The protein encoded by this gene plays a role in the maturation of glycosylphosphatidylinositol (GPI) anchors on GPI-anchored proteins. Mutations in this gene are associated with an autosomal recessive syndrome characterized by hyperphosphatasia and intellectual disability. [provided by RefSeq, Jul 2017] See more...

Aliases for PGAP2 Gene

Aliases for PGAP2 Gene

  • Post-GPI Attachment To Proteins 2 2 3 5
  • FRAG1 2 3 4
  • Mental Retardation, Non-Syndromic, Autosomal Recessive, 21 2 3
  • Mental Retardation, Non-Syndromic, Autosomal Recessive, 17 2 3
  • Post-GPI Attachment To Proteins Factor 2 3 4
  • FGF Receptor Activating Protein 1 2 3
  • CWH43-N 2 3
  • Cell Wall Biogenesis 43 N-Terminal Homolog (S. Cerevisiae) 2
  • Cell Wall Biogenesis 43 N-Terminal Homolog 3
  • FGF Receptor-Activating Protein 1 4
  • HPMRS3 3
  • MRT17 3
  • MRT21 3
  • PGAP2 5

External Ids for PGAP2 Gene

Previous HGNC Symbols for PGAP2 Gene

  • MRT21
  • MRT17

Previous GeneCards Identifiers for PGAP2 Gene

  • GC11P003787
  • GC11P003818
  • GC11P003552

Summaries for PGAP2 Gene

Entrez Gene Summary for PGAP2 Gene

  • The protein encoded by this gene plays a role in the maturation of glycosylphosphatidylinositol (GPI) anchors on GPI-anchored proteins. Mutations in this gene are associated with an autosomal recessive syndrome characterized by hyperphosphatasia and intellectual disability. [provided by RefSeq, Jul 2017]

GeneCards Summary for PGAP2 Gene

PGAP2 (Post-GPI Attachment To Proteins 2) is a Protein Coding gene. Diseases associated with PGAP2 include Hyperphosphatasia With Mental Retardation Syndrome 3 and Hyperphosphatasia-Intellectual Disability Syndrome. Gene Ontology (GO) annotations related to this gene include protein transporter activity.

UniProtKB/Swiss-Prot Summary for PGAP2 Gene

  • Involved in the lipid remodeling steps of GPI-anchor maturation. Required for stable expression of GPI-anchored proteins at the cell surface.

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PGAP2 Gene

Genomics for PGAP2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PGAP2 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
GH11J003795 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 600.7 -0.5 -523 4 RNF2 CEBPG SP1 CREB1 GATAD2A HNRNPL ATF7 PRDM10 REST ZNF629 PGAP2 NUP98 TRIM68 ART5 piR-32214-073 CHRNA10
GH11J003807 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 605.9 +11.0 11022 2.6 GATAD2A CTCF PRDM10 LEF1 IKZF1 KDM1A ZNF692 RCOR2 JUND DDX20 PGAP2 lnc-NUP98-2 NUP98 RHOG
GH11J003818 Enhancer 0.7 Ensembl ENCODE 7 +19.2 19224 1.9 TEAD4 KDM1A FOXA1 HDAC2 BCOR ADNP ZMYM3 RNF2 SP1 ZNF148 RHOG RNU7-50P PGAP2 lnc-RHOG-1 lnc-NUP98-2 NUP98
GH11J003801 Enhancer 0.6 Ensembl ENCODE 7.1 +4.6 4555 1 IKZF1 ZBTB33 NR3C1 PGAP2 NUP98 lnc-NUP98-2 RHOG
GH11J003803 Enhancer 0.3 Ensembl ENCODE 5.8 +6.4 6380 1 PGAP2 NUP98 lnc-NUP98-2 RHOG
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PGAP2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PGAP2

Genomic Locations for PGAP2 Gene

Genomic Locations for PGAP2 Gene
chr11:3,797,724-3,826,371
(GRCh38/hg38)
Size:
28,648 bases
Orientation:
Plus strand
chr11:3,818,954-3,847,601
(GRCh37/hg19)
Size:
28,648 bases
Orientation:
Plus strand

Genomic View for PGAP2 Gene

Genes around PGAP2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PGAP2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PGAP2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PGAP2 Gene

Proteins for PGAP2 Gene

  • Protein details for PGAP2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UHJ9-PGAP2_HUMAN
    Recommended name:
    Post-GPI attachment to proteins factor 2
    Protein Accession:
    Q9UHJ9
    Secondary Accessions:
    • E9PJG5
    • H7BXL9
    • Q6UC77
    • Q96G66
    • Q9UF01
    • Q9Y4N1

    Protein attributes for PGAP2 Gene

    Size:
    254 amino acids
    Molecular mass:
    29400 Da
    Quaternary structure:
    • Interacts with PGAP2IP.
    Miscellaneous:
    • [Isoform 1]: This isoform is predicted to contain an additional transmembrane domain at position 85-105. If this domain exists, the topology of the protein would be modified, possibly challenging the GPI-anchor remodeling function of the protein.

    Alternative splice isoforms for PGAP2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PGAP2 Gene

Post-translational modifications for PGAP2 Gene

No Post-translational modifications

No data available for DME Specific Peptides for PGAP2 Gene

Domains & Families for PGAP2 Gene

Gene Families for PGAP2 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Potential drug targets
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Transporters

Protein Domains for PGAP2 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PGAP2 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ54959 (B7Z2X5_HUMAN)
  • FGF receptor-activating protein 1 (PGAP2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9UHJ9

UniProtKB/Swiss-Prot:

PGAP2_HUMAN :
  • Belongs to the PGAP2 family.
Family:
  • Belongs to the PGAP2 family.
genes like me logo Genes that share domains with PGAP2: view

Function for PGