AP4B1 — 477 ClinVar variants

All ClinVar germline AP4B1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 238 flagged for review →

34 Pathogenic · 7 Pathogenic/Likely pathogenic · 19 Likely pathogenic · 17 Conflicting · 14 Benign · 8 Benign/Likely benign · 134 Likely benign · 244 Uncertain significance

Full AP4B1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 238

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 5

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

Predictors lean, ClinVar uncertain 132

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

Predictors split 101

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

All AP4B1 variants

Pathogenic 34

  • c.114-2A>C Multiple submitters hereditary spastic paraplegia 47
  • c.114-2A>G Multiple submitters Inborn genetic diseases
  • p.Arg102Ter Multiple submitters hereditary spastic paraplegia 47
  • p.Arg353Ter Multiple submitters hereditary spastic paraplegia 47
  • p.Arg393Ter Multiple submitters hereditary spastic paraplegia 47
  • p.Arg449Ter Multiple submitters Inborn genetic diseases
  • p.Cys18fs Multiple submitters hereditary spastic paraplegia 47
  • p.Cys298Ter Multiple submitters hereditary spastic paraplegia 47
  • p.Gln414Ter Multiple submitters hereditary spastic paraplegia 47
  • p.Tyr135_Arg137delinsTer Multiple submitters Inborn genetic diseases
  • c.1510+2T>C Single submitter hereditary spastic paraplegia 47
  • p.Ala105fs Single submitter hereditary spastic paraplegia 47
  • p.Ala367fs Single submitter hereditary spastic paraplegia 47
  • p.Ala375delinsLeuTer Single submitter hereditary spastic paraplegia 47
  • p.Arg497fs Single submitter hereditary spastic paraplegia 47
  • p.Asn149Ter Single submitter hereditary spastic paraplegia 47
  • p.Asn178fs Single submitter
  • p.Asp131fs Single submitter hereditary spastic paraplegia 47
  • p.Cys293fs Single submitter hereditary spastic paraplegia 47
  • p.Cys73Ter Single submitter hereditary spastic paraplegia 47
  • p.Gln118Ter Single submitter hereditary spastic paraplegia 47
  • p.Gln394fs Single submitter hereditary spastic paraplegia 47
  • p.Glu388Ter Single submitter hereditary spastic paraplegia 47
  • p.Glu467Ter Single submitter hereditary spastic paraplegia 47
  • p.Gly309fs Single submitter hereditary spastic paraplegia 47
  • p.Ile371fs Single submitter hereditary spastic paraplegia 47
  • p.Ile440fs Single submitter hereditary spastic paraplegia 47
  • p.Leu442fs Single submitter hereditary spastic paraplegia 47
  • p.Lys329Ter Single submitter hereditary spastic paraplegia 47
  • c.667del No assertion criteria hereditary spastic paraplegia 47
  • p.Arg487Ter No assertion criteria hereditary spastic paraplegia 47
  • p.His148fs No assertion criteria
  • p.Ser323fs No assertion criteria hereditary spastic paraplegia 47
  • p.Tyr455Ter No assertion criteria hereditary spastic paraplegia 47

Pathogenic/Likely pathogenic 7

  • p.Arg206Ter Multiple submitters hereditary spastic paraplegia 47
  • p.Arg406Ter Multiple submitters hereditary spastic paraplegia
  • p.Arg514Ter Multiple submitters hereditary spastic paraplegia 47
  • p.Gln331fs Multiple submitters hereditary spastic paraplegia 47
  • p.Thr387fs Multiple submitters Inborn genetic diseases
  • p.Tyr519Ter Multiple submitters AP4B1-related disorder
  • p.Glu163delinsValTer No assertion criteria hereditary spastic paraplegia 47

Likely pathogenic 19

Conflicting classifications of pathogenicity 17

  • c.1115-2A>G Single submitter hereditary spastic paraplegia 47
  • c.114-10C>T Single submitter hereditary spastic paraplegia 47
  • c.338+5G>A Single submitter hereditary spastic paraplegia 47
  • p.Ala216Asp Single submitter Inborn genetic diseases ⚠
  • p.Arg206Gln Single submitter Inborn genetic diseases ⚠
  • p.Arg520Cys Single submitter Inborn genetic diseases ⚠
  • p.Arg583His Single submitter hereditary spastic paraplegia ⚠
  • p.Gln189= Single submitter hereditary spastic paraplegia 47
  • p.Gln270= Single submitter hereditary spastic paraplegia 47
  • p.Leu17= Single submitter hereditary spastic paraplegia
  • p.Met1fs Single submitter hereditary spastic paraplegia 47
  • p.Pro308= Single submitter hereditary spastic paraplegia
  • p.Val193Ile Single submitter Inborn genetic diseases ⚠
  • p.Val252Ala Single submitter Inborn genetic diseases ⚠
  • p.Val300Leu Single submitter hereditary spastic paraplegia 47 ⚠
  • p.Val348= Single submitter hereditary spastic paraplegia
  • p.Val524Ala Single submitter Inborn genetic diseases ⚠

