PGAP3 Gene (Protein Coding)

Post-GPI Attachment To Proteins Phospholipase 3

GC17M039676
GIFtS:
38
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 asso... See more...

Aliases for PGAP3 Gene

Aliases for PGAP3 Gene

  • Post-GPI Attachment To Proteins Phospholipase 3 2 3 5
  • CAB2 2 3 4
  • Post-GPI Attachment To Proteins Factor 3 3 4
  • Gene Coamplified With ERBB2 Protein 3 4
  • Post-GPI Attachment To Proteins 3 2 3
  • Per1-Like Domain Containing 1 2 3
  • COS16 Homolog 3 4
  • PERLD1 3 4
  • PP1498 2 3
  • HCOS16 3 4
  • PER1-Like Domain-Containing Protein 1 4
  • AGLA546 3
  • MGC9753 2
  • PGAP3 5
  • PER1 2

External Ids for PGAP3 Gene

Previous HGNC Symbols for PGAP3 Gene

  • PERLD1

Previous GeneCards Identifiers for PGAP3 Gene

  • GC17M035081
  • GC17M037827
  • GC17M033621

Summaries for PGAP3 Gene

Entrez Gene Summary for PGAP3 Gene

  • 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]

GeneCards Summary for PGAP3 Gene

PGAP3 (Post-GPI Attachment To Proteins Phospholipase 3) is a Protein Coding gene. Diseases associated with PGAP3 include Hyperphosphatasia With Mental Retardation Syndrome 4 and Diaphragmatic Hernia, Congenital. Gene Ontology (GO) annotations related to this gene include hydrolase activity, acting on ester bonds.

UniProtKB/Swiss-Prot Summary for PGAP3 Gene

  • Involved in the lipid remodeling steps of GPI-anchor maturation. Lipid remodeling steps consist in the generation of 2 saturated fatty chains at the sn-2 position of GPI-anchors proteins. Required for phospholipase A2 activity that removes an acyl-chain at the sn-2 position of GPI-anchors during the remodeling of GPI.

Additional gene information for PGAP3 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PGAP3 Gene

Genomics for PGAP3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for PGAP3 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PGAP3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PGAP3

Genomic Locations for PGAP3 Gene

Genomic Locations for PGAP3 Gene
chr17:39,671,122-39,696,797
(GRCh38/hg38)
Size:
25,676 bases
Orientation:
Minus strand
chr17:37,827,375-37,853,050
(GRCh37/hg19)
Size:
25,676 bases
Orientation:
Minus strand

Genomic View for PGAP3 Gene

Genes around PGAP3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PGAP3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PGAP3 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for PGAP3 Gene

Proteins for PGAP3 Gene

Products:

  1. Antibody
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  • Protein details for PGAP3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96FM1-PGAP3_HUMAN
    Recommended name:
    Post-GPI attachment to proteins factor 3
    Protein Accession:
    Q96FM1
    Secondary Accessions:
    • B4DGK7
    • Q86Z03
    • Q8NBJ8

    Protein attributes for PGAP3 Gene

    Size:
    320 amino acids
    Molecular mass:
    36475 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAC55580.1; Type=Frameshift; Evidence={ECO:0000305};
    Miscellaneous:
    • When transfected in S.cerevisiae, it can complement the absence of yeast of PER1 protein, suggesting a conserved role in lipid remodeling steps of GPI-anchor maturation.

    Alternative splice isoforms for PGAP3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PGAP3 Gene

Protein Expression for PGAP3 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for PGAP3 Gene

  • Glycosylation at Asn40
  • Glycosylation from GlyConnect
    • PGAP3_HUMAN (1621)

Other Protein References for PGAP3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PGAP3 Gene

Domains & Families for PGAP3 Gene

Gene Families for PGAP3 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for PGAP3 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PGAP3 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ52489, highly similar to Homo sapiens per1-like domain containing 1 (PERLD1), mRNA (B4DGK7_HUMAN)
  • cDNA FLJ61173, highly similar to Homo sapiens per1-like domain containing 1 (PERLD1), mRNA (B4DVJ3_HUMAN)
  • PER1-like domain-containing protein 1 (PGAP3_HUMAN)
  • Per1-like domain containing 1, isoform CRA_a (Q9HBS1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q96FM1

UniProtKB/Swiss-Prot:

PGAP3_HUMAN :
  • Belongs to the PGAP3 family.
Family:
  • Belongs to the PGAP3 family.
genes like me logo Genes that share domains with PGAP3: view

Function for PGAP3 Gene

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  2. CRISPR
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  6. Cell Line

Molecular function for PGAP3 Gene

UniProtKB/Swiss-Prot Function:
Involved in the lipid remodeling steps of GPI-anchor maturation. Lipid remodeling steps consist in the generation of 2 saturated fatty chains at the sn-2 position of GPI-anchors proteins. Required for phospholipase A2 activity that removes an acyl-chain at the sn-2 position of GPI-anchors during the remodeling of GPI.

