AP4M1 — 476 ClinVar variants

All ClinVar germline AP4M1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 171 flagged for review →

31 Pathogenic · 9 Pathogenic/Likely pathogenic · 25 Likely pathogenic · 19 Conflicting · 31 Benign · 7 Benign/Likely benign · 169 Likely benign · 185 Uncertain significance

Full AP4M1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 171

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 vs ClinVar 2

ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.

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 88

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

Predictors split 76

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

All AP4M1 variants

Pathogenic 31

  • p.Arg268Ter Multiple submitters hereditary spastic paraplegia 50
  • p.Arg306Ter Multiple submitters hereditary spastic paraplegia
  • p.Arg318Ter Multiple submitters AP4M1-related disorder
  • p.Arg338Ter Multiple submitters hereditary spastic paraplegia 50
  • p.Asn73fs Multiple submitters hereditary spastic paraplegia 50
  • p.Gln183Ter Multiple submitters hereditary spastic paraplegia 50
  • p.Ser308Ter Multiple submitters hereditary spastic paraplegia 50
  • p.Val281fs Multiple submitters hereditary spastic paraplegia 50
  • c.52_58+6del Single submitter hereditary spastic paraplegia 50
  • c.974+1G>A Single submitter hereditary spastic paraplegia 50
  • c.974+2dup Single submitter intellectual disability
  • p.Arg338fs Single submitter hereditary spastic paraplegia 50
  • p.Arg441fs Single submitter hereditary spastic paraplegia 50
  • p.Asn185fs Single submitter hereditary spastic paraplegia 50
  • p.Asp118fs Single submitter Spastic paraplegia
  • p.Asp190fs Single submitter hereditary spastic paraplegia 50
  • p.Asp23fs Single submitter hereditary spastic paraplegia 50
  • p.Asp288fs Single submitter hereditary spastic paraplegia 50
  • p.Asp43fs Single submitter hereditary spastic paraplegia 50
  • p.Gln135Ter Single submitter hereditary spastic paraplegia 50
  • p.Glu233Ter Single submitter hereditary spastic paraplegia 50
  • p.Gly243Ser Single submitter Inborn genetic diseases ⚠
  • p.Leu298Pro Single submitter hereditary spastic paraplegia 50
  • p.Lys18fs Single submitter congenital nervous system disorder
  • p.Phe77fs Single submitter
  • p.Pro246fs Single submitter
  • p.Thr395fs Single submitter hereditary spastic paraplegia 50
  • p.Trp304Ter Single submitter hereditary spastic paraplegia 50
  • p.Tyr110Ter Single submitter
  • p.Tyr65fs Single submitter
  • p.Val259fs Single submitter hereditary spastic paraplegia 50

Pathogenic/Likely pathogenic 9

  • c.1137+1G>T Multiple submitters hereditary spastic paraplegia 50
  • p.Cys319Arg Multiple submitters Inborn genetic diseases
  • p.Gln373Ter Multiple submitters intellectual disability
  • p.Gln4Ter Multiple submitters hereditary spastic paraplegia 50
  • p.Glu193Lys Multiple submitters AP-4 deficiency syndrome
  • p.Leu377fs Multiple submitters
  • p.Lys11fs Multiple submitters hereditary spastic paraplegia 50
  • p.Trp439Ter Multiple submitters hereditary spastic paraplegia 50
  • p.Val48fs Multiple submitters hereditary spastic paraplegia 50

