Seroatlas · Human Serome Atlas

PGAP1

GPI inositol-deacylase

Also known as: Bst1, FLJ12377, PGAP1_HUMAN, SPG67

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: Q75T13
Gene: PGAP1
Ensembl: ENSG00000197121
Chromosome: 2
Canonical length: 922 aa
Protein class: Disease related genes, Human disease related genes, Metabolic proteins, Predicted intracellular proteins, Predicted membrane proteins

OverviewNCBI Gene

The protein encoded by this gene functions early in the glycosylphosphatidylinositol (GPI) biosynthetic pathway, catalyzing the inositol deacylation of GPI. The encoded protein is required for the production of GPI that can attach to proteins, and this may be an important factor in the transport of GPI-anchored proteins from the endoplasmic reticulum to the Golgi. Defects in this gene are a cause an autosomal recessive form of cognitive impairment. [provided by RefSeq, Jul 2017]

Canonical amino-acid sequenceUniProt

922 residues, UniProt reviewed canonical sequence.

>Q75T13|PGAP1
     1  MFLHSVNLWN LAFYVFMVFL ATLGLWDVFF GFEENKCSMS YMFEYPEYQK IELPKKLAKR
    61  YPAYELYLYG EGSYAEEHKI LPLTGIPVLF LPGNAGSYKQ VRSIGSIALR KAEDIDFKYH
   121  FDFFSVNFNE ELVALYGGSL QKQTKFVHEC IKTILKLYKG QEFAPKSVAI IGHSMGGLVA
   181  RALLTLKNFK HDLINLLITQ ATPHVAPVMP LDRFITDFYT TVNNYWILNA RHINLTTLSV
   241  AGGFRDYQVR SGLTFLPKLS HHTSALSVVS SAVPKTWVST DHLSIVWCKQ LQLTTVRAFF
   301  DLIDADTKQI TQNSKKKLSV LYHHFIRHPS KHFEENPAII SDLTGTSMWV LVKVSKWTYV
   361  AYNESEKIYF TFPLENHRKI YTHVYCQSTM LDTNSWIFAC INSTSMCLQG VDLSWKAELL
   421  PTIKYLTLRL QDYPSLSHLV VYVPSVRGSK FVVDCEFFKK EKRYIQLPVT HLFSFGLSSR
   481  KVVLNTNGLY YNLELLNFGQ IYQAFKINVV SKCSAVKEEI TSIYRLHIPW SYEDSLTIAQ
   541  APSSTEISLK LHIAQPENNT HVALFKMYTS SDCRYEVTVK TSFSQILGQV VRFHGGALPA
   601  YVVSNILLAY RGQLYSLFST GCCLEYATML DKEAKPYKVD PFVIIIKFLL GYKWFKELWD
   661  VLLLPELDAV ILTCQSMCFP LISLILFLFG TCTAYWSGLL SSASVRLLSS LWLALKRPSE
   721  LPKDIKMISP DLPFLTIVLI IVSWTTCGAL AILLSYLYYV FKVVHLQASL TTFKNSQPVN
   781  PKHSRRSEKK SNHHKDSSIH HLRLSANDAE DSLRMHSTVI NLLTWIVLLS MPSLIYWLKN
   841  LRYYFKLNPD PCKPLAFILI PTMAILGNTY TVSIKSSKLL KTTSQFPLPL AVGVIAFGSA
   901  HLYRLPCFVF IPLLLHALCN FM

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PGAP1 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability: Other membrane
Secreted: No
Transmembrane segments: 7
Mean surface accessibility (rSASA): 0.24
Highest tissue expression: 12 nTPM

Expression across tissuesHPA

Tissue

retina: 12 nTPM
skin: 12 nTPM
ovary: 8.7 nTPM
pituitary gland: 8.5 nTPM
adrenal gland: 7.9 nTPM
hypothalamus: 7.5 nTPM

Single-cell type

corticotrophs: 430 nCPM
lactotrophs: 375 nCPM
somatotrophs: 320 nCPM
vascular smooth muscle cells: 212 nCPM
thyrotrophs: 202 nCPM
other brain neurons: 189 nCPM

Immune cell

T-reg: 0.9 nTPM
memory CD4 T-cell: 0.7 nTPM
memory CD8 T-cell: 0.7 nTPM
naive CD4 T-cell: 0.6 nTPM
naive CD8 T-cell: 0.5 nTPM
gdT-cell: 0.2 nTPM

Brain region

hypothalamus: 46 nTPM
midbrain: 37 nTPM
cerebral cortex: 32 nTPM
basal ganglia: 29 nTPM
cerebellum: 24 nTPM
pons: 21 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about PGAP1.

Disease | AllUniProt

Conditions PGAP1 is implicated in, by any mechanism.

Neurodevelopmental disorder with dysmorphic features, spasticity, and brain abnormalities (NEDDSBA) MIM:615802

Disease | GeneticClinVar

47 pathogenic / likely-pathogenic of 488 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Intellectual disability, autosomal recessive 42
Inborn genetic diseases
Cerebral visual impairment and intellectual disability
See cases

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance): 0.6
gnomAD pLI: 0
gnomAD missense Z: 1.26
DepMap mean gene effect: -0.03
DepMap dependency class: none

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 5% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

hydrolase activity, acting on ester bonds
deacylase activity
phosphatidylinositol deacylase activity

Cellular components

Protein domainsUniProt · Pfam · InterPro

Alpha/Beta hydrolase fold
GPI inositol-deacylase PGAP1-like alpha/beta domain
GPI inositol-deacylase
GPI inositol-deacylase, transmembrane domain
PGAP1-like alpha/beta domain
GPI inositol-deacylase beta-sandwich domain
GPI inositol-deacylase transmembrane domain
GPI inositol-deacylase beta-sandwich domain

KeywordsUniProt

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads PGAP1 as an antibody target. Whether an autoantibody or antibody against PGAP1 could matter depends on whether native PGAP1 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PGAP1 is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label PGAP1 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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