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Aliases for PGAP3 Gene

Aliases for PGAP3 Gene

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

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 3) is a Protein Coding gene. Diseases associated with PGAP3 include Hyperphosphatasia With Mental Retardation Syndrome 4 and Hyperphosphatasia-Intellectual Disability Syndrome. Gene Ontology (GO) annotations related to this gene include hydrolase activity, acting on ester bonds.

UniProtKB/Swiss-Prot 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 (Probable).

Additional gene information for PGAP3 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PGAP3 Gene

Genomics for PGAP3 Gene

GeneHancer (GH) Regulatory Elements for PGAP3 Gene

Promoters and enhancers for PGAP3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH17I039686 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 565.3 +8.6 8567 3 PKNOX1 SMAD1 FOXA2 MLX ARID4B SIN3A DMAP1 YY1 POLR2B E2F8 PGAP3 ERBB2 MED1 LOC105371762 MIEN1 GRB7 STARD3 SNORA21 MED24 GC17P039685
GH17I039694 Enhancer 1.3 Ensembl ENCODE dbSUPER 568.3 +1.0 1018 2.9 FOXA2 MLX ARID4B SIN3A DMAP1 ZNF48 ETS1 YY1 TCF12 ZNF207 PGAP3 MIEN1 GRB7 NEUROD2 LRRC3C ORMDL3 ERBB2
GH17I039698 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 17.5 -6.6 -6577 8.8 PKNOX1 FOXA2 ARID4B SIN3A DMAP1 ZBTB7B YY1 FOS SP3 SP5 ERBB2 GRB7 PGAP3 MIEN1 NEUROD2 THRA ORMDL3 GSDMB MIR4728
GH17I039658 Promoter/Enhancer 2.9 VISTA EPDnew FANTOM5 Ensembl ENCODE dbSUPER 16.1 +33.1 33107 10.4 HDGF MLX ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 SLC30A9 ZNF766 TCAP PNMT PGAP3 STARD3 CDK12 LOC105371762 STAC2 FBXL20 MSL1
GH17I039673 Enhancer 2 VISTA FANTOM5 Ensembl ENCODE dbSUPER 21 +19.1 19140 7.4 HDGF PKNOX1 FOXA2 SMAD1 ARID4B DMAP1 ZNF48 ZNF121 GLIS2 ATF7 PGAP3 STARD3 NEUROD2 RAPGEFL1 ORMDL3 ERBB2 GRB7 GSDMB PNMT GC17P039685
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PGAP3 on UCSC Golden Path with GeneCards custom track

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)

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 StructureGene Density

RefSeq DNA sequence for PGAP3 Gene

Proteins for PGAP3 Gene

  • 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
    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.
    SequenceCaution:
    • Sequence=BAC55580.1; Type=Frameshift; Positions=164, 174, 176, 197; Evidence={ECO:0000305};

    Alternative splice isoforms for PGAP3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PGAP3 Gene

Post-translational modifications for PGAP3 Gene

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
  • Predicted secreted proteins

Protein Domains for PGAP3 Gene

InterPro:
ProtoNet:

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

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 (Probable).

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

miRNA for PGAP3 Gene

miRTarBase miRNAs that target PGAP3

Inhibitory RNA Products

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 3
cytosol 2

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

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 --
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

No Compound Related Data Available

Transcripts for PGAP3 Gene

Unigene Clusters for PGAP3 Gene

Post-GPI attachment to proteins 3:
Representative Sequences:

Inhibitory RNA Products

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
ECgene alternative splicing isoforms for
PGAP3

Expression for PGAP3 Gene

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



Protein tissue co-expression partners for PGAP3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PGAP3 Gene:

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(4.6)
  • Intestine(4.2)

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 33 34
  • 99.48 (n)
cow
(Bos Taurus)
Mammalia PGAP3 33 34
  • 90.39 (n)
dog
(Canis familiaris)
Mammalia PGAP3 33 34
  • 89.13 (n)
mouse
(Mus musculus)
Mammalia Pgap3 33 16 34
  • 86.75 (n)
rat
(Rattus norvegicus)
Mammalia Perld1 33
  • 86.75 (n)
oppossum
(Monodelphis domestica)
Mammalia PGAP3 34
  • 75 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PGAP3 34
  • 67 (a)
OneToOne
chicken
(Gallus gallus)
Aves PGAP3 33 34
  • 76.19 (n)
lizard
(Anolis carolinensis)
Reptilia PGAP3 34
  • 69 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pgap3 33
  • 71.19 (n)
zebrafish
(Danio rerio)
Actinopterygii zgc:171485 33
  • 68.1 (n)
PGAP3 34
  • 67 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG3271 33 34
  • 52.04 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP005392 33
  • 51.37 (n)
worm
(Caenorhabditis elegans)
Secernentea R01B10.4 34
  • 31 (a)
OneToOne
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AFR678C 33
  • 45.64 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0C02101g 33
  • 41.61 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PER1 33 34 36
  • 40.4 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT1G16560 33
  • 45.53 (n)
rice
(Oryza sativa)
Liliopsida Os05g0220100 33
  • 47.13 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU08609 33
  • 48.76 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPAC823.07 33
  • 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 squirt (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)

Paralogs for PGAP3 Gene

No data available for Paralogs for PGAP3 Gene

Variants for PGAP3 Gene

Sequence variations from dbSNP and Humsavar for PGAP3 Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs183208638 pathogenic, Hyperphosphatasia with mental retardation syndrome 4 39,672,244(-) G/A 3_prime_UTR_variant, genic_downstream_transcript_variant
rs200598755 pathogenic, likely-pathogenic, Hyperphosphatasia with mental retardation syndrome 4, not provided 39,673,660(-) C/T intron_variant
rs202146344 pathogenic, uncertain-significance, Hyperphosphatasia with mental retardation syndrome 4, not specified 39,684,709(-) G/A 5_prime_UTR_variant, coding_sequence_variant, intron_variant, missense_variant, non_coding_transcript_variant
rs371549948 pathogenic, Hyperphosphatasia with mental retardation syndrome 4, Hyperphosphatasia with mental retardation syndrome 4 (HPMRS4) [MIM:615716] 39,684,715(-) G/A/C 5_prime_UTR_variant, coding_sequence_variant, intron_variant, missense_variant, non_coding_transcript_variant
rs587777251 pathogenic, Hyperphosphatasia with mental retardation syndrome 4, Hyperphosphatasia with mental retardation syndrome 4 (HPMRS4) [MIM:615716] 39,685,926(-) C/T 5_prime_UTR_variant, coding_sequence_variant, missense_variant, non_coding_transcript_variant

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

(4) MalaCards diseases for PGAP3 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, 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

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 58
  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 22 58
  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 22 58
  4. 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 58
  5. Fatty acid remodeling of GPI-anchored proteins is required for their raft association. (PMID: 17314402) Maeda Y … Kinoshita T (Molecular biology of the cell 2007) 2 3 58

Products for PGAP3 Gene

  • Addgene plasmids for PGAP3

Sources for PGAP3 Gene

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