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PIGO phosphatidylinositol glycan anchor biosynthesis class O [ Homo sapiens (human) ]

Gene ID: 84720, updated on 3-Nov-2024

Summary

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Official Symbol
PIGOprovided by HGNC
Official Full Name
phosphatidylinositol glycan anchor biosynthesis class Oprovided by HGNC
Primary source
HGNC:HGNC:23215
See related
Ensembl:ENSG00000165282 MIM:614730; AllianceGenome:HGNC:23215
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
HPMRS2
Summary
This gene encodes a protein that is involved in glycosylphosphatidylinositol (GPI)-anchor biosynthesis. The GPI-anchor is a glycolipid which contains three mannose molecules in its core backbone. The GPI-anchor is found on many blood cells and serves to anchor proteins to the cell surface. This protein is involved in the transfer of ethanolaminephosphate (EtNP) to the third mannose in GPI. At least three alternatively spliced transcripts encoding two distinct isoforms have been found for this gene. [provided by RefSeq, Jan 2011]
Expression
Ubiquitous expression in thyroid (RPKM 6.9), testis (RPKM 4.4) and 25 other tissues See more
Orthologs
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Genomic context

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See PIGO in Genome Data Viewer
Location:
9p13.3
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (35088688..35096591, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (35107866..35115769, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (35088685..35096588, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene valosin containing protein Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19859 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28317 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28318 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28319 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:35078961-35079568 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:35079644-35079809 Neighboring gene FA complementation group G Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:35080785-35081391 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28320 Neighboring gene PIGO antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28321 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28322 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28323 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28324 Neighboring gene stomatin like 2 Neighboring gene GATA motif-containing MPRA enhancer 90 Neighboring gene atos homolog B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19860 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19861 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:35113841-35114670 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19862

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. Mutations in PIGO, a member of the GPI-anchor-synthesis pathway, cause hyperphosphatasia with mental retardation. Krawitz PM, et al. Am J Hum Genet, 2012 Jul 13. PMID 22683086, Free PMC Article
  2. PIGO mutations in intractable epilepsy and severe developmental delay with mild elevation of alkaline phosphatase levels. Nakamura K, et al. Epilepsia, 2014 Feb. PMID 24417746
  3. Phenotype-genotype correlations of PIGO deficiency with variable phenotypes from infantile lethality to mild learning difficulties. Tanigawa J, et al. Hum Mutat, 2017 Jul. PMID 28337824
  4. Vitamin B6-responsive epilepsy due to inherited GPI deficiency. Kuki I, et al. Neurology, 2013 Oct 15. PMID 24049131
  5. Analysis of exome data for 4293 trios suggests GPI-anchor biogenesis defects are a rare cause of developmental disorders. Pagnamenta AT, et al. Eur J Hum Genet, 2017 Jun. PMID 28327575, Free PMC Article

See all (33) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. PIGO deficiency shows variable phenotypes from infantile lethality to mild learning difficulties
    Title: Phenotype-genotype correlations of PIGO deficiency with variable phenotypes from infantile lethality to mild learning difficulties.
  2. Disease associated PIGO missense mutations resulted in decreased activity in vitro.
    Title: Analysis of exome data for 4293 trios suggests GPI-anchor biogenesis defects are a rare cause of developmental disorders.
  3. Novel PIGO mutations expand the clinical spectrum of PIGO abnormalities to include epileptic encephalopathy with mild elevation of alkaline phosphatase (ALP).
    Title: PIGO mutations in intractable epilepsy and severe developmental delay with mild elevation of alkaline phosphatase levels.
  4. Our data identify PIGO as the second gene associated with HPMRS and suggest that a deficiency in GPI-anchor synthesis is the underlying molecular pathomechanism of HPMRS.
    Title: Mutations in PIGO, a member of the GPI-anchor-synthesis pathway, cause hyperphosphatasia with mental retardation.
  5. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
  6. Observational study of gene-disease association. (HuGE Navigator)
    Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
  7. 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.
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

Associated conditions

Description Tests
Hyperphosphatasia with intellectual disability syndrome 2
MedGen: C3553637 OMIM: 614749 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)

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

  • MGC3079, FLJ00135, MGC20536, DKFZp434M222

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables mannose-ethanolamine phosphotransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables mannose-ethanolamine phosphotransferase activity IMP
Inferred from Mutant Phenotype
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 ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
is_active_in endoplasmic reticulum membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endoplasmic reticulum membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in membrane HDA PubMed 

General protein information

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Preferred Names
GPI ethanolamine phosphate transferase 3
Names
phosphatidylinositol-glycan biosynthesis class O 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.

