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    PGAP3 post-GPI attachment to proteins phospholipase 3 [ Homo sapiens (human) ]

    Gene ID: 93210, updated on 10-Dec-2024

    Summary

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    Official Symbol
    PGAP3provided by HGNC
    Official Full Name
    post-GPI attachment to proteins phospholipase 3provided by HGNC
    Primary source
    HGNC:HGNC:23719
    See related
    Ensembl:ENSG00000161395 MIM:611801; AllianceGenome:HGNC:23719
    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
    CAB2; PERLD1; PP1498; hCOS16; AGLA546
    Summary
    This gene encodes a glycosylphosphatidylinositol (GPI)-specific phospholipase that primarily localizes to the Golgi apparatus. This ubiquitously expressed gene is predicted to encode a seven-transmembrane protein that removes unsaturated fatty acids from the sn-2 position of GPI. The remodeling of the constituent fatty acids on GPI is thought to be important for the proper association between GPI-anchored proteins and lipid rafts. The tethering of proteins to plasma membranes via posttranslational GPI-anchoring is thought to play a role in protein sorting and trafficking. Mutations in this gene cause an autosomal recessive form of neurologic hyperphosphatasia with cognitive disability (HPMRS4). Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2017]
    Expression
    Ubiquitous expression in thyroid (RPKM 14.6), skin (RPKM 9.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PGAP3 in Genome Data Viewer
    Location:
    17q12
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (39671122..39688057, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (40534687..40551623, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (37827375..37844310, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:37822021-37822758 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:37822759-37823496 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8461 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12101 Neighboring gene titin-cap Neighboring gene VISTA enhancer hs1769 Neighboring gene phenylethanolamine N-methyltransferase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:37835782-37836282 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12103 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr17:37845149-37846109 Neighboring gene erb-b2 receptor tyrosine kinase 2 Neighboring gene Sharpr-MPRA regulatory region 353 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:37857299-37857800 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:37857801-37858300 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:37861047-37861919 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:37882556-37883528 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8463 Neighboring gene microRNA 4728 Neighboring gene migration and invasion enhancer 1

    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. Defining the phenotype of PGAP3-congenital disorder of glycosylation; a review of 65 cases. Altassan R, et al. Mol Genet Metab, 2023 Nov. PMID 37647829, Free PMC Article
    2. Genome-wide association study identifies PERLD1 as asthma candidate gene. Anantharaman R, et al. BMC Med Genet, 2011 Dec 21. PMID 22188591, Free PMC Article
    3. Mutations in PGAP3 impair GPI-anchor maturation, causing a subtype of hyperphosphatasia with mental retardation. Howard MF, et al. Am J Hum Genet, 2014 Feb 6. PMID 24439110, Free PMC Article
    4. Rare Noncoding Mutations Extend the Mutational Spectrum in the PGAP3 Subtype of Hyperphosphatasia with Mental Retardation Syndrome. Knaus A, et al. Hum Mutat, 2016 Aug. PMID 27120253, Free PMC Article
    5. PGAP3-related hyperphosphatasia with mental retardation syndrome: Report of 10 new patients and a homozygous founder mutation. Abdel-Hamid MS, et al. Clin Genet, 2018 Jan. PMID 28390064

    See all (32) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. High PGAP3 expression is associated with lymph node metastasis and low CD8[+]T cell in patients with HER2[+] breast cancer.
      Title: High PGAP3 expression is associated with lymph node metastasis and low CD8(+)T cell in patients with HER2(+) breast cancer.
    2. Defining the phenotype of PGAP3-congenital disorder of glycosylation; a review of 65 cases.
      Title: Defining the phenotype of PGAP3-congenital disorder of glycosylation; a review of 65 cases.
    3. Genetic analysis of sinonasal undifferentiated carcinoma discovers recurrent SWI/SNF alterations and a novel PGAP3-SRPK1 fusion gene.
      Title: Genetic analysis of sinonasal undifferentiated carcinoma discovers recurrent SWI/SNF alterations and a novel PGAP3-SRPK1 fusion gene.
    4. The novel circular RNA circ-PGAP3 retards cervical cancer growth by regulating the miR-769-5p/p53 axis.
      Title: The novel circular RNA circ-PGAP3 retards cervical cancer growth by regulating the miR-769-5p/p53 axis.
    5. Hyperphosphatasia with mental retardation syndrome type 4 in three unrelated South African patients.
      Title: Hyperphosphatasia with mental retardation syndrome type 4 in three unrelated South African patients.
    6. The Asthma-associated PER1-like domain-containing protein 1 (PERLD1) Haplotype Influences Soluble Glycosylphosphatidylinositol Anchor Protein (sGPI-AP) Levels in Serum and Immune Cell Proliferation.
      Title: The Asthma-associated PER1-like domain-containing protein 1 (PERLD1) Haplotype Influences Soluble Glycosylphosphatidylinositol Anchor Protein (sGPI-AP) Levels in Serum and Immune Cell Proliferation.
    7. Data show that biallelic loss of function mutations in the post-GPI attachment to proteins 3 (PGAP3) gene were detected in all patients.
      Title: PGAP3-related hyperphosphatasia with mental retardation syndrome: Report of 10 new patients and a homozygous founder mutation.
    8. A screening approach with sequence specific baits for transcripts of genes of the GPI pathway identified pathogenic noncoding mutations in PGAP3 subtype of hyperphosphatasia with mental retardation syndrome. Besides five missense mutations, an intronic mutation was found causing an aberrant splice product and a mutation in the 3'UTR that is associated with substantially lower mRNA levels.
      Title: Rare Noncoding Mutations Extend the Mutational Spectrum in the PGAP3 Subtype of Hyperphosphatasia with Mental Retardation Syndrome.
    9. Impairment of PGAP3 causes a subtype of hyperphosphatasia with intellectual disabilities, a congenital disorder of glycosylation that is also referred to as Mabry syndrome.
      Title: Mutations in PGAP3 impair GPI-anchor maturation, causing a subtype of hyperphosphatasia with mental retardation.
    10. Data show that glycosylphosphatidylinositol-anchored proteins (GPI-APs) are secreted into the medium by cells overexpressing PGAP3.
      Title: Apical sorting of lysoGPI-anchored proteins occurs independent of association with detergent-resistant membranes but dependent on their N-glycosylation.
    Submit: New GeneRIF Correction See all GeneRIFs (15)

    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 4
    MedGen: C3810354 OMIM: 615716 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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC9753

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables hydrolase activity, acting on ester bonds IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables hydrolase activity, acting on ester bonds IMP
    Inferred from Mutant Phenotype
    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 IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in GPI anchor metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Golgi membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in endoplasmic reticulum membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    post-GPI attachment to proteins factor 3
    Names
    COS16 homolog
    gene coamplified with ERBB2 protein
    per1-like domain containing 1
    post-GPI attachment to proteins 3

    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_034125.1 RefSeqGene

      Range
      5014..21949
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001291726.2 → NP_001278655.1  post-GPI attachment to proteins factor 3 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001278655.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the 5' coding region, compared to variant 1. It encodes a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      AK075474, BC010652, DC389056
      Consensus CDS
      CCDS77013.1
      UniProtKB/Swiss-Prot
      Q96FM1
      Related
      ENSP00000367250.4, ENST00000378011.8
      Conserved Domains (1) summary
      pfam04080
      Location:54 → 255
      Per1; Per1-like

    2. NM_001291728.2 → NP_001278657.1  post-GPI attachment to proteins factor 3 isoform 3 precursor

      See identical proteins and their annotated locations for NP_001278657.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an in-frame exon in the 3' coding region, compared to variant 1. It encodes a shorter protein (isoform 3), compared to isoform 1.
      Source sequence(s)
      AK294639, BC010652
      Consensus CDS
      CCDS77015.1
      UniProtKB/TrEMBL
      B4DVJ3, B6ZDN2
      Related
      ENSP00000415765.2, ENST00000429199.6
      Conserved Domains (1) summary
      pfam04080
      Location:54 → 285
      Per1; Per1-like

    3. NM_001291730.2 → NP_001278659.1  post-GPI attachment to proteins factor 3 isoform 4 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks two in-frame exons in the 3' coding region, compared to variant 1. It encodes a shorter protein (isoform 4), compared to isoform 1.
      Source sequence(s)
      BC010652, BG472165, DC389056
      UniProtKB/Swiss-Prot
      Q96FM1
      Conserved Domains (1) summary
      cl02172
      Location:54 → 185
      Per1; Per1-like

    4. NM_001291732.2 → NP_001278661.1  post-GPI attachment to proteins factor 3 isoform 5 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks three in-frame exons in the 3' coding region, compared to variant 1. It encodes a shorter protein (isoform 5), compared to isoform 1.
      Source sequence(s)
      BC010652, DC389056
      UniProtKB/Swiss-Prot
      Q96FM1
      Conserved Domains (1) summary
      cl02172
      Location:54 → 164
      Per1; Per1-like

    5. NM_001291733.2 → NP_001278662.1  post-GPI attachment to proteins factor 3 isoform 6 precursor

      See identical proteins and their annotated locations for NP_001278662.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) lacks four exons in the 3' coding region, compared to variant 1. It encodes a shorter protein (isoform 6) with a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AK289612, BC010652, DC389056
      Consensus CDS
      CCDS77014.1
      UniProtKB/TrEMBL
      J3KTJ2, J3QKU0
      Related
      ENSP00000463234.1, ENST00000579146.5
      Conserved Domains (1) summary
      cl02172
      Location:54 → 146
      Per1; Per1-like

    6. NM_033419.5 → NP_219487.3  post-GPI attachment to proteins factor 3 isoform 1 precursor

      See identical proteins and their annotated locations for NP_219487.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      BC010652, DC389056
      Consensus CDS
      CCDS32641.1
      UniProtKB/Swiss-Prot
      B4DGK7, Q86Z03, Q8NBJ8, Q96FM1
      UniProtKB/TrEMBL
      B4DVJ3, B6ZDN2
      Related
      ENSP00000300658.4, ENST00000300658.9
      Conserved Domains (1) summary
      cl02172
      Location:54 → 306
      Per1; Per1-like

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      39671122..39688057 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011525480.2 → XP_011523782.1  post-GPI attachment to proteins factor 3 isoform X1

      Conserved Domains (1) summary
      pfam04080
      Location:54 → 231
      Per1; Per1-like

    2. XM_047437082.1 → XP_047293038.1  post-GPI attachment to proteins factor 3 isoform X2

    3. XM_047437083.1 → XP_047293039.1  post-GPI attachment to proteins factor 3 isoform X3

      UniProtKB/TrEMBL
      J3KTJ2
      Related
      ENSP00000463011.1, ENST00000584620.5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      40534687..40551623 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054317811.1 → XP_054173786.1  post-GPI attachment to proteins factor 3 isoform X1

    2. XM_054317812.1 → XP_054173787.1  post-GPI attachment to proteins factor 3 isoform X2

    3. XM_054317813.1 → XP_054173788.1  post-GPI attachment to proteins factor 3 isoform X3

      UniProtKB/TrEMBL
      J3KTJ2
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96FM1.2 GenPept UniProtKB/Swiss-Prot:Q96FM1

    Gene LinkOut

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

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