p.Glu107fs Single submitter syndromic X-linked intellectual disability 5
- p.Phe94fs Single submitter syndromic X-linked intellectual disability 5
- p.Ser23Ter Single submitter Inborn genetic diseases
- p.Thr31fs Single submitter
- p.Trp18Ter Single submitter
- c.1-2A>G No assertion criteria syndromic X-linked intellectual disability 5
- c.180-5_180-2del No assertion criteria syndromic X-linked intellectual disability 5
- p.Gln36Ter No assertion criteria syndromic X-linked intellectual disability 5
- p.Glu76Ter No assertion criteria syndromic X-linked intellectual disability 5
Pathogenic/Likely pathogenic 1
- c.-1+1G>A Multiple submitters syndromic X-linked intellectual disability 5
Likely pathogenic 6
- c.179+1G>A Single submitter
- c.288+5G>A Single submitter syndromic X-linked intellectual disability 5
- p.Glu121fs Single submitter syndromic X-linked intellectual disability 5
- p.Leu22fs Single submitter syndromic X-linked intellectual disability 5
- p.Phe7fs Single submitter syndromic X-linked intellectual disability 5
- p.Gln2Ter No assertion criteria X-linked syndromic intellectual disability
Conflicting classifications of pathogenicity 1
- p.His84= Single submitter
Benign 12
- c.288+73T>A Multiple submitters
- c.179+11del Single submitter
- c.179+12G>T Single submitter
- c.180-5T>C Single submitter
- c.289-10del Single submitter
- c.289-10dup Single submitter
- c.426+193T>C Single submitter
- c.426+206A>G Single submitter
- c.426+226A>G Single submitter
- c.-1+227G>C Single submitter
- p.Leu49= Single submitter
- p.Phe94= Single submitter
Benign/Likely benign 3
- c.289-8C>T Multiple submitters Inborn genetic diseases
- p.Ser96= Multiple submitters Inborn genetic diseases
- p.Val38Ile Multiple submitters Inborn genetic diseases ⚠
Likely benign 24
- c.427-9C>A Multiple submitters
- c.436-5C>T Multiple submitters
- p.Tyr86= Multiple submitters
- c.180-18A>G Single submitter
- c.289-10T>C Single submitter
- c.289-11T>C Single submitter
- c.289-9C>T Single submitter
- c.426+15C>G Single submitter
- c.426+8A>C Single submitter
- c.426+9C>T Single submitter
- c.436-19_436-18del Single submitter
- c.-12C>T Single submitter
- p.Asp24= Single submitter
- p.Asp74= Single submitter
- p.Gln36= Single submitter
- p.Glu124= Single submitter
- p.Glu50= Single submitter
- p.Glu76= Single submitter
- p.Ile103= Single submitter
- p.Leu15= Single submitter
- p.Leu22= Single submitter
- p.Pro21= Single submitter
- p.Ter161= Single submitter
- p.Thr160= Single submitter
Uncertain significance 28
- p.Asn129Thr Multiple submitters ⚠
- p.Gly158Arg Multiple submitters Inborn genetic diseases ⚠
- p.Ile134Thr Multiple submitters Inborn genetic diseases ⚠
- p.Ile82Val Multiple submitters Inborn genetic diseases ⚠
- p.Leu54Val Multiple submitters Inborn genetic diseases ⚠
- c.179+3A>G Single submitter
- c.-1+15G>T Single submitter
- c.*1C>T Single submitter Inborn genetic diseases
- c.*241A>C Single submitter syndromic X-linked intellectual disability 5
- p.Ala40Val Single submitter ⚠
- p.Asn129Ile Single submitter ⚠
- p.Cys67Arg Single submitter ⚠
- p.Cys68Tyr Single submitter ⚠
- p.Gln36Arg Single submitter Inborn genetic diseases ⚠
- p.Glu135Ala Single submitter intellectual disability ⚠
- p.Glu142= Single submitter
- p.Glu155Val Single submitter ⚠
- p.Glu50Gln Single submitter ⚠
- p.Gly158Glu Single submitter ⚠
- p.Gly95Ser Single submitter ⚠
- p.Ile134Val Single submitter ⚠
- p.Ile157Thr Single submitter ⚠
- p.Leu139Arg Single submitter ⚠
- p.Leu15Arg Single submitter ⚠
- p.Leu80= Single submitter
- p.Leu80_Ile83del Single submitter AP1S2-related disorder
- p.Thr125Pro Single submitter Inborn genetic diseases ⚠
- p.Val87Met Single submitter ⚠