PGAP1 — 469 ClinVar variants

All ClinVar germline PGAP1 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 183 flagged for review →

23 Pathogenic · 5 Pathogenic/Likely pathogenic · 22 Likely pathogenic · 16 Conflicting · 47 Benign · 8 Benign/Likely benign · 146 Likely benign · 202 Uncertain significance

Full PGAP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 183

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 8

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

Predictors lean, ClinVar uncertain 148

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

Predictors split 27

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

All PGAP1 variants

Pathogenic 23

  • p.Arg786fs Multiple submitters Inborn genetic diseases
  • p.Gln466Ter Multiple submitters intellectual disability, autosomal recessive 42
  • p.Ile465fs Multiple submitters intellectual disability, autosomal recessive 42
  • c.1221-3A>G Single submitter intellectual disability, autosomal recessive 42
  • c.1501-2A>G Single submitter intellectual disability, autosomal recessive 42
  • c.1952+1G>C Single submitter intellectual disability, autosomal recessive 42
  • c.861-2A>G Single submitter intellectual disability, autosomal recessive 42
  • c.927+1G>A Single submitter intellectual disability, autosomal recessive 42
  • p.Asn223fs Single submitter Inborn genetic diseases
  • p.Asn7fs Single submitter intellectual disability, autosomal recessive 42
  • p.Cys623fs Single submitter intellectual disability, autosomal recessive 42
  • p.Cys623Ter Single submitter intellectual disability, autosomal recessive 42
  • p.Gln143Ter Single submitter intellectual disability, autosomal recessive 42
  • p.Leu259Ter Single submitter intellectual disability, autosomal recessive 42
  • p.Lys308fs Single submitter Cerebral visual impairment and intellectual disability
  • p.Phe734_Leu735insTer Single submitter Inborn genetic diseases
  • p.Pro92del Single submitter Cerebral visual impairment and intellectual disability
  • p.Pro92fs Single submitter intellectual disability, autosomal recessive 42
  • p.Ser535Ter Single submitter
  • p.Tyr524Ter Single submitter intellectual disability, autosomal recessive 42
  • p.Val516fs Single submitter intellectual disability, autosomal recessive 42
  • c.1090-2A>G No assertion criteria intellectual disability, autosomal recessive 42
  • c.1952+1G>T No assertion criteria intellectual disability, autosomal recessive 42

Pathogenic/Likely pathogenic 5

  • p.Arg231Ter Multiple submitters
  • p.Gln555Ter Multiple submitters PGAP1-related disorders
  • p.Leu197del Multiple submitters intellectual disability, autosomal recessive 42
  • p.Leu681fs Multiple submitters intellectual disability, autosomal recessive 42
  • p.Tyr758Ter Multiple submitters intellectual disability, autosomal recessive 42

Likely pathogenic 22

Conflicting classifications of pathogenicity 16

  • c.808-7_808-3del Single submitter intellectual disability, autosomal recessive 42
  • c.927+4T>C Single submitter Inborn genetic diseases
  • p.Ala164= Single submitter intellectual disability, autosomal recessive 42
  • p.Ala541Thr Single submitter Inborn genetic diseases ⚠
  • p.Ala703Thr Single submitter Inborn genetic diseases ⚠
  • p.Arg574Gln Single submitter Inborn genetic diseases ⚠
  • p.Asn195= Single submitter intellectual disability, autosomal recessive 42
  • p.Asn792Ser Single submitter Inborn genetic diseases ⚠
  • p.Asp212= Single submitter intellectual disability, autosomal recessive 42
  • p.Asp796= Single submitter intellectual disability, autosomal recessive 42
  • p.Glu546= Single submitter intellectual disability, autosomal recessive 42
  • p.Leu564Ser Single submitter intellectual disability, autosomal recessive 42 ⚠
  • p.Leu823Val Single submitter Inborn genetic diseases ⚠
  • p.Thr220Met Single submitter Inborn genetic diseases ⚠
  • p.Tyr626His Single submitter hereditary spastic paraplegia ⚠
  • p.Val763Ile Single submitter intellectual disability, autosomal recessive 42 ⚠