Likely pathogenic 25

  • c.930-1G>C Multiple submitters hereditary spastic paraplegia 50
  • c.1138-1G>A Single submitter hereditary spastic paraplegia 50
  • c.351+1G>A Single submitter hereditary spastic paraplegia 50
  • c.463-2A>T Single submitter hereditary spastic paraplegia 50
  • c.58+1_58+2del Single submitter hereditary spastic paraplegia 50
  • c.58+2T>G Single submitter hereditary spastic paraplegia 50
  • c.607-2_607-1del Single submitter hereditary spastic paraplegia 50
  • p.Ala87fs Single submitter
  • p.Cys319Tyr Single submitter
  • p.Lys36fs Single submitter hereditary spastic paraplegia 50
  • p.Ser167fs Single submitter hereditary spastic paraplegia 50
  • p.Ser301fs Single submitter hereditary spastic paraplegia 50
  • p.Ser408del Single submitter
  • p.Thr125fs Single submitter hereditary spastic paraplegia 50
  • p.Tyr119Ter Single submitter hereditary spastic paraplegia 50
  • p.Tyr284Ser Single submitter hereditary spastic paraplegia 50
  • p.Val68fs Single submitter hereditary spastic paraplegia 50
  • c.1026-1G>T No assertion criteria Spastic paraplegia
  • c.974+1G>T No assertion criteria Spastic paraplegia
  • p.Arg227His No assertion criteria Spastic paraplegia ⚠
  • p.Gln161Ter No assertion criteria
  • p.Glu232fs No assertion criteria Spastic paraplegia
  • p.Glu31fs No assertion criteria Spastic paraplegia
  • p.Leu175fs No assertion criteria Spastic paraplegia
  • p.Phe6fs No assertion criteria

Conflicting classifications of pathogenicity 19

  • c.544-6T>G Single submitter Inborn genetic diseases
  • c.607-2A>G Single submitter hereditary spastic paraplegia
  • c.728-21TC[5] Single submitter hereditary spastic paraplegia 50
  • c.929+5G>A Single submitter hereditary spastic paraplegia 50
  • p.Ala448Thr Single submitter hereditary spastic paraplegia 50 ⚠
  • p.Arg310= Single submitter hereditary spastic paraplegia
  • p.Arg318Gln Single submitter hereditary spastic paraplegia 50 ⚠
  • p.Arg441Ter Single submitter hereditary spastic paraplegia 50
  • p.Cys431= Single submitter hereditary spastic paraplegia 50
  • p.Glu111Asp Single submitter hereditary spastic paraplegia 50 ⚠
  • p.Glu99Lys Single submitter hereditary spastic paraplegia 50 ⚠
  • p.Gly376= Single submitter hereditary spastic paraplegia 50
  • p.Gly63= Single submitter hereditary spastic paraplegia 50
  • p.Met380Ile Single submitter hereditary spastic paraplegia 50 ⚠
  • p.Phe409Leu Single submitter hereditary spastic paraplegia 50 ⚠
  • p.Ser348= Single submitter hereditary spastic paraplegia 50
  • p.Thr136Met Single submitter hereditary spastic paraplegia 50 ⚠
  • p.Val250= Single submitter hereditary spastic paraplegia 50
  • p.Val74Ile Single submitter hereditary spastic paraplegia 50 ⚠

Benign 31

Benign/Likely benign 7

  • p.Ala448= Multiple submitters hereditary spastic paraplegia 50
  • p.Gly247Ala Multiple submitters hereditary spastic paraplegia 50
  • p.Leu175= Multiple submitters hereditary spastic paraplegia 50
  • p.Leu334= Multiple submitters hereditary spastic paraplegia
  • p.Pro350= Multiple submitters hereditary spastic paraplegia 50
  • p.Pro76= Multiple submitters hereditary spastic paraplegia
  • p.Ser287= Multiple submitters hereditary spastic paraplegia 50

Likely benign 169

  • c.1137+7G>A Multiple submitters hereditary spastic paraplegia 50
  • c.147+242G>A Multiple submitters
  • c.59-14C>G Multiple submitters hereditary spastic paraplegia 50
  • c.975-14C>T Multiple submitters hereditary spastic paraplegia 50
  • c.*387C>T Multiple submitters
  • p.Asp251= Multiple submitters hereditary spastic paraplegia 50
  • p.Asp381= Multiple submitters hereditary spastic paraplegia 50
  • p.Ser257= Multiple submitters hereditary spastic paraplegia 50
  • p.Thr415= Multiple submitters hereditary spastic paraplegia 50
  • p.Val210= Multiple submitters hereditary spastic paraplegia 50
  • p.Val259= Multiple submitters hereditary spastic paraplegia 50
  • c.1025+18C>G Single submitter hereditary spastic paraplegia 50
  • c.1025+19C>G Single submitter hereditary spastic paraplegia 50
  • c.1025+20A>G Single submitter hereditary spastic paraplegia 50
  • c.1026-10C>G Single submitter hereditary spastic paraplegia 50
  • c.1026-20C>G Single submitter hereditary spastic paraplegia 50
  • c.1137+10G>C Single submitter hereditary spastic paraplegia 50
  • c.1137+16C>T Single submitter hereditary spastic paraplegia 50
  • c.1138-15C>T Single submitter hereditary spastic paraplegia 50
  • c.1138-17G>T Single submitter hereditary spastic paraplegia 50
  • c.1138-4A>G Single submitter hereditary spastic paraplegia 50
  • c.1138-8C>G Single submitter hereditary spastic paraplegia 50
  • c.147+10G>A Single submitter hereditary spastic paraplegia 50
  • c.147+12C>T Single submitter hereditary spastic paraplegia 50
  • c.147+16_147+22dup Single submitter hereditary spastic paraplegia 50
  • c.147+18dup Single submitter hereditary spastic paraplegia 50
  • c.148-10T>C Single submitter hereditary spastic paraplegia 50
  • c.148-11C>T Single submitter hereditary spastic paraplegia 50
  • c.148-18T>C Single submitter hereditary spastic paraplegia 50
  • c.254+14G>A Single submitter hereditary spastic paraplegia 50
  • c.254+15del Single submitter hereditary spastic paraplegia 50
  • c.254+17T>C Single submitter hereditary spastic paraplegia 50
  • c.254+20G>A Single submitter hereditary spastic paraplegia 50
  • c.255-10G>A Single submitter hereditary spastic paraplegia 50
  • c.255-12G>A Single submitter hereditary spastic paraplegia 50
  • c.255-12G>C Single submitter hereditary spastic paraplegia 50
  • c.351+17C>T Single submitter hereditary spastic paraplegia 50
  • c.351+18C>T Single submitter hereditary spastic paraplegia 50
  • c.351+19C>T Single submitter hereditary spastic paraplegia 50
  • c.351+8T>G Single submitter
  • c.351+9C>G Single submitter hereditary spastic paraplegia 50
  • c.351+9C>T Single submitter
  • c.352-12C>T Single submitter hereditary spastic paraplegia 50
  • c.352-18_352-17dup Single submitter hereditary spastic paraplegia 50
  • c.462+15A>G Single submitter hereditary spastic paraplegia 50
  • c.462+20_462+22del Single submitter hereditary spastic paraplegia 50
  • c.463-15T>C Single submitter hereditary spastic paraplegia 50
  • c.463-6T>C Single submitter
  • c.543+11_543+14dup Single submitter hereditary spastic paraplegia 50
  • c.543+11G>C Single submitter hereditary spastic paraplegia 50
  • c.544-11C>T Single submitter hereditary spastic paraplegia 50
  • c.544-13C>T Single submitter hereditary spastic paraplegia 50
  • c.544-16TC[3] Single submitter hereditary spastic paraplegia 50
  • c.544-7_544-6del Single submitter hereditary spastic paraplegia 50
  • c.58+14T>C Single submitter hereditary spastic paraplegia 50
