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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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PGAP1
post-GPI attachment to proteins inositol deacylase 1
Chromosome 2 Β· 2q33.1
NCBI Gene: 80055Ensembl: ENSG00000197121.16HGNC: HGNC:25712UniProt: Q75T13
31PubMed Papers
21Diseases
0Drugs
47Pathogenic Variants
FUNCTIONAL ROLE
Transporter
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
deacylase activityendoplasmic reticulumendoplasmic reticulum membraneGPI anchor biosynthetic processautosomal recessive non-syndromic intellectual disabilitygenetic disorderRare genetic intellectual disability with developmental anomalyautosomal recessive spastic paraplegia type 67
✦AI Summary

PGAP1 (post-GPI attachment to proteins inositol deacylase 1) is an endoplasmic reticulum-localized serine hydrolase that catalyzes removal of the acyl chain from the 2-OH position of the inositol ring in glycosylphosphatidylinositol-anchored proteins (GPI-APs) 1. This deacylation initiates the post-attachment remodeling phase essential for GPI-AP biogenesis and facilitates ER-to-Golgi transport of properly modified GPI-APs 21. Structural studies reveal PGAP1's distinctive guitar-shaped substrate-binding cavity and drawing compass-like conformational movement during catalysis, with glycan-mediated interactions conferring substrate specificity 1. Clinically, PGAP1 deficiency causes spastic paraplegia-67, an autosomal recessive neurodevelopmental disorder characterized by psychomotor retardation, dysmorphic features, spasticity, brain atrophy, and delayed myelination 34. Affected individuals also present with cerebral visual impairment, intellectual disability, microcephaly, and increased susceptibility to respiratory complications including recurrent apneas 35. Loss-of-function PGAP1 variants prevent GPI-AP remodeling, demonstrable through reduced resistance to phosphatidylinositol-specific phospholipase C treatment in patient-derived lymphoblastoid cells 5. Beyond neurological manifestations, PGAP1 appears involved in immune regulation and fibrotic disease pathways 67, suggesting broader disease relevance.

Sources cited
1
PGAP1 is an inositol deacylase catalyzing removal of acyl chains from GPI-APs; reveals structural basis of catalysis and substrate specificity
PMID: 38167496
2
PGAP1 initiates post-attachment remodeling of GPI-APs and participates in ER-to-Golgi transport
PMID: 24784135
3
Compound heterozygous PGAP1 mutations cause psychomotor retardation, brain atrophy, delayed myelination, and recurrent apneas
PMID: 27206732
4
PGAP1 variants cause spastic paraplegia-67 with neurodevelopmental delay, dysmorphic features, spasticity, and brain abnormalities
PMID: 40785186
5
PGAP1 compound heterozygous variants cause cerebral visual impairment and intellectual disability; functional loss demonstrated in cell models
PMID: 25804403
6
PGAP1 identified as Th17-related gene with diagnostic value in systemic sclerosis; shows altered expression in fibrotic disease
PMID: 41619156
7
PGAP1 is part of IL-7 signature module associated with disease activity in primary SjΓΆgren's syndrome
PMID: 38114349
Disease Associationsβ“˜21
autosomal recessive non-syndromic intellectual disabilityOpen Targets
0.66Moderate
genetic disorderOpen Targets
0.51Moderate
Rare genetic intellectual disability with developmental anomalyOpen Targets
0.43Moderate
autosomal recessive spastic paraplegia type 67Open Targets
0.37Weak
hereditary spastic paraplegiaOpen Targets
0.19Weak
thyroid cancerOpen Targets
0.18Weak
Neurodevelopmental disorderOpen Targets
0.15Weak
myopiaOpen Targets
0.11Weak
pathological myopiaOpen Targets
0.11Weak
autosomal recessive spondylocostal dysostosisOpen Targets
0.06Suggestive
spondyloepiphyseal dysplasia tarda, Kohn typeOpen Targets
0.06Suggestive
3-M syndromeOpen Targets
0.05Suggestive
holoprosencephalyOpen Targets
0.05Suggestive
spondylocostal dysostosis 2, autosomal recessiveOpen Targets
0.05Suggestive
Prata-Liberal-Goncalves syndromeOpen Targets
0.05Suggestive
spinal cord injuryOpen Targets
0.05Suggestive
spondylocamptodactyly syndromeOpen Targets
0.05Suggestive
multiple epiphyseal dysplasiaOpen Targets
0.04Suggestive
microphthalmia, isolated, with coloboma 5Open Targets
0.04Suggestive
autosomal dominant brachyolmiaOpen Targets
0.04Suggestive
Neurodevelopmental disorder with dysmorphic features, spasticity, and brain abnormalitiesUniProt
Pathogenic Variants47
NM_024989.4(PGAP1):c.1394_1397del (p.Ile465fs)Pathogenic
Intellectual disability, autosomal recessive 42|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 465
NM_024989.4(PGAP1):c.2042del (p.Leu681fs)Pathogenic
Intellectual disability, autosomal recessive 42|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 681
NM_024989.4(PGAP1):c.586CTT[1] (p.Leu197del)Pathogenic
Intellectual disability, autosomal recessive 42
β˜…β˜…β˜†β˜†2024β†’ Residue 197
NM_024989.4(PGAP1):c.1663C>T (p.Gln555Ter)Pathogenic
Intellectual disability, autosomal recessive 42
β˜…β˜…β˜†β˜†2023β†’ Residue 555
NM_024989.4(PGAP1):c.1396C>T (p.Gln466Ter)Pathogenic
Intellectual disability, autosomal recessive 42|not provided
β˜…β˜…β˜†β˜†2023β†’ Residue 466
NM_024989.4(PGAP1):c.2357_2358insTA (p.Arg786fs)Pathogenic
not provided|Intellectual disability, autosomal recessive 42|Inborn genetic diseases
β˜…β˜…β˜†β˜†2023β†’ Residue 786
NM_024989.4(PGAP1):c.2274C>G (p.Tyr758Ter)Pathogenic
Intellectual disability, autosomal recessive 42
β˜…β˜…β˜†β˜†2022β†’ Residue 758
NM_024989.4(PGAP1):c.691C>T (p.Arg231Ter)Pathogenic
not provided|See cases
β˜…β˜…β˜†β˜†2021β†’ Residue 231
NM_024989.4(PGAP1):c.1897G>T (p.Glu633Ter)Likely pathogenic
Intellectual disability, autosomal recessive 42
β˜…β˜†β˜†β˜†2024β†’ Residue 633
NM_024989.4(PGAP1):c.1604C>A (p.Ser535Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 535
NM_024989.4(PGAP1):c.1869C>A (p.Cys623Ter)Pathogenic
Intellectual disability, autosomal recessive 42
β˜…β˜†β˜†β˜†2024β†’ Residue 623
NM_024989.4(PGAP1):c.1546_1549del (p.Val516fs)Pathogenic
Intellectual disability, autosomal recessive 42
β˜…β˜†β˜†β˜†2024β†’ Residue 516
NM_024989.4(PGAP1):c.1867del (p.Cys623fs)Pathogenic
Intellectual disability, autosomal recessive 42
β˜…β˜†β˜†β˜†2024β†’ Residue 623
NM_024989.4(PGAP1):c.574del (p.Asp192fs)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 192
NM_024989.4(PGAP1):c.861-2A>GPathogenic
Intellectual disability, autosomal recessive 42
β˜…β˜†β˜†β˜†2024
NM_024989.4(PGAP1):c.2286+1G>ALikely pathogenic
Intellectual disability, autosomal recessive 42
β˜…β˜†β˜†β˜†2024
NM_024989.4(PGAP1):c.1351-2A>GLikely pathogenic
Intellectual disability, autosomal recessive 42
β˜…β˜†β˜†β˜†2023
NM_024989.4(PGAP1):c.275del (p.Pro92fs)Pathogenic
Intellectual disability, autosomal recessive 42
β˜…β˜†β˜†β˜†2023β†’ Residue 92
NM_024989.4(PGAP1):c.2051T>A (p.Leu684Ter)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 684
NM_024989.4(PGAP1):c.2287-1G>ALikely pathogenic
Intellectual disability, autosomal recessive 42
β˜…β˜†β˜†β˜†2023
View on ClinVar β†—
Related Genes
TMED10Protein interaction89%PGAP3Protein interaction88%PIGWProtein interaction83%CD55Protein interaction82%PIGSProtein interaction81%PIGTProtein interaction78%
Tissue Expression6 tissues
Brain
100%
Ovary
89%
Bone Marrow
68%
Heart
64%
Lung
56%
Liver
24%
Gene Interaction Network
Click a node to explore
PGAP1TMED10PGAP3PIGWCD55PIGSPIGT
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q75T13
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.69LoF Tolerant
pLIβ“˜
0.02Tolerant
Observed/Expected LoF0.47 [0.33–0.69]
RankingsWhere PGAP1 stands among ~20K protein-coding genes
  • #11,771of 20,598
    Most Researched31
  • #1,394of 5,498
    Most Pathogenic Variants47
  • #5,224of 17,882
    Most Constrained (LOEUF)0.69
Genes detectedPGAP1
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Compound heterozygous variants in PGAP1 causing severe psychomotor retardation, brain atrophy, recurrent apneas and delayed myelination: a case report and literature review.
PMID: 27206732
BMC Neurol Β· 2016
1.00
2
Metabolic traits shape responses to LSD1-directed therapy in glioblastoma tumor-initiating cells.
PMID: 40408499
Sci Adv Β· 2025
0.90
3
What is new in CDG?
PMID: 28484880
J Inherit Metab Dis Β· 2017
0.80
4
PGAP1-Related Encephalopathy in an Infant With Neurodevelopmental Delay: Novel Variant and Review of Literature.
PMID: 40785186
Int J Dev Neurosci Β· 2025
0.70
5
Molecular basis of the inositol deacylase PGAP1 involved in quality control of GPI-AP biogenesis.
PMID: 38167496
Nat Commun Β· 2024
0.60