Genomic

  1. NG_031990.1 RefSeqGene

    Range
    5011..12914
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001201484.2 → NP_001188413.1  GPI ethanolamine phosphate transferase 3 isoform 2

    See identical proteins and their annotated locations for NP_001188413.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and coding region compared to variant 1. The resulting isoform (2) has the same N- and C-termini but lacks an internal segment compared to isoform 1. Variants 2 and 3 both encode the same isoform (2).
    Source sequence(s)
    AL353795, BC065282, BE139632, BU727886, CR985224
    Consensus CDS
    CCDS6576.1
    UniProtKB/TrEMBL
    A0A8V8TPZ0
    Related
    ENSP00000298004.5, ENST00000298004.9
    Conserved Domains (2) summary
    COG1524
    Location:42 → 299
    Npp1; Predicted pyrophosphatase or phosphodiesterase, AlkP superfamily [General function prediction only]
    cd16023
    Location:65 → 344
    GPI_EPT_3; GPI ethanolamine phosphate transferase 3, PIG-O

  2. NM_032634.4 → NP_116023.2  GPI ethanolamine phosphate transferase 3 isoform 1

    See identical proteins and their annotated locations for NP_116023.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
    Source sequence(s)
    AL353795, AY358472, BC029271, BE139632, BU727886, CR985224
    Consensus CDS
    CCDS6575.1
    UniProtKB/Swiss-Prot
    B1AML3, Q6P154, Q6UX80, Q8TDS8, Q8TEQ8, Q96CS9, Q9BVN9, Q9Y4B0
    UniProtKB/TrEMBL
    A0A8V8TPI4
    Related
    ENSP00000367880.3, ENST00000378617.4
    Conserved Domains (2) summary
    COG1524
    Location:42 → 299
    Npp1; Predicted pyrophosphatase or phosphodiesterase, AlkP superfamily [General function prediction only]
    cd16023
    Location:65 → 344
    GPI_EPT_3; GPI ethanolamine phosphate transferase 3, PIG-O

  3. NM_152850.4 → NP_690577.2  GPI ethanolamine phosphate transferase 3 isoform 2

    See identical proteins and their annotated locations for NP_690577.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding region compared to variant 1. The resulting isoform (2) has the same N- and C-termini but lacks an internal segment compared to isoform 1. Variants 2 and 3 both encode the same isoform (2).
    Source sequence(s)
    BC036916, BE139632, BU727886, CR991745
    Consensus CDS
    CCDS6576.1
    UniProtKB/TrEMBL
    A0A8V8TPZ0
    Related
    ENSP00000354678.2, ENST00000361778.7
    Conserved Domains (2) summary
    COG1524
    Location:42 → 299
    Npp1; Predicted pyrophosphatase or phosphodiesterase, AlkP superfamily [General function prediction only]
    cd16023
    Location:65 → 344
    GPI_EPT_3; GPI ethanolamine phosphate transferase 3, PIG-O

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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    35088688..35096591 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005251619.4 → XP_005251676.1  GPI ethanolamine phosphate transferase 3 isoform X1

    See identical proteins and their annotated locations for XP_005251676.1

    UniProtKB/Swiss-Prot
    B1AML3, Q6P154, Q6UX80, Q8TDS8, Q8TEQ8, Q96CS9, Q9BVN9, Q9Y4B0
    UniProtKB/TrEMBL
    A0A8V8TPI4
    Related
    ENSP00000514894.1, ENST00000700257.1
    Conserved Domains (2) summary
    COG1524
    Location:42 → 299
    Npp1; Predicted pyrophosphatase or phosphodiesterase, AlkP superfamily [General function prediction only]
    cd16023
    Location:65 → 344
    GPI_EPT_3; GPI ethanolamine phosphate transferase 3, PIG-O

  2. XM_047423974.1 → XP_047279930.1  GPI ethanolamine phosphate transferase 3 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    35107866..35115769 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054364022.1 → XP_054219997.1  GPI ethanolamine phosphate transferase 3 isoform X1

    UniProtKB/Swiss-Prot
    B1AML3, Q6P154, Q6UX80, Q8TDS8, Q8TEQ8, Q96CS9, Q9BVN9, Q9Y4B0

  2. XM_054364023.1 → XP_054219998.1  GPI ethanolamine phosphate transferase 3 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8TEQ8.3 GenPept UniProtKB/Swiss-Prot:Q8TEQ8

Gene LinkOut

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