  • c.59-11C>T Single submitter hereditary spastic paraplegia 50
  • c.59-14C>T Single submitter hereditary spastic paraplegia 50
  • c.59-16T>C Single submitter hereditary spastic paraplegia 50
  • c.59-17G>A Single submitter hereditary spastic paraplegia 50
  • c.59-8C>T Single submitter hereditary spastic paraplegia 50
  • c.606+18A>C Single submitter hereditary spastic paraplegia 50
  • c.606+200C>T Single submitter
  • c.606+20C>T Single submitter hereditary spastic paraplegia 50
  • c.607-12C>T Single submitter hereditary spastic paraplegia 50
  • c.607-13C>T Single submitter hereditary spastic paraplegia 50
  • c.607-286T>C Single submitter
  • c.607-5C>T Single submitter hereditary spastic paraplegia 50
  • c.607-94G>A Single submitter
  • c.673+11T>C Single submitter hereditary spastic paraplegia 50
  • c.673+18A>G Single submitter hereditary spastic paraplegia 50
  • c.674-19_674-17del Single submitter hereditary spastic paraplegia 50
  • c.674-19A>T Single submitter hereditary spastic paraplegia 50
  • c.674-5G>A Single submitter hereditary spastic paraplegia 50
  • c.674-6C>T Single submitter hereditary spastic paraplegia 50
  • c.674-8_674-6del Single submitter hereditary spastic paraplegia 50
  • c.728-12C>T Single submitter hereditary spastic paraplegia 50
  • c.728-17T>C Single submitter hereditary spastic paraplegia 50
  • c.728-21TC[6] Single submitter hereditary spastic paraplegia 50
  • c.728-8C>T Single submitter hereditary spastic paraplegia 50
  • c.834+8T>C Single submitter hereditary spastic paraplegia 50
  • c.929+10T>C Single submitter hereditary spastic paraplegia 50
  • c.930-11C>T Single submitter hereditary spastic paraplegia 50
  • c.930-4C>G Single submitter hereditary spastic paraplegia 50
  • c.930-6A>C Single submitter hereditary spastic paraplegia 50
  • c.930-9C>T Single submitter
  • c.974+16G>A Single submitter hereditary spastic paraplegia 50
  • c.975-13G>A Single submitter hereditary spastic paraplegia 50
  • c.975-13G>T Single submitter hereditary spastic paraplegia 50
  • c.975-15C>T Single submitter hereditary spastic paraplegia 50
  • c.975-16C>T Single submitter hereditary spastic paraplegia 50
  • c.975-19G>A Single submitter hereditary spastic paraplegia 50
  • c.975-8C>T Single submitter hereditary spastic paraplegia 50
  • c.975-9C>T Single submitter hereditary spastic paraplegia 50
  • c.-10C>T Single submitter
  • c.*219G>T Single submitter
  • c.*23C>T Single submitter hereditary spastic paraplegia
  • p.Ala157= Single submitter hereditary spastic paraplegia 50
  • p.Ala200= Single submitter hereditary spastic paraplegia 50
  • p.Ala30= Single submitter hereditary spastic paraplegia 50
  • p.Ala327= Single submitter hereditary spastic paraplegia 50
  • p.Arg131= Single submitter hereditary spastic paraplegia 50
  • p.Arg21= Single submitter
  • p.Arg297= Single submitter hereditary spastic paraplegia 50
  • p.Arg413Leu Single submitter hereditary spastic paraplegia 50
  • p.Arg429= Single submitter hereditary spastic paraplegia 50
  • p.Asn73= Single submitter hereditary spastic paraplegia 50
  • p.Asp262= Single submitter hereditary spastic paraplegia 50
  • p.Asp28= Single submitter hereditary spastic paraplegia 50
  • p.Asp288= Single submitter hereditary spastic paraplegia 50
  • p.Asp289= Single submitter hereditary spastic paraplegia 50
  • p.Asp447= Single submitter hereditary spastic paraplegia 50
  • p.Gln273= Single submitter hereditary spastic paraplegia 50