Phenotypes From GWAS Catalog for PGAP3 Gene

Gene Ontology (GO) - Molecular Function for PGAP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016788 hydrolase activity, acting on ester bonds IMP 17021251
genes like me logo Genes that share ontologies with PGAP3: view
genes like me logo Genes that share phenotypes with PGAP3: view

Human Phenotype Ontology for PGAP3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PGAP3 Gene

MGI Knock Outs for PGAP3:

Animal Model Products

  • Taconic Biosciences Mouse Models for PGAP3

CRISPR Products

miRNA for PGAP3 Gene

miRTarBase miRNAs that target PGAP3

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PGAP3

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for PGAP3 Gene

Localization for PGAP3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PGAP3 Gene

Golgi apparatus membrane. Multi-pass membrane protein. Endoplasmic reticulum membrane. Multi-pass membrane protein. Note=Mainly localizes to Golgi apparatus. {ECO:0000305}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PGAP3 gene
Compartment Confidence
endoplasmic reticulum 5
plasma membrane 4
golgi apparatus 4
cytosol 2
extracellular 1
cytoskeleton 1
mitochondrion 1
nucleus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PGAP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IEA --
GO:0005783 endoplasmic reticulum IEA --
GO:0005789 endoplasmic reticulum membrane IEA --
GO:0005794 Golgi apparatus IEA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with PGAP3: view

Pathways & Interactions for PGAP3 Gene

PathCards logo

SuperPathways for PGAP3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PGAP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006505 GPI anchor metabolic process IMP 17021251
GO:0006506 GPI anchor biosynthetic process IEA,IMP 29374258
genes like me logo Genes that share ontologies with PGAP3: view

No data available for Pathways by source and SIGNOR curated interactions for PGAP3 Gene

Drugs & Compounds for PGAP3 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for PGAP3 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for PGAP3 Gene

6 REFSEQ mRNAs :
14 NCBI additional mRNA sequence :
11 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PGAP3

Alternative Splicing Database (ASD) splice patterns (SP) for PGAP3 Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7a · 7b · 7c ^ 8 ^ 9a · 9b · 9c
SP1: - - - - -
SP2: - - - - - -
SP3: - - - - - - - -
SP4: -
SP5: - - - - -
SP6: - - - - - - - - - -
SP7: - - -
SP8: - - -
SP9: - - - -
SP10:

Relevant External Links for PGAP3 Gene

GeneLoc Exon Structure for
PGAP3

Expression for PGAP3 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PGAP3 Gene

mRNA expression in normal human tissues for PGAP3 Gene
mRNA expression by BioGPS for PGAP3 GenemRNA expression by GTEx for PGAP3 Gene

Protein differential expression in normal tissues from HIPED for PGAP3 Gene

This gene is overexpressed in Placenta (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PGAP3 Gene



Protein tissue co-expression partners for PGAP3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PGAP3

SOURCE GeneReport for Unigene cluster for PGAP3 Gene:

Hs.462971

mRNA Expression by UniProt/SwissProt for PGAP3 Gene:

Q96FM1-PGAP3_HUMAN
Tissue specificity: Ubiquitously expressed, with highest levels in thyroid and placenta.

Evidence on tissue expression from TISSUES for PGAP3 Gene

  • Nervous system(4.7)
  • Intestine(4.3)
  • Skin(2.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PGAP3 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • integumentary
  • nervous
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • cerebellum
  • cheek
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • nose
  • outer ear
  • skull
  • tooth
Thorax:
  • heart
Abdomen:
  • biliary tract
  • intestine
  • kidney
  • large intestine
  • liver
Pelvis:
  • anus
  • rectum
Limb:
  • digit
  • finger
  • foot
  • hand
  • lower limb
  • nail
  • toe
  • upper limb
General:
  • hair
  • skin
genes like me logo Genes that share expression patterns with PGAP3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for PGAP3 Gene

