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

    Gene ID: 5277, updated on 14-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
    mouse all
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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 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
    		Compare labs
    Neurodevelopmental disorder with epilepsy and hemochromatosis
    MedGen: CN307964 OMIM: 301072 GeneReviews: Not available
    		Compare labs
    Paroxysmal nocturnal hemoglobinuria 1
    MedGen: C3806670 OMIM: 300818 GeneReviews: Not available
    		Compare labs

    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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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