  • p.Gln4= Single submitter hereditary spastic paraplegia 50
  • p.Glu31= Single submitter hereditary spastic paraplegia 50
  • p.Glu355= Single submitter
  • p.Glu358= Single submitter hereditary spastic paraplegia 50
  • p.Glu410= Single submitter hereditary spastic paraplegia 50
  • p.Glu81= Single submitter hereditary spastic paraplegia 50
  • p.Gly120= Single submitter hereditary spastic paraplegia 50
  • p.Gly243= Single submitter hereditary spastic paraplegia 50
  • p.Gly247= Single submitter hereditary spastic paraplegia 50
  • p.Gly401= Single submitter hereditary spastic paraplegia 50
  • p.Gly91= Single submitter hereditary spastic paraplegia 50
  • p.Gly98= Single submitter hereditary spastic paraplegia 50
  • p.Ile269= Single submitter hereditary spastic paraplegia 50
  • p.Leu112= Single submitter hereditary spastic paraplegia 50
  • p.Leu130= Single submitter hereditary spastic paraplegia 50
  • p.Leu15= Single submitter hereditary spastic paraplegia 50
  • p.Leu195= Single submitter hereditary spastic paraplegia 50
  • p.Leu206= Single submitter hereditary spastic paraplegia 50
  • p.Leu321= Single submitter hereditary spastic paraplegia 50
  • p.Leu328= Single submitter hereditary spastic paraplegia 50
  • p.Leu393= Single submitter
  • p.Leu419= Single submitter hereditary spastic paraplegia 50
  • p.Leu64= Single submitter hereditary spastic paraplegia 50
  • p.Leu66= Single submitter hereditary spastic paraplegia 50
  • p.Leu80= Single submitter hereditary spastic paraplegia 50
  • p.Leu82= Single submitter hereditary spastic paraplegia 50
  • p.Leu90= Single submitter hereditary spastic paraplegia 50
  • p.Leu97= Single submitter hereditary spastic paraplegia 50
  • p.Phe20= Single submitter hereditary spastic paraplegia 50
  • p.Phe219= Single submitter
  • p.Phe409= Single submitter hereditary spastic paraplegia 50
  • p.Pro173= Single submitter hereditary spastic paraplegia 50
  • p.Pro389= Single submitter hereditary spastic paraplegia 50
  • p.Pro436= Single submitter hereditary spastic paraplegia 50
  • p.Ser10= Single submitter hereditary spastic paraplegia 50
  • p.Ser151= Single submitter hereditary spastic paraplegia 50
  • p.Ser176= Single submitter hereditary spastic paraplegia 50
  • p.Ser222= Single submitter hereditary spastic paraplegia 50
  • p.Ser3= Single submitter hereditary spastic paraplegia 50
  • p.Ser349= Single submitter hereditary spastic paraplegia 50
  • p.Ser396= Single submitter hereditary spastic paraplegia 50
  • p.Ser408= Single submitter hereditary spastic paraplegia 50
  • p.Ser446= Single submitter hereditary spastic paraplegia 50
  • p.Ser62= Single submitter
  • p.Thr127= Single submitter hereditary spastic paraplegia 50
  • p.Thr136= Single submitter hereditary spastic paraplegia 50
  • p.Thr231= Single submitter hereditary spastic paraplegia 50
  • p.Thr280= Single submitter hereditary spastic paraplegia 50
  • p.Val187= Single submitter hereditary spastic paraplegia 50
  • p.Val192= Single submitter hereditary spastic paraplegia 50
  • p.Val197= Single submitter hereditary spastic paraplegia 50
  • p.Val281= Single submitter hereditary spastic paraplegia 50
  • p.Val330= Single submitter hereditary spastic paraplegia 50
  • p.Val450= Single submitter hereditary spastic paraplegia 50
  • p.Asn185= No assertion criteria AP4M1-related disorder
  • p.Gly371= No assertion criteria AP4M1-related disorder
  • p.Leu347= No assertion criteria AP4M1-related disorder

Uncertain significance 185