Orthologs for PGAP3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PGAP3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia PGAP3 30 31
  • 99.48 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia PGAP3 30 31
  • 90.39 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia PGAP3 30 31
  • 89.13 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Pgap3 30 17 31
  • 86.75 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Perld1 30
  • 86.75 (n)
Oppossum
(Monodelphis domestica)
 Mammalia PGAP3 31
  • 75 (a)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia PGAP3 31
  • 67 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves PGAP3 30 31
  • 76.19 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia PGAP3 31
  • 69 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia pgap3 30
  • 71.19 (n)
Zebrafish
(Danio rerio)
 Actinopterygii zgc:171485 30
  • 68.1 (n)
PGAP3 31
  • 67 (a)
 OneToOne
Fruit Fly
(Drosophila melanogaster)
 Insecta CG3271 30 31
  • 52.04 (n)
 OneToOne
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP005392 30
  • 51.37 (n)
Worm
(Caenorhabditis elegans)
 Secernentea R01B10.4 31
  • 31 (a)
 OneToOne
A. gosspyii yeast
(Eremothecium gossypii)
 Saccharomycetes AGOS_AFR678C 30
  • 45.64 (n)
K. Lactis Yeast
(Kluyveromyces lactis)
 Saccharomycetes KLLA0C02101g 30
  • 41.61 (n)
Baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes PER1 30 31 33
  • 40.4 (n)
 OneToOne
Thale Cress
(Arabidopsis thaliana)
 eudicotyledons AT1G16560 30
  • 45.53 (n)
Rice
(Oryza sativa)
 Liliopsida Os05g0220100 30
  • 47.13 (n)
Bread mold
(Neurospora crassa)
 Ascomycetes NCU08609 30
  • 48.76 (n)
Fission Yeast
(Schizosaccharomyces pombe)
 Schizosaccharomycetes SPAC823.07 30
  • 42.09 (n)
Species where no ortholog for PGAP3 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for PGAP3 Gene

ENSEMBL:
Gene Tree for PGAP3 (if available)
TreeFam:
Gene Tree for PGAP3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PGAP3: view image

Paralogs for PGAP3 Gene

No data available for Paralogs for PGAP3 Gene

Variants for PGAP3 Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PGAP3 Gene

SNP ID Clinical significance and condition Chr 17 pos Variation AA Info Type
679984 Benign: not provided 39,674,647(-) A/G SYNONYMOUS_VARIANT,INTRON_VARIANT
708595 Likely Benign: not provided 39,684,714(-) C/T SYNONYMOUS_VARIANT,INTRON_VARIANT
709315 Likely Benign: not provided 39,673,997(-) C/T MISSENSE_VARIANT,INTRON_VARIANT
714858 Benign: not provided 39,684,705(-) G/A SYNONYMOUS_VARIANT,INTRON_VARIANT
715314 Benign: not provided 39,673,525(-) T/C MISSENSE_VARIANT,INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for PGAP3 Gene

Structural Variations from Database of Genomic Variants (DGV) for PGAP3 Gene

Variant ID Type Subtype PubMed ID
dgv40n68 CNV loss 17160897
esv3640547 CNV loss 21293372
nsv1146669 OTHER inversion 26484159
nsv457738 CNV loss 19166990
nsv516757 CNV loss 19592680
nsv528093 CNV loss 19592680
nsv574991 CNV loss 21841781

Variation tolerance for PGAP3 Gene

Residual Variation Intolerance Score: 75.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.88; 35.11% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PGAP3 Gene

Human Gene Mutation Database (HGMD)
PGAP3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PGAP3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PGAP3 Gene

Disorders for PGAP3 Gene

MalaCards: The human disease database

(10) MalaCards diseases for PGAP3 Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search PGAP3 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

PGAP3_HUMAN
  • Hyperphosphatasia with mental retardation syndrome 4 (HPMRS4) [MIM:615716]: An autosomal recessive neurologic disorder characterized by profound developmental delay, severe mental retardation, no speech, psychomotor delay, postnatal microcephaly, and elevated serum alkaline phosphatase. {ECO:0000269 PubMed:24439110}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for PGAP3

Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with PGAP3: view

No data available for Genatlas for PGAP3 Gene

Publications for PGAP3 Gene

  1. PER1 is required for GPI-phospholipase A2 activity and involved in lipid remodeling of GPI-anchored proteins. (PMID: 17021251) Fujita M … Jigami Y (Molecular biology of the cell 2006) 2 3 4
  2. MGC9753 gene, located within PPP1R1B-STARD3-ERBB2-GRB7 amplicon on human chromosome 17q12, encodes the seven-transmembrane receptor with extracellular six-cystein domain. (PMID: 12739007) Katoh M … Katoh M (International journal of oncology 2003) 3 4 23
  3. Identification of the CAB2/hCOS16 gene required for the repair of DNA double-strand breaks on a core amplified region of the 17q12 locus in breast and gastric cancers. (PMID: 12460457) Nezu M … Terada M (Japanese journal of cancer research : Gann 2002) 3 4 23
  4. Identification of a Golgi GPI-N-acetylgalactosamine transferase with tandem transmembrane regions in the catalytic domain. (PMID: 29374258) Hirata T … Kinoshita T (Nature communications 2018) 3 4
  5. Mutations in PGAP3 impair GPI-anchor maturation, causing a subtype of hyperphosphatasia with mental retardation. (PMID: 24439110) Howard MF … Krawitz PM (American journal of human genetics 2014) 3 4

ExternalLinks

View latest publications for PGAP3 gene in Mastermind

Products for PGAP3 Gene

  • Addgene plasmids for PGAP3

Sources for PGAP3 Gene