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PIGA phosphatidylinositol glycan anchor biosynthesis class A [ Homo sapiens (human) ]

Gene ID: 5277, updated on 1-Jun-2020

Summary

Official Symbol
PIGAprovided by HGNC
Official Full Name
phosphatidylinositol glycan anchor biosynthesis class Aprovided by HGNC
Primary source
HGNC:HGNC:8957
See related
Ensembl:ENSG00000165195 MIM:311770
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
GPI3; PNH1; PIG-A; MCAHS2
Summary
This gene encodes a protein required for synthesis of N-acetylglucosaminyl phosphatidylinositol (GlcNAc-PI), the first intermediate in the biosynthetic pathway of GPI anchor. The GPI anchor is a glycolipid found on many blood cells and which serves to anchor proteins to the cell surface. Paroxysmal nocturnal hemoglobinuria, an acquired hematologic disorder, has been shown to result from mutations in this gene. Alternate splice variants have been characterized. A related pseudogene is located on chromosome 12. [provided by RefSeq, Jun 2010]
Expression
Ubiquitous expression in bone marrow (RPKM 9.8), urinary bladder (RPKM 3.0) and 24 other tissues See more
Orthologs

Genomic context

See PIGA in Genome Data Viewer
Location:
Xp22.2
Exon count:
7
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) X NC_000023.11 (15319451..15335554, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (15337573..15353676, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ankyrin repeat and SOCS box containing 9 Neighboring gene ankyrin repeat and SOCS box containing 11 Neighboring gene PIR-FIGF readthrough Neighboring gene vascular endothelial growth factor D Neighboring gene pirin

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Multiple congenital anomalies-hypotonia-seizures syndrome 2
MedGen: C3275508 OMIM: 300868 GeneReviews: Not available
Compare labs
Paroxysmal nocturnal hemoglobinuria 1
MedGen: C3806670 OMIM: 300818 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2014-11-04)

ClinGen Genome Curation Page
Haploinsufficency

Some evidence for dosage pathogenicity (Last evaluated (2014-11-04)

ClinGen Genome Curation PagePubMed

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
UDP-glycosyltransferase activity TAS
Traceable Author Statement
more info
 
phosphatidylinositol N-acetylglucosaminyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
phosphatidylinositol N-acetylglucosaminyltransferase activity TAS
Traceable Author Statement
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
GPI anchor biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
GPI anchor biosynthetic process TAS
Traceable Author Statement
more info
PubMed 
cellular response to leukemia inhibitory factor IEA
Inferred from Electronic Annotation
more info
 
positive regulation of metabolic process TAS
Traceable Author Statement
more info
PubMed 
preassembly of GPI anchor in ER membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
phosphatidylinositol N-acetylglucosaminyltransferase subunit A
Names
GLCNAC-PI synthesis protein
GPI anchor biosynthesis
class A GlcNAc-inositol phospholipid assembly protein
phosphatidylinositol-glycan biosynthesis, class A protein
NP_002632.1
NP_065206.3
XP_011543841.1

NCBI Reference Sequences (RefSeq)

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

  1. NG_009786.1 RefSeqGene

    Range
    4985..21088
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_160

mRNA and Protein(s)

  1. NM_002641.4NP_002632.1  phosphatidylinositol N-acetylglucosaminyltransferase subunit A isoform 1

    See identical proteins and their annotated locations for NP_002632.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
    Source sequence(s)
    BQ026877, D11466
    Consensus CDS
    CCDS14165.1
    UniProtKB/Swiss-Prot
    P37287
    Related
    ENSP00000369820.3, ENST00000333590.5
    Conserved Domains (1) summary
    cd03796
    Location:34432
    GT1_PIG-A_like; This family is most closely related to the GT1 family of glycosyltransferases. Phosphatidylinositol glycan-class A (PIG-A), an X-linked gene in humans, is necessary for the synthesis of N-acetylglucosaminyl-phosphatidylinositol, a very early intermediate ...
  2. NM_020473.3NP_065206.3  phosphatidylinositol N-acetylglucosaminyltransferase subunit A isoform 3

    See identical proteins and their annotated locations for NP_065206.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region and uses an alternate start codon, compared to variant 1. The resulting isoform (3) has a distinct and shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AK303538, BC038236, BQ026877, DA951065
    Consensus CDS
    CCDS48086.2
    UniProtKB/Swiss-Prot
    P37287
    Related
    ENSP00000489540.1, ENST00000634582.1
    Conserved Domains (1) summary
    cl10013
    Location:5198
    Glycosyltransferase_GTB_type; Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate ...

RNA

  1. NR_033835.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate splice site in the 5' region, compared to variant 1. This variant is represented as non-coding because the use of the supported start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK098047, BC038236, BQ026877, DC347872
    Related
    ENST00000635598.1
  2. NR_033836.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) uses an alternate splice site in the 5' region, compared to variant 1. This variant is represented as non-coding because it lacks a significant portion of the 5' coding region, as found in variant 1, and multiple upstream ORFs are present, which are predicted to interfere with the translation of the longest ORF.
    Source sequence(s)
    BC038236, BQ026877, CX870731, DA951065
    Related
    ENST00000638131.1

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p13 Primary Assembly

    Range
    15319451..15335554 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011545539.2XP_011543841.1  phosphatidylinositol N-acetylglucosaminyltransferase subunit A isoform X1

    Conserved Domains (2) summary
    COG0438
    Location:3170
    RfaB; Glycosyltransferase involved in cell wall bisynthesis [Cell wall/membrane/envelope biogenesis]
    cl10013
    Location:6201
    Glycosyltransferase_GTB_type; Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate ...

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_020472.1: Suppressed sequence

    Description
    NM_020472.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
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