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

Gene ID: 93210, updated on 11-Apr-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (39671122..39688057, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (40534687..40551623, complement)
105.20220307 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. Hyperphosphatasia with mental retardation syndrome type 4 in three unrelated South African patients. Bezuidenhout H, et al. Am J Med Genet A, 2020 Oct. PMID 32845056
  2. 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. Sio YY, et al. Sci Rep, 2020 Jan 20. PMID 31959860, Free PMC Article
  3. 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
  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. 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

See all (29) 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
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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

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_2023_10

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

    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

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

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