Benign 47

Benign/Likely benign 8

  • c.1729-12G>A Multiple submitters intellectual disability, autosomal recessive 42
  • c.860+12C>A Multiple submitters intellectual disability, autosomal recessive 42
  • p.Asn868= Multiple submitters intellectual disability, autosomal recessive 42
  • p.Gln585Glu Multiple submitters intellectual disability, autosomal recessive 42
  • p.Leu302= Multiple submitters hereditary spastic paraplegia
  • p.Leu700= Multiple submitters intellectual disability, autosomal recessive 42
  • p.Pro912Ser Multiple submitters intellectual disability, autosomal recessive 42
  • p.Thr883Ala Multiple submitters intellectual disability, autosomal recessive 42

Likely benign 146

  • c.148-8A>T Multiple submitters intellectual disability, autosomal recessive 42
  • c.649+12T>C Multiple submitters intellectual disability, autosomal recessive 42
  • c.650-6C>T Multiple submitters intellectual disability, autosomal recessive 42
  • p.Gln585= Multiple submitters intellectual disability, autosomal recessive 42
  • p.Glu65= Multiple submitters intellectual disability, autosomal recessive 42
  • p.Ile104Val Multiple submitters intellectual disability, autosomal recessive 42
  • p.Phe498= Multiple submitters intellectual disability, autosomal recessive 42
  • c.1034-164G>A Single submitter
  • c.1089+16A>G Single submitter intellectual disability, autosomal recessive 42
  • c.1090-4G>A Single submitter intellectual disability, autosomal recessive 42
  • c.1173+10T>C Single submitter intellectual disability, autosomal recessive 42
  • c.1173+10T>G Single submitter
  • c.1173+16C>T Single submitter intellectual disability, autosomal recessive 42
  • c.1174-133G>A Single submitter
  • c.1174-20_1174-16del Single submitter intellectual disability, autosomal recessive 42
  • c.1220+10_1220+11del Single submitter intellectual disability, autosomal recessive 42
  • c.1220+18A>G Single submitter intellectual disability, autosomal recessive 42
  • c.1273-18_1273-16del Single submitter intellectual disability, autosomal recessive 42
  • c.1351-13T>A Single submitter intellectual disability, autosomal recessive 42
  • c.1351-22_1351-19del Single submitter intellectual disability, autosomal recessive 42
  • c.1351-58G>T Single submitter
  • c.1426+174A>C Single submitter
  • c.1426+17T>A Single submitter intellectual disability, autosomal recessive 42
  • c.147+9C>T Single submitter intellectual disability, autosomal recessive 42
  • c.148-18A>G Single submitter intellectual disability, autosomal recessive 42
  • c.148-9T>A Single submitter intellectual disability, autosomal recessive 42
  • c.1500+14A>T Single submitter intellectual disability, autosomal recessive 42
  • c.1501-18G>A Single submitter intellectual disability, autosomal recessive 42
  • c.1552+133_1552+134insAGAA Single submitter
  • c.1553-16T>A Single submitter intellectual disability, autosomal recessive 42
  • c.1620-19A>G Single submitter intellectual disability, autosomal recessive 42
  • c.1620-28A>G Single submitter
  • c.1728+8G>T Single submitter intellectual disability, autosomal recessive 42
  • c.1729-4C>T Single submitter intellectual disability, autosomal recessive 42
  • c.1862-19A>T Single submitter intellectual disability, autosomal recessive 42
  • c.1952+133del Single submitter
  • c.1953-13C>A Single submitter intellectual disability, autosomal recessive 42
  • c.1953-14T>G Single submitter intellectual disability, autosomal recessive 42
  • c.1953-259del Single submitter
  • c.2150+9_2150+10insA Single submitter intellectual disability, autosomal recessive 42
  • c.2286+11T>C Single submitter intellectual disability, autosomal recessive 42
  • c.2286+13A>G Single submitter intellectual disability, autosomal recessive 42
  • c.2286+20C>G Single submitter intellectual disability, autosomal recessive 42
  • c.2286+293del Single submitter
  • c.2286+6T>G Single submitter
  • c.2287-12T>C Single submitter intellectual disability, autosomal recessive 42
  • c.2287-15A>G Single submitter intellectual disability, autosomal recessive 42
  • c.2287-20G>A Single submitter intellectual disability, autosomal recessive 42
  • c.2338-13T>C Single submitter intellectual disability, autosomal recessive 42
  • c.2338-16C>T Single submitter intellectual disability, autosomal recessive 42
  • c.2525+161G>T Single submitter
  • c.2526-19T>C Single submitter intellectual disability, autosomal recessive 42
  • c.2526-4A>G Single submitter intellectual disability, autosomal recessive 42
  • c.2630+191dup Single submitter
  • c.2630+20C>A Single submitter intellectual disability, autosomal recessive 42
  • c.2631-7T>C Single submitter intellectual disability, autosomal recessive 42
  • c.301+10_301+12del Single submitter intellectual disability, autosomal recessive 42
  • c.301+14G>A Single submitter intellectual disability, autosomal recessive 42
  • c.301+15A>C Single submitter intellectual disability, autosomal recessive 42
  • c.301+17G>T Single submitter intellectual disability, autosomal recessive 42
  • c.301+18T>C Single submitter intellectual disability, autosomal recessive 42
  • c.301+7C>T Single submitter intellectual disability, autosomal recessive 42
  • c.302-17A>G Single submitter intellectual disability, autosomal recessive 42
  • c.302-20T>G Single submitter intellectual disability, autosomal recessive 42
  • c.477+12G>A Single submitter intellectual disability, autosomal recessive 42
  • c.477+14A>G Single submitter
  • c.478-131T>G Single submitter
  • c.478-15G>T Single submitter intellectual disability, autosomal recessive 42
  • c.649+275_649+277dup Single submitter
  • c.649+301del Single submitter
  • c.649+301dup Single submitter
  • c.649+8C>G Single submitter intellectual disability, autosomal recessive 42
  • c.807+14A>G Single submitter intellectual disability, autosomal recessive 42
  • c.860+16T>C Single submitter intellectual disability, autosomal recessive 42
  • c.860+99del Single submitter
  • c.927+15A>G Single submitter intellectual disability, autosomal recessive 42
  • c.927+17T>C Single submitter intellectual disability, autosomal recessive 42
  • c.927+280_927+281dup Single submitter
  • c.927+9T>A Single submitter intellectual disability, autosomal recessive 42
  • c.928-17A>G Single submitter intellectual disability, autosomal recessive 42
  • c.928-19G>A Single submitter intellectual disability, autosomal recessive 42
  • c.928-20T>G Single submitter intellectual disability, autosomal recessive 42
  • c.*203T>C Single submitter
  • p.Ala12= Single submitter intellectual disability, autosomal recessive 42
  • p.Ala182= Single submitter intellectual disability, autosomal recessive 42
  • p.Ala305= Single submitter intellectual disability, autosomal recessive 42
  • p.Ala539= Single submitter intellectual disability, autosomal recessive 42
  • p.Ala63= Single submitter intellectual disability, autosomal recessive 42
  • p.Ala63Thr Single submitter intellectual disability, autosomal recessive 42
  • p.Arg297= Single submitter intellectual disability, autosomal recessive 42
  • p.Arg447His Single submitter Inborn genetic diseases
  • p.Asn336= Single submitter intellectual disability, autosomal recessive 42
  • p.Asn394= Single submitter intellectual disability, autosomal recessive 42
  • p.Asn807= Single submitter intellectual disability, autosomal recessive 42
  • p.Asp454= Single submitter intellectual disability, autosomal recessive 42
  • p.Cys623= Single submitter intellectual disability, autosomal recessive 42
