PGAP1 post-GPI attachment to proteins inositol deacylase 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PGAP1provided by HGNC
Official Full Name: post-GPI attachment to proteins inositol deacylase 1provided by HGNC
Primary source: HGNC:HGNC:25712
See related: Ensembl:ENSG00000197121 MIM:611655; AllianceGenome:HGNC:25712
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: Bst1; MRT42; SPG67; NEDDSBA; ISPD3024
Summary: 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]
Expression: Ubiquitous expression in adrenal (RPKM 6.0), brain (RPKM 5.4) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2q33.1

Exon count:: 30

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (196833004..196926707, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (197316688..197410380, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (197697728..197791431, complement)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Molecular basis of the inositol deacylase PGAP1 involved in quality control of GPI-AP biogenesis.
Title: Molecular basis of the inositol deacylase PGAP1 involved in quality control of GPI-AP biogenesis.
Downregulation of lncRNA NEAT1 interacts with miR-374b-5p/PGAP1 axis to aggravate the development of osteoarthritis.
Title: Downregulation of lncRNA NEAT1 interacts with miR-374b-5p/PGAP1 axis to aggravate the development of osteoarthritis.
LncRNA LEMD1-AS1 relieves chondrocyte inflammation by targeting miR-944/PGAP1 in osteoarthritis.
Title: LncRNA LEMD1-AS1 relieves chondrocyte inflammation by targeting miR-944/PGAP1 in osteoarthritis.
Study confirms homozygous loss-of function mutations in PGAP1 as a cause of severe encephalopathy.
Title: Loss of function of PGAP1 as a cause of severe encephalopathy identified by Whole Exome Sequencing: Lessons of the bioinformatics pipeline.
PGAP1 mutation and a proven functional loss of PGAP1 were found in a patient with cerebral visual impairment and intellectual diasability.
Title: Cerebral visual impairment and intellectual disability caused by PGAP1 variants.
results add PGAP1 to the growing list of GPI abnormalities and indicate that not only the cell surface expression levels of GPI-APs but also the fine structure of GPI-anchors is important for the normal neurological development
Title: Null mutation in PGAP1 impairing Gpi-anchor maturation in patients with intellectual disability and encephalopathy.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
PGAP1 encoded an ER-associated, 922-amino acid membrane protein bearing a lipase consensus motif.
Title: Inositol deacylation of glycosylphosphatidylinositol-anchored proteins is mediated by mammalian PGAP1 and yeast Bst1p.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Intellectual disability, autosomal recessive 42 MedGen: C4014343 OMIM: 615802 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Genetic analysis of the pathogenic molecular sub-phenotype interferon-alpha identifies multiple novel loci involved in systemic lupus erythematosus. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D2S2327 (e-PCR), detects polymorphism
- UniSTS:22841

NoName (e-PCR)
- UniSTS:483661

D11S3114 (e-PCR)
- UniSTS:152207

WI-11026 (e-PCR)
- UniSTS:16784

L17809 (e-PCR)
- UniSTS:39087

RH45473 (e-PCR)
- UniSTS:82117

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables hydrolase activity, acting on ester bonds	TAS Traceable Author Statement more info
enables phosphatidylinositol deacylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables phosphatidylinositol deacylase activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in GPI anchor metabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in anterior/posterior axis specification	IEA Inferred from Electronic Annotation more info
involved_in attachment of GPI anchor to protein	TAS Traceable Author Statement more info
involved_in embryonic pattern specification	IEA Inferred from Electronic Annotation more info
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in forebrain regionalization	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of ER to Golgi vesicle-mediated transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein transport	IEA Inferred from Electronic Annotation more info
involved_in sensory perception of sound	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in endoplasmic reticulum	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum	ISS Inferred from Sequence or Structural Similarity more info
located_in endoplasmic reticulum membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: GPI inositol-deacylase

Names: post-GPI attachment to proteins 1; post-GPI attachment to proteins factor 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_046780.1 RefSeqGene

Range

5289..98992

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001321099.2 → NP_001308028.1 GPI inositol-deacylase isoform 2

Status: REVIEWED

Source sequence(s)

AB128038, AC012486, AC017035, BX648642, DN992948

UniProtKB/Swiss-Prot

Q75T13

Conserved Domains (1) summary

pfam07819
Location:1 → 128

PGAP1; PGAP1-like protein
NM_001321100.2 → NP_001308029.1 GPI inositol-deacylase isoform 3

Status: REVIEWED

Source sequence(s)

AB128038, AC012486, DN992948

UniProtKB/Swiss-Prot

Q75T13
NM_024989.4 → NP_079265.2 GPI inositol-deacylase isoform 1

See identical proteins and their annotated locations for NP_079265.2

Status: REVIEWED

Source sequence(s)

AB128038, AC012486, AK022439

Consensus CDS

CCDS2318.1

UniProtKB/Swiss-Prot

Q4G0R8, Q4ZG47, Q53SM0, Q6AW92, Q6UWV4, Q75T13, Q9HA24

Related

ENSP00000346809.3, ENST00000354764.9

Conserved Domains (1) summary

pfam07819
Location:83 → 302

PGAP1; PGAP1-like protein

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

196833004..196926707 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017004993.2 → XP_016860482.1 GPI inositol-deacylase isoform X1

UniProtKB/Swiss-Prot

Q75T13

Conserved Domains (1) summary

pfam07819
Location:1 → 128

PGAP1; PGAP1-like protein
XM_017004992.1 → XP_016860481.1 GPI inositol-deacylase isoform X1

UniProtKB/Swiss-Prot

Q75T13

Conserved Domains (1) summary

pfam07819
Location:1 → 128

PGAP1; PGAP1-like protein
XM_047445910.1 → XP_047301866.1 GPI inositol-deacylase isoform X2