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PIGZ phosphatidylinositol glycan anchor biosynthesis class Z [ Homo sapiens (human) ]

Gene ID: 80235, updated on 3-Apr-2024

Summary

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Official Symbol
PIGZprovided by HGNC
Official Full Name
phosphatidylinositol glycan anchor biosynthesis class Zprovided by HGNC
Primary source
HGNC:HGNC:30596
See related
Ensembl:ENSG00000119227 MIM:611671; AllianceGenome:HGNC:30596
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
SMP3; PIG-Z; GPI-MT-IV
Summary
The glycosylphosphatidylinositol (GPI) anchor is a glycolipid found on many blood cells that serves to anchor proteins to the cell surface. This gene encodes a protein that is localized to the endoplasmic reticulum, and is involved in GPI anchor biosynthesis. As shown for the yeast homolog, which is a member of a family of dolichol-phosphate-mannose (Dol-P-Man)-dependent mannosyltransferases, this protein can also add a side-branching fourth mannose to GPI precursors during the assembly of GPI anchors. [provided by RefSeq, Jul 2008]
Expression
Broad expression in colon (RPKM 5.3), brain (RPKM 1.9) and 20 other tissues See more
Orthologs
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Genomic context

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See PIGZ in Genome Data Viewer
Location:
3q29
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (196946356..196968833, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (199672412..199695067, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (196673227..196695704, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene nuclear cap binding protein subunit 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:196668731-196669404 Neighboring gene NCBP2 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:196669405-196670078 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:196670753-196671426 Neighboring gene NCBP2 antisense 2 (head to head) Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:196674955-196675702 Neighboring gene Sharpr-MPRA regulatory region 11589 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:196695281-196695816 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:196695817-196696352 Neighboring gene collagen alpha-1(I) chain-like Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:196696353-196696888 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21106 Neighboring gene 40S ribosomal protein SA-like

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. Human Smp3p adds a fourth mannose to yeast and human glycosylphosphatidylinositol precursors in vivo. Taron BW, et al. J Biol Chem, 2004 Aug 20. PMID 15208306
  2. Common origin and evolution of glycosyltransferases using Dol-P-monosaccharides as donor substrate. Oriol R, et al. Mol Biol Evol, 2002 Sep. PMID 12200473
  3. Enzymes and auxiliary factors for GPI lipid anchor biosynthesis and post-translational transfer to proteins. Eisenhaber B, et al. Bioessays, 2003 Apr. PMID 12655644
  4. The essential Smp3 protein is required for addition of the side-branching fourth mannose during assembly of yeast glycosylphosphatidylinositols. Grimme SJ, et al. J Biol Chem, 2001 Jul 20. PMID 11356840
  5. SUMOylation of DDX39A Alters Binding and Export of Antiviral Transcripts to Control Innate Immunity. Shi P, et al. J Immunol, 2020 Jul 1. PMID 32393512

See all (11) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. publication also discusses human SMP3
    Title: The essential Smp3 protein is required for addition of the side-branching fourth mannose during assembly of yeast glycosylphosphatidylinositols.
Submit: New GeneRIF Correction

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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

Clone Names

  • FLJ12768, MGC52163

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables alpha-1,2-mannosyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables alpha-1,2-mannosyltransferase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables mannosyltransferase activity EXP
Inferred from Experiment
more info
 PubMed 
enables mannosyltransferase activity IGI
Inferred from Genetic 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 IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in GPI anchor biosynthetic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in preassembly of GPI anchor in ER membrane TAS
Traceable Author Statement
more info
  
Component Evidence Code Pubs
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in endoplasmic reticulum membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
GPI mannosyltransferase 4
Names
GPI mannosyltransferase IV
SMP3 mannosyltransferase
dol-P-Man dependent GPI mannosyltransferase
phosphatidylinositol glycan, class Z
phosphatidylinositol-glycan biosynthesis class Z protein

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.

mRNA and Protein(s)

  1. NM_025163.4 → NP_079439.2  GPI mannosyltransferase 4

    See identical proteins and their annotated locations for NP_079439.2

    Status: REVIEWED

    Source sequence(s)
    AK022830, AK296867, BC018804, BG760692, BX493581
    Consensus CDS
    CCDS3324.1
    UniProtKB/Swiss-Prot
    Q86VD9, Q9H9G6
    Related
    ENSP00000413405.1, ENST00000412723.6
    Conserved Domains (1) summary
    cl21590
    Location:44 → 391
    PMT_2; Dolichyl-phosphate-mannose-protein mannosyltransferase

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

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    196946356..196968833 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011513192.3 → XP_011511494.1  GPI mannosyltransferase 4 isoform X2

    See identical proteins and their annotated locations for XP_011511494.1

    Conserved Domains (1) summary
    cl21590
    Location:83 → 430
    PMT_2; Dolichyl-phosphate-mannose-protein mannosyltransferase

  2. XM_047448993.1 → XP_047304949.1  GPI mannosyltransferase 4 isoform X2

  3. XM_024453767.2 → XP_024309535.1  GPI mannosyltransferase 4 isoform X1

    Conserved Domains (1) summary
    cl21590
    Location:109 → 456
    PMT_2; Dolichyl-phosphate-mannose-protein mannosyltransferase

  4. XM_024453766.2 → XP_024309534.1  GPI mannosyltransferase 4 isoform X1

    Conserved Domains (1) summary
    cl21590
    Location:109 → 456
    PMT_2; Dolichyl-phosphate-mannose-protein mannosyltransferase

  5. XM_017007241.2 → XP_016862730.1  GPI mannosyltransferase 4 isoform X1

    Conserved Domains (1) summary
    cl21590
    Location:109 → 456
    PMT_2; Dolichyl-phosphate-mannose-protein mannosyltransferase

  6. XM_017007243.2 → XP_016862732.1  GPI mannosyltransferase 4 isoform X3

    UniProtKB/TrEMBL
    B4DL68
    Conserved Domains (1) summary
    cl21590
    Location:5 → 241
    PMT_2; Dolichyl-phosphate-mannose-protein mannosyltransferase

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    199672412..199695067 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054347966.1 → XP_054203941.1  GPI mannosyltransferase 4 isoform X1

  2. XM_054347970.1 → XP_054203945.1  GPI mannosyltransferase 4 isoform X2

  3. XM_054347969.1 → XP_054203944.1  GPI mannosyltransferase 4 isoform X2

  4. XM_054347968.1 → XP_054203943.1  GPI mannosyltransferase 4 isoform X1

  5. XM_054347967.1 → XP_054203942.1  GPI mannosyltransferase 4 isoform X1

  6. XM_054347965.1 → XP_054203940.1  GPI mannosyltransferase 4 isoform X1

  7. XM_054347971.1 → XP_054203946.1  GPI mannosyltransferase 4 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q86VD9.4 GenPept UniProtKB/Swiss-Prot:Q86VD9

Gene LinkOut

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