Benign 14

Benign/Likely benign 8

  • c.618-13G>C Multiple submitters hereditary spastic paraplegia 47
  • p.His268Arg Multiple submitters hereditary spastic paraplegia
  • p.Ile397Val Multiple submitters Inborn genetic diseases
  • p.Ile575Val Multiple submitters Inborn genetic diseases
  • p.Leu304= Multiple submitters Inborn genetic diseases
  • p.Met51Leu Multiple submitters hereditary spastic paraplegia 47
  • p.Pro80= Multiple submitters Inborn genetic diseases
  • p.Tyr455= Multiple submitters Inborn genetic diseases

Likely benign 134

  • c.1199-222A>G Multiple submitters
  • c.1792+85A>G Multiple submitters
  • c.339-87A>C Multiple submitters
  • c.618-321G>T Multiple submitters
  • p.Ala715= Multiple submitters Inborn genetic diseases
  • p.Glu190= Multiple submitters Inborn genetic diseases
  • p.Glu428= Multiple submitters hereditary spastic paraplegia 47
  • p.Glu504= Multiple submitters
  • p.Ile303= Multiple submitters hereditary spastic paraplegia 47
  • p.Ile575= Multiple submitters hereditary spastic paraplegia 47
  • p.Ile669= Multiple submitters Inborn genetic diseases
  • p.Ile734Val Multiple submitters hereditary spastic paraplegia 47
  • p.Leu160= Multiple submitters Inborn genetic diseases
  • p.Pro198= Multiple submitters Inborn genetic diseases
  • p.Pro536= Multiple submitters Inborn genetic diseases
  • p.Thr256Ile Multiple submitters Inborn genetic diseases
  • p.Thr357= Multiple submitters hereditary spastic paraplegia 47
  • p.Thr668= Multiple submitters hereditary spastic paraplegia 47
  • p.Thr89= Multiple submitters Inborn genetic diseases
  • c.1114+14C>T Single submitter hereditary spastic paraplegia 47
  • c.1114+98T>C Single submitter
  • c.1114+9C>T Single submitter hereditary spastic paraplegia 47
  • c.1115-103del Single submitter
  • c.1115-116dup Single submitter
  • c.1115-13C>T Single submitter hereditary spastic paraplegia 47
  • c.113+10A>G Single submitter hereditary spastic paraplegia 47
  • c.113+13T>G Single submitter hereditary spastic paraplegia 47
  • c.113+20G>T Single submitter hereditary spastic paraplegia 47
  • c.114-13G>T Single submitter hereditary spastic paraplegia 47
  • c.114-14T>C Single submitter hereditary spastic paraplegia 47
  • c.114-6G>T Single submitter hereditary spastic paraplegia 47
  • c.114-9G>A Single submitter hereditary spastic paraplegia 47
  • c.1198+7C>A Single submitter hereditary spastic paraplegia 47
  • c.1199-13G>A Single submitter hereditary spastic paraplegia 47
  • c.1199-18C>T Single submitter hereditary spastic paraplegia 47
  • c.1302+11A>G Single submitter hereditary spastic paraplegia 47
  • c.1302+14C>G Single submitter hereditary spastic paraplegia 47
  • c.1302+234TTTTG[2] Single submitter
  • c.1302+8G>A Single submitter hereditary spastic paraplegia 47
  • c.1303-11T>C Single submitter hereditary spastic paraplegia 47
  • c.1303-160A>G Single submitter
  • c.1510+12A>G Single submitter hereditary spastic paraplegia 47
  • c.1510+9T>C Single submitter
  • c.1511-19A>G Single submitter hereditary spastic paraplegia 47
  • c.1792+11T>C Single submitter hereditary spastic paraplegia 47
  • c.1792+16A>G Single submitter hereditary spastic paraplegia 47
  • c.1792+8C>T Single submitter hereditary spastic paraplegia 47
  • c.1793-9C>A Single submitter hereditary spastic paraplegia 47
  • c.338+19G>C Single submitter hereditary spastic paraplegia 47
  • c.339-12T>C Single submitter hereditary spastic paraplegia 47
  • c.339-16A>C Single submitter hereditary spastic paraplegia 47
  • c.339-16A>G Single submitter hereditary spastic paraplegia 47
  • c.339-7T>C Single submitter hereditary spastic paraplegia 47
  • c.469+17C>A Single submitter hereditary spastic paraplegia 47
  • c.470-14G>A Single submitter hereditary spastic paraplegia 47
  • c.470-20A>G Single submitter hereditary spastic paraplegia 47
  • c.617+16C>T Single submitter hereditary spastic paraplegia 47
  • c.617+17A>G Single submitter hereditary spastic paraplegia 47
  • c.617+8T>C Single submitter hereditary spastic paraplegia 47
  • c.618-12T>C Single submitter hereditary spastic paraplegia 47
  • c.618-13G>A Single submitter hereditary spastic paraplegia 47
  • c.618-16T>G Single submitter hereditary spastic paraplegia 47
  • c.618-20T>C Single submitter hereditary spastic paraplegia 47
  • c.618-4A>T Single submitter hereditary spastic paraplegia 47
  • c.-66C>G Single submitter
  • c.*301T>C Single submitter
  • p.Ala366= Single submitter hereditary spastic paraplegia 47
  • p.Ala595= Single submitter hereditary spastic paraplegia 47
  • p.Arg393= Single submitter hereditary spastic paraplegia 47
  • p.Arg487= Single submitter hereditary spastic paraplegia 47
  • p.Arg624His Single submitter Inborn genetic diseases
  • p.Asn341= Single submitter hereditary spastic paraplegia 47
  • p.Asn452= Single submitter hereditary spastic paraplegia 47
  • p.Asp211= Single submitter hereditary spastic paraplegia 47
  • p.Asp358= Single submitter
  • p.Asp432= Single submitter hereditary spastic paraplegia 47
  • p.Asp61= Single submitter hereditary spastic paraplegia 47
  • p.Cys491= Single submitter
  • p.Cys502= Single submitter hereditary spastic paraplegia 47
  • p.Cys73= Single submitter
  • p.Glu607= Single submitter hereditary spastic paraplegia 47
  • p.Gly152= Single submitter hereditary spastic paraplegia 47
  • p.Gly435= Single submitter hereditary spastic paraplegia 47
  • p.His268= Single submitter hereditary spastic paraplegia 47
  • p.His642= Single submitter hereditary spastic paraplegia 47
  • p.Ile261= Single submitter hereditary spastic paraplegia 47
  • p.Ile532= Single submitter hereditary spastic paraplegia 47
  • p.Leu112= Single submitter hereditary spastic paraplegia 47
  • p.Leu129= Single submitter hereditary spastic paraplegia 47
  • p.Leu142= Single submitter hereditary spastic paraplegia 47
  • p.Leu203= Single submitter
  • p.Leu204= Single submitter hereditary spastic paraplegia 47
  • p.Leu282= Single submitter Inborn genetic diseases
  • p.Leu282= Single submitter hereditary spastic paraplegia 47
  • p.Leu297= Single submitter hereditary spastic paraplegia 47
  • p.Leu423= Single submitter hereditary spastic paraplegia 47
  • p.Leu545= Single submitter hereditary spastic paraplegia 47
  • p.Leu563= Single submitter hereditary spastic paraplegia 47
  • p.Leu67= Single submitter hereditary spastic paraplegia 47
  • p.Leu698= Single submitter
  • p.Leu70= Single submitter hereditary spastic paraplegia 47
  • p.Leu727= Single submitter hereditary spastic paraplegia 47
  • p.Leu78= Single submitter hereditary spastic paraplegia 47
  • p.Lys278= Single submitter Inborn genetic diseases
  • p.Lys633= Single submitter hereditary spastic paraplegia 47
  • p.Lys680= Single submitter hereditary spastic paraplegia 47
  • p.Phe311= Single submitter Inborn genetic diseases
  • p.Phe405= Single submitter hereditary spastic paraplegia 47
  • p.Phe469= Single submitter hereditary spastic paraplegia 47
  • p.Pro124= Single submitter hereditary spastic paraplegia 47
  • p.Pro424= Single submitter hereditary spastic paraplegia 47
  • p.Pro548= Single submitter hereditary spastic paraplegia 47
  • p.Pro613= Single submitter hereditary spastic paraplegia 47
  • p.Pro654= Single submitter hereditary spastic paraplegia 47
  • p.Pro99= Single submitter Inborn genetic diseases
  • p.Ser313= Single submitter hereditary spastic paraplegia 47
  • p.Ser592Ala Single submitter Inborn genetic diseases
  • p.Thr379= Single submitter hereditary spastic paraplegia 47
  • p.Thr562= Single submitter Inborn genetic diseases
  • p.Thr717= Single submitter hereditary spastic paraplegia 47
  • p.Thr74= Single submitter hereditary spastic paraplegia 47
  • p.Tyr135= Single submitter hereditary spastic paraplegia 47
  • p.Tyr225= Single submitter Inborn genetic diseases
  • p.Tyr29= Single submitter hereditary spastic paraplegia 47
  • p.Tyr519= Single submitter
  • p.Tyr69= Single submitter hereditary spastic paraplegia 47
  • p.Val194= Single submitter
  • p.Val218= Single submitter hereditary spastic paraplegia 47
  • p.Val333= Single submitter hereditary spastic paraplegia 47
  • p.Val621= Single submitter hereditary spastic paraplegia 47
  • p.Val68= Single submitter hereditary spastic paraplegia 47
  • p.Val726Leu Single submitter Inborn genetic diseases
  • c.-35G>C No assertion criteria
  • p.Asn561= No assertion criteria AP4B1-related disorder

Uncertain significance 244