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

Gene ID: 5277, updated on 27-Nov-2024

Summary

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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; AllianceGenome:HGNC:8957
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; NEDEPH
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
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Genomic context

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See PIGA in Genome Data Viewer
Location:
Xp22.2
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (15319451..15335554, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (14902337..14918440, complement)
RS_2024_09 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 Sharpr-MPRA regulatory region 14330 Neighboring gene ankyrin repeat and SOCS box containing 11 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29446 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29447 Neighboring gene PIR-FIGF readthrough Neighboring gene vascular endothelial growth factor D Neighboring gene pirin Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20672 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:15510866-15511368 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:15511369-15511872

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. PIG-A mutations in paroxysmal nocturnal hemoglobinuria and in normal hematopoiesis. Brodsky RA, et al. Leuk Lymphoma, 2006 Jul. PMID 16923549
  2. Early frameshift mutation in PIGA identified in a large XLID family without neonatal lethality. Belet S, et al. Hum Mutat, 2014 Mar. PMID 24357517
  3. A novel germline PIGA mutation in Ferro-Cerebro-Cutaneous syndrome: a neurodegenerative X-linked epileptic encephalopathy with systemic iron-overload. Swoboda KJ, et al. Am J Med Genet A, 2014 Jan. PMID 24259288, Free PMC Article
  4. The small population of PIG-A mutant cells in myelodysplastic syndromes do not arise from multipotent hematopoietic stem cells. Pu JJ, et al. Haematologica, 2012 Aug. PMID 22315493, Free PMC Article
  5. The phenotype of a germline mutation in PIGA: the gene somatically mutated in paroxysmal nocturnal hemoglobinuria. Johnston JJ, et al. Am J Hum Genet, 2012 Feb 10. PMID 22305531, Free PMC Article

See all (66) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis.
    Title: PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis.
  2. Congenital diaphragmatic hernia in siblings with PIGA-related congenital disorder of glycosylation.
    Title: Congenital diaphragmatic hernia in siblings with PIGA-related congenital disorder of glycosylation.
  3. PIG-A gene mutation as a mutagenicity biomarker among coke oven workers.
    Title: PIG-A gene mutation as a mutagenicity biomarker among coke oven workers.
  4. Constitutional PIGA mutations cause a novel subtype of hemochromatosis in patients with neurologic dysfunction.
    Title: Constitutional PIGA mutations cause a novel subtype of hemochromatosis in patients with neurologic dysfunction.
  5. Mutations in PIGA cause a CD52-/GPI-anchor-deficient phenotype complicating alemtuzumab treatment in T-cell prolymphocytic leukemia.
    Title: Mutations in PIGA cause a CD52-/GPI-anchor-deficient phenotype complicating alemtuzumab treatment in T-cell prolymphocytic leukemia.
  6. Implication of PIGA genotype on erythrocytes phenotype in Paroxysmal Nocturnal Hemoglobinuria.
    Title: Implication of PIGA genotype on erythrocytes phenotype in Paroxysmal Nocturnal Hemoglobinuria.
  7. PIGA-related epileptic encephalopathy demonstrating intrafamilial phenotypic heterogeneity.
    Title: PIGA-related epileptic encephalopathy demonstrating intrafamilial phenotypic heterogeneity.
  8. Evaluation of PIG-A-mutated granulocytes and ex-vivo binucleated micronucleated lymphocytes frequencies after breast cancer radiotherapy in humans.
    Title: Evaluation of PIG-A-mutated granulocytes and ex-vivo binucleated micronucleated lymphocytes frequencies after breast cancer radiotherapy in humans.
  9. Early-onset epileptic encephalopathy related to germline PIGA mutations: A series of 5 cases.
    Title: Early-onset epileptic encephalopathy related to germline PIGA mutations: A series of 5 cases.
  10. Identification of acquired PIGA mutations and additional variants by next-generation sequencing in paroxysmal nocturnal hemoglobinuria.
    Title: Identification of acquired PIGA mutations and additional variants by next-generation sequencing in paroxysmal nocturnal hemoglobinuria.
Submit: New GeneRIF Correction See all GeneRIFs (37)

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
Multiple congenital anomalies-hypotonia-seizures syndrome 2
MedGen: C3275508 OMIM: 300868 GeneReviews: Not available
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Neurodevelopmental disorder with epilepsy and hemochromatosis
MedGen: CN307964 OMIM: 301072 GeneReviews: Not available
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Paroxysmal nocturnal hemoglobinuria 1
MedGen: C3806670 OMIM: 300818 GeneReviews: Not available
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables UDP-glycosyltransferase activity TAS
Traceable Author Statement
more info
  
enables phosphatidylinositol N-acetylglucosaminyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables phosphatidylinositol N-acetylglucosaminyltransferase activity TAS
Traceable Author Statement
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in GPI anchor biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in GPI anchor biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
involved_in GPI anchor biosynthetic process TAS
Traceable Author Statement
more info
  
involved_in cellular response to leukemia inhibitory factor IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
  
part_of glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex IPI
Inferred from Physical Interaction
more info
 PubMed 
located_in membrane HDA PubMed 

General protein information

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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
XP_054183185.1

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

  1. NG_009786.1 RefSeqGene

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

mRNA and Protein(s)

  1. NM_002641.4 → NP_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
    B4E0V2, P37287, Q16025, Q16250
    UniProtKB/TrEMBL
    A0A2K4Z9P8, A0A2K4Z9Q9, A0A2K4Z9S0, A0A2K4Z9S8, A0A2K4Z9T1, A0A2K4Z9T4, A0A2K4Z9T5, A0A2K4Z9T7, A0A2K4Z9T8, A0A2K4Z9U3, A0A2K4Z9V6, A0A2K4Z9V8, A0A2K4Z9W0, A0A2K4Z9W1, A0A2K4Z9W2, A0A2K4Z9W5, A0A2K4Z9W7, A0A2K4Z9W8, A0A2K4Z9X1, A0A2K4Z9X3, A0A2K4Z9X9, A0A2K4Z9Y1, A0A2K4Z9Z2, A0A2K4ZA02, B2RCE0
    Related
    ENSP00000369820.3, ENST00000333590.6
    Conserved Domains (1) summary
    cd03796
    Location:34 → 432
    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_020473.3 → NP_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/TrEMBL
    A0A2K4Z9X5
    Related
    ENSP00000489540.1, ENST00000634582.1
    Conserved Domains (1) summary
    cl10013
    Location:5 → 198
    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: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

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

mRNA and Protein(s)

  1. XM_011545539.3 → XP_011543841.1  phosphatidylinositol N-acetylglucosaminyltransferase subunit A isoform X1

    UniProtKB/TrEMBL
    A0A2K4Z9X5
    Conserved Domains (2) summary
    COG0438
    Location:3 → 170
    RfaB; Glycosyltransferase involved in cell wall bisynthesis [Cell wall/membrane/envelope biogenesis]
    cl10013
    Location:6 → 201
    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 ...

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    14902337..14918440 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054327210.1 → XP_054183185.1  phosphatidylinositol N-acetylglucosaminyltransferase subunit A isoform X1

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.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P37287.1 GenPept UniProtKB/Swiss-Prot:P37287

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