PLP1 — 469 ClinVar variants

All ClinVar germline PLP1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 151 flagged for review →

65 Pathogenic · 14 Pathogenic/Likely pathogenic · 97 Likely pathogenic · 19 Conflicting · 24 Benign · 9 Benign/Likely benign · 93 Likely benign · 148 Uncertain significance

Full PLP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 151

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 4

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.

Predicted LoF vs a conflicting call 2

ClinVar submitters conflict, and it's a predicted loss-of-function change in a gene where LoF causes disease — flagged for review, not resolved (verify NMD-escape for C-terminal truncations). Non-missense.

Predictors lean, ClinVar uncertain 69

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

Predictors split 71

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

All PLP1 variants

Pathogenic 65

  • c.191+1G>A Multiple submitters hereditary spastic paraplegia 2
  • c.4+1del Multiple submitters hereditary spastic paraplegia 2
  • c.454-1G>A Multiple submitters Pelizaeus-Merzbacher spectrum disorder
  • p.Asp203Asn Multiple submitters Pelizaeus-Merzbacher spectrum disorder
  • p.Gln69Ter Multiple submitters hereditary spastic paraplegia 2
  • p.Met1Arg Multiple submitters Inborn genetic diseases
  • p.Met1Thr Multiple submitters Inborn genetic diseases
  • p.Met1Val Multiple submitters PLP1-related disorder
  • c.191+1G>T Single submitter
  • c.4+1G>A Single submitter hereditary spastic paraplegia 2
  • c.4+1G>T Single submitter hereditary spastic paraplegia 2
  • c.453+159G>A Single submitter Pelizaeus-Merzbacher spectrum disorder
  • c.453+1G>C Single submitter
  • c.454-1G>T Single submitter Pelizaeus-Merzbacher spectrum disorder
  • c.454-2A>G Single submitter Pelizaeus-Merzbacher spectrum disorder
  • c.454-314T>G Single submitter hereditary spastic paraplegia 2
  • c.622+1G>A Single submitter Pelizaeus-Merzbacher spectrum disorder
  • c.697-1G>A Single submitter hereditary spastic paraplegia 2
  • c.697-2A>C Single submitter Pelizaeus-Merzbacher spectrum disorder
  • c.762+2T>C Single submitter
  • p.Ala243Val Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Arg127fs Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Arg205fs Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Cys139fs Single submitter hereditary spastic paraplegia 2
  • p.Cys228Ter Single submitter
  • p.Cys7Ter Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Gln121Ter Single submitter hereditary spastic paraplegia 2
  • p.Gln129fs Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Gln185Ter Single submitter hereditary spastic paraplegia 2
  • p.Gln56Ter Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Gln99Ter Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Glu136fs Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Glu136Ter Single submitter hereditary spastic paraplegia 2
  • p.Glu48fs Single submitter hereditary spastic paraplegia 2
  • p.Glu59Ter Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Gly120fs Single submitter
  • p.Gly143fs Single submitter hereditary spastic paraplegia 2
  • p.Gly74Ter Single submitter hereditary spastic paraplegia 2
  • p.Gly95fs Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Ile197fs Single submitter hereditary spastic paraplegia 2
  • p.Leu224Phe Single submitter hereditary spastic paraplegia 2
  • p.Leu225fs Single submitter
  • p.Met1fs Single submitter hereditary spastic paraplegia 2
  • p.Met1Ile Single submitter hereditary spastic paraplegia 2
  • p.Met1Lys Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Pro216Ser Single submitter Pelizaeus-Merzbacher spectrum disorder ⚠
  • p.Pro216Thr Single submitter Pelizaeus-Merzbacher spectrum disorder ⚠
  • p.Ser126fs Single submitter hereditary spastic paraplegia 2
  • p.Ser222Cys Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Trp163Ter Single submitter hereditary spastic paraplegia 2
  • p.Tyr60fs Single submitter hereditary spastic paraplegia 2
  • p.Tyr60Ter Single submitter hereditary spastic paraplegia 2
  • p.Tyr70Ter Single submitter PLP1-related disorder
  • p.Val12fs Single submitter hereditary spastic paraplegia 2
  • p.Cys139fs Single submitter hereditary spastic paraplegia 2
  • p.Trp145Ter Single submitter hereditary spastic paraplegia 2
  • p.Ala247fs Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Ala242Val No assertion criteria Pelizaeus-Merzbacher disease, connatal ⚠
  • p.Asp203His No assertion criteria Pelizaeus-Merzbacher spectrum disorder
  • p.Asp57Tyr No assertion criteria Pelizaeus-Merzbacher spectrum disorder ⚠
  • p.Gly208Val No assertion criteria Auditory neuropathy spectrum disorder
  • p.Gly221Cys No assertion criteria Pelizaeus-Merzbacher disease, connatal
  • p.Gly74Arg No assertion criteria Pelizaeus-Merzbacher spectrum disorder
  • p.Thr156Ile No assertion criteria Pelizaeus-Merzbacher spectrum disorder ⚠
  • p.Thr182Pro No assertion criteria Pelizaeus-Merzbacher spectrum disorder

Pathogenic/Likely pathogenic 14

  • c.453+2T>C Multiple submitters Pelizaeus-Merzbacher spectrum disorder
  • c.454-10A>G Multiple submitters PLP1-related disorder
  • c.696+1G>A Multiple submitters Inborn genetic diseases
  • p.Gly246Ala Multiple submitters hereditary spastic paraplegia 2
  • p.His148Tyr Multiple submitters hereditary spastic paraplegia ⚠
  • p.His238fs Multiple submitters hereditary spastic paraplegia 2
  • p.Ile187Thr Multiple submitters hereditary spastic paraplegia 2
  • p.Lys151= Multiple submitters Pelizaeus-Merzbacher spectrum disorder
  • p.Phe237Ser Multiple submitters PLP1-related disorder ⚠
  • p.Pro15Leu Multiple submitters Pelizaeus-Merzbacher spectrum disorder
  • p.Ser226Pro Multiple submitters Pelizaeus-Merzbacher spectrum disorder ⚠
  • p.Trp145Ter Multiple submitters hereditary spastic paraplegia 2
  • p.Tyr58Cys Multiple submitters Pelizaeus-Merzbacher spectrum disorder
  • p.Val252fs Multiple submitters Pelizaeus-Merzbacher spectrum disorder

Likely pathogenic 97

  • p.Cys220Gly Multiple submitters Pelizaeus-Merzbacher spectrum disorder
  • p.Gln69Leu Multiple submitters Pelizaeus-Merzbacher spectrum disorder
  • p.His130Tyr Multiple submitters hereditary spastic paraplegia 2 ⚠
  • p.Ile47Thr Multiple submitters Pelizaeus-Merzbacher spectrum disorder
  • p.Leu210Phe Multiple submitters PLP1-related disorder ⚠
  • p.Leu31Arg Multiple submitters Pelizaeus-Merzbacher spectrum disorder
  • p.Leu85Arg Multiple submitters Pelizaeus-Merzbacher spectrum disorder
  • p.Phe32Leu Multiple submitters Pelizaeus-Merzbacher spectrum disorder ⚠
  • p.Pro216Leu Multiple submitters Pelizaeus-Merzbacher spectrum disorder ⚠
  • p.Trp163Arg Multiple submitters Pelizaeus-Merzbacher spectrum disorder
  • p.Val219Phe Multiple submitters Pelizaeus-Merzbacher spectrum disorder ⚠
  • c.192-2A>C Single submitter Pelizaeus-Merzbacher spectrum disorder
  • c.192-2A>G Single submitter Pelizaeus-Merzbacher spectrum disorder
  • c.453+164G>A Single submitter Pelizaeus-Merzbacher spectrum disorder
  • c.453+1G>T Single submitter hereditary spastic paraplegia 2
  • c.453+28_453+46del Single submitter Pelizaeus-Merzbacher spectrum disorder
  • c.453+3G>C Single submitter
  • c.453+4A>G Single submitter Pelizaeus-Merzbacher spectrum disorder
  • c.454-314T>A Single submitter Pelizaeus-Merzbacher spectrum disorder
  • c.5-1G>A Single submitter hereditary spastic paraplegia 2
  • p.Ile197fs Single submitter Pelizaeus-Merzbacher spectrum disorder
  • c.623-2A>C Single submitter Pelizaeus-Merzbacher spectrum disorder
  • c.697-54_711delinsTTTATT Single submitter Pelizaeus-Merzbacher spectrum disorder
  • c.762+3G>T Single submitter Pelizaeus-Merzbacher spectrum disorder
  • c.763-1G>T Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Ala115fs Single submitter hereditary spastic paraplegia 2
  • p.Ala21Val Single submitter
  • p.Ala243Glu Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Ala247fs Single submitter
  • p.Ala248Glu Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Ala76Pro Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Arg137Leu Single submitter ⚠
  • p.Arg205Gly Single submitter PLP1-related disorder
  • p.Asp203Gly Single submitter hereditary spastic paraplegia 2
  • p.Cys169Arg Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Cys184Tyr Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Cys201fs Single submitter PLP1-related disorder
  • p.Cys220Arg Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Cys220Phe Single submitter PLP1-related disorder
  • p.Cys228Tyr Single submitter
  • p.Cys33Tyr Single submitter
  • p.Cys35Arg Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Cys35Ter Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Cys35Tyr Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Gln129Ter Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Gln185fs Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Glu232Lys Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Glu38del Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Gly217Asp Single submitter hereditary spastic paraplegia 2
  • p.Gly246Trp Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Gly28Glu Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Gly42Asp Single submitter Pelizaeus-Merzbacher spectrum disorder ⚠
  • p.Gly74Glu Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Leu19Pro Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Leu224Ile Single submitter hereditary spastic paraplegia 2
  • p.Leu239Pro Single submitter
  • p.Leu251Pro Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Leu254= Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Leu254Pro Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Leu31Pro Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Leu40His Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Leu46Pro Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Leu81Arg Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Leu85Pro Single submitter PLP1-related disorder
  • p.Leu86fs Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Leu87Pro Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Lys122fs Single submitter PLP1-related disorder
  • p.Lys144Ter Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Lys151Asn Single submitter Pelizaeus-Merzbacher spectrum disorder ⚠
  • p.Met206Arg Single submitter Pelizaeus-Merzbacher spectrum disorder ⚠
  • p.Met206Thr Single submitter PLP1-related disorder ⚠
  • p.Phe215fs Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Phe237Val Single submitter Pelizaeus-Merzbacher spectrum disorder ⚠
  • p.Phe244Val Single submitter Pelizaeus-Merzbacher spectrum disorder ⚠
  • p.Phe51Val Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Pro173Ser Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Ser170Phe Single submitter hereditary spastic paraplegia 2
  • p.Ser18fs Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Ser253Cys Single submitter Pelizaeus-Merzbacher spectrum disorder ⚠
  • p.Ser253Phe Single submitter Pelizaeus-Merzbacher spectrum disorder ⚠
  • p.Ter278Trp Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Thr116Lys Single submitter Pelizaeus-Merzbacher spectrum disorder ⚠
  • p.Thr41Pro Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Thr43Ile Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Trp181_Thr183del Single submitter
  • p.Trp212Ter Single submitter PLP1-related disorder
  • p.Tyr177Ter Single submitter
  • p.Tyr207Asn Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Tyr207His Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Tyr263Ter Single submitter hereditary spastic paraplegia 2
  • p.Val138fs Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Val153fs Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Val219Gly Single submitter Pelizaeus-Merzbacher spectrum disorder
  • p.Arg9Ter No assertion criteria Spasticity
  • p.Cys141fs No assertion criteria hereditary spastic paraplegia 2
  • p.Leu142fs No assertion criteria Pelizaeus-Merzbacher spectrum disorder
  • p.Lys122Arg No assertion criteria hereditary spastic paraplegia 2 ⚠

Conflicting classifications of pathogenicity 19

Benign 24

Benign/Likely benign 9

  • c.5-15C>G Multiple submitters hereditary spastic paraplegia 2
  • c.622+28C>G Multiple submitters Pelizaeus-Merzbacher spectrum disorder
  • c.763-20C>A Multiple submitters hereditary spastic paraplegia 2
  • c.-31C>T Multiple submitters Pelizaeus-Merzbacher spectrum disorder
  • p.Gln56= Multiple submitters Pelizaeus-Merzbacher spectrum disorder
  • p.Gly154Ser Multiple submitters polycystic kidney disease 1
  • p.Gly198= Multiple submitters hereditary spastic paraplegia 2
  • p.Ser222= Multiple submitters hereditary spastic paraplegia 2
  • p.Thr193= Multiple submitters hereditary spastic paraplegia 2

Likely benign 93

  • c.622+15G>A Multiple submitters hereditary spastic paraplegia 2
  • p.Leu85= Multiple submitters hereditary spastic paraplegia 2
  • p.Phe79= Multiple submitters hereditary spastic paraplegia 2
  • p.Tyr82= Multiple submitters hereditary spastic paraplegia 2
  • p.Val267Ile Multiple submitters hereditary spastic paraplegia 2
  • c.191+19A>G Single submitter hereditary spastic paraplegia 2
  • c.192-10G>A Single submitter hereditary spastic paraplegia 2
  • c.192-19T>A Single submitter hereditary spastic paraplegia 2
  • c.192-69T>C Single submitter
  • c.192-9T>A Single submitter hereditary spastic paraplegia 2
  • c.4+16T>C Single submitter hereditary spastic paraplegia 2
  • c.4+66A>C Single submitter
  • c.453+123C>T Single submitter
  • c.453+16A>G Single submitter hereditary spastic paraplegia 2
  • c.453+37G>T Single submitter hereditary spastic paraplegia 2
  • c.453+416T>G Single submitter
  • c.453+43G>A Single submitter hereditary spastic paraplegia 2
  • c.453+44A>G Single submitter hereditary spastic paraplegia 2
  • c.453+9C>T Single submitter hereditary spastic paraplegia 2
  • c.454-15T>C Single submitter hereditary spastic paraplegia 2
  • c.454-16A>C Single submitter hereditary spastic paraplegia 2
  • c.454-16A>G Single submitter hereditary spastic paraplegia 2
  • c.5-10T>A Single submitter hereditary spastic paraplegia 2
  • c.5-12C>T Single submitter hereditary spastic paraplegia 2
  • c.5-13dup Single submitter hereditary spastic paraplegia 2
  • c.5-16C>A Single submitter hereditary spastic paraplegia 2
  • c.5-17C>T Single submitter hereditary spastic paraplegia 2
  • c.5-6C>T Single submitter hereditary spastic paraplegia 2
  • c.5-8T>C Single submitter hereditary spastic paraplegia 2
  • c.622+14C>T Single submitter hereditary spastic paraplegia 2
  • c.622+8A>G Single submitter hereditary spastic paraplegia 2
  • c.623-19C>T Single submitter hereditary spastic paraplegia 2
  • c.696+17G>T Single submitter hereditary spastic paraplegia 2
  • c.697-12A>C Single submitter hereditary spastic paraplegia 2
  • c.697-12A>G Single submitter hereditary spastic paraplegia 2
  • c.762+9A>G Single submitter hereditary spastic paraplegia 2
  • c.763-16C>T Single submitter hereditary spastic paraplegia 2
  • c.763-17_763-14del Single submitter hereditary spastic paraplegia 2
  • c.-143-51C>T Single submitter
  • c.-143-77_-143-68del Single submitter
  • c.*6C>T Single submitter
  • p.Ala115= Single submitter hereditary spastic paraplegia 2
  • p.Ala188= Single submitter hereditary spastic paraplegia 2
  • p.Ala202= Single submitter hereditary spastic paraplegia 2
  • p.Ala214= Single submitter hereditary spastic paraplegia 2
  • p.Ala248= Single submitter hereditary spastic paraplegia 2
  • p.Asn223= Single submitter hereditary spastic paraplegia 2
  • p.Cys10= Single submitter hereditary spastic paraplegia 2
  • p.Cys109= Single submitter hereditary spastic paraplegia 2
  • p.Cys33= Single submitter hereditary spastic paraplegia 2
  • p.Cys6= Single submitter hereditary spastic paraplegia 2
  • p.Glu136= Single submitter hereditary spastic paraplegia 2
  • p.Glu5= Single submitter hereditary spastic paraplegia 2
  • p.Glu89= Single submitter hereditary spastic paraplegia 2
  • p.Gly102= Single submitter hereditary spastic paraplegia 2
  • p.Gly112= Single submitter hereditary spastic paraplegia 2
  • p.Gly119= Single submitter hereditary spastic paraplegia 2
  • p.Gly13= Single submitter hereditary spastic paraplegia 2
  • p.Gly143= Single submitter Inborn genetic diseases
  • p.Gly217= Single submitter hereditary spastic paraplegia 2
  • p.Gly90= Single submitter hereditary spastic paraplegia 2
  • p.Gly95= Single submitter Inborn genetic diseases
  • p.Ile47= Single submitter hereditary spastic paraplegia 2
  • p.Leu142= Single submitter hereditary spastic paraplegia 2
  • p.Leu159= Single submitter hereditary spastic paraplegia 2
  • p.Leu4= Single submitter hereditary spastic paraplegia 2
  • p.Leu40= Single submitter hereditary spastic paraplegia 2
  • p.Leu46= Single submitter hereditary spastic paraplegia 2
  • p.Leu87= Single submitter hereditary spastic paraplegia 2
  • p.Phe265= Single submitter hereditary spastic paraplegia 2
  • p.Ser114= Single submitter hereditary spastic paraplegia 2
  • p.Ser199= Single submitter hereditary spastic paraplegia 2
  • p.Thr106= Single submitter hereditary spastic paraplegia 2
  • p.Thr160= Single submitter hereditary spastic paraplegia 2
  • p.Thr182= Single submitter hereditary spastic paraplegia 2
  • p.Thr236= Single submitter hereditary spastic paraplegia 2
  • p.Thr41= Single submitter hereditary spastic paraplegia 2
  • p.Thr41Ile Single submitter Inborn genetic diseases
  • p.Thr93= Single submitter hereditary spastic paraplegia 2
  • p.Thr94= Single submitter hereditary spastic paraplegia 2
  • p.Tyr104= Single submitter hereditary spastic paraplegia 2
  • p.Tyr177= Single submitter hereditary spastic paraplegia 2
  • p.Val162= Single submitter hereditary spastic paraplegia 2
  • p.Val174= Single submitter hereditary spastic paraplegia 2
  • p.Val245= Single submitter hereditary spastic paraplegia 2
  • p.Val267= Single submitter hereditary spastic paraplegia 2
  • p.Val97= Single submitter hereditary spastic paraplegia 2
  • p.Leu4= Single submitter
  • p.Leu40= Single submitter hereditary spastic paraplegia 2
  • p.Leu87= Single submitter hereditary spastic paraplegia 2
  • p.Val245= Single submitter hereditary spastic paraplegia 2
  • c.4+74G>T No assertion criteria PLP1-related disorder
  • c.453+55C>T No assertion criteria PLP1-related disorder

Uncertain significance 148