  • p.Gln292= Single submitter intellectual disability, autosomal recessive 42
  • p.Gln767= Single submitter intellectual disability, autosomal recessive 42
  • p.Gln885= Single submitter intellectual disability, autosomal recessive 42
  • p.Glu461= Single submitter intellectual disability, autosomal recessive 42
  • p.Glu557= Single submitter intellectual disability, autosomal recessive 42
  • p.Gly410= Single submitter intellectual disability, autosomal recessive 42
  • p.His191= Single submitter intellectual disability, autosomal recessive 42
  • p.His328= Single submitter intellectual disability, autosomal recessive 42
  • p.His332= Single submitter intellectual disability, autosomal recessive 42
  • p.Ile538= Single submitter intellectual disability, autosomal recessive 42
  • p.Ile799Val Single submitter Inborn genetic diseases
  • p.Leu193= Single submitter intellectual disability, autosomal recessive 42
  • p.Leu228= Single submitter intellectual disability, autosomal recessive 42
  • p.Leu235= Single submitter intellectual disability, autosomal recessive 42
  • p.Leu283= Single submitter intellectual disability, autosomal recessive 42
  • p.Leu321= Single submitter Inborn genetic diseases
  • p.Leu650= Single submitter
  • p.Leu672= Single submitter intellectual disability, autosomal recessive 42
  • p.Leu713= Single submitter intellectual disability, autosomal recessive 42
  • p.Leu828= Single submitter intellectual disability, autosomal recessive 42
  • p.Leu890= Single submitter intellectual disability, autosomal recessive 42
  • p.Leu914= Single submitter intellectual disability, autosomal recessive 42
  • p.Lys142= Single submitter intellectual disability, autosomal recessive 42
  • p.Lys317= Single submitter intellectual disability, autosomal recessive 42
  • p.Lys36= Single submitter intellectual disability, autosomal recessive 42
  • p.Lys653= Single submitter intellectual disability, autosomal recessive 42
  • p.Phe13= Single submitter intellectual disability, autosomal recessive 42
  • p.Phe43= Single submitter intellectual disability, autosomal recessive 42
  • p.Phe908= Single submitter intellectual disability, autosomal recessive 42
  • p.Pro210= Single submitter intellectual disability, autosomal recessive 42
  • p.Pro274= Single submitter intellectual disability, autosomal recessive 42
  • p.Pro62= Single submitter intellectual disability, autosomal recessive 42
  • p.Pro680= Single submitter intellectual disability, autosomal recessive 42
  • p.Pro733= Single submitter intellectual disability, autosomal recessive 42
  • p.Pro854= Single submitter intellectual disability, autosomal recessive 42
  • p.Pro906= Single submitter
  • p.Ser403= Single submitter intellectual disability, autosomal recessive 42
  • p.Ser784= Single submitter intellectual disability, autosomal recessive 42
  • p.Thr371= Single submitter intellectual disability, autosomal recessive 42
  • p.Thr486= Single submitter intellectual disability, autosomal recessive 42
  • p.Thr581= Single submitter intellectual disability, autosomal recessive 42
  • p.Thr691= Single submitter intellectual disability, autosomal recessive 42
  • p.Thr771= Single submitter intellectual disability, autosomal recessive 42
  • p.Tyr903= Single submitter intellectual disability, autosomal recessive 42
  • p.Val208= Single submitter intellectual disability, autosomal recessive 42
  • p.Val28= Single submitter hereditary spastic paraplegia
  • p.Val354= Single submitter intellectual disability, autosomal recessive 42
  • p.Val602= Single submitter
  • p.Val670Ile Single submitter Inborn genetic diseases
  • p.Lys550= No assertion criteria PGAP1-related disorder

Uncertain significance 202