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

    Gene ID: 84720, updated on 27-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
    mouse all
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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
    • 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
    		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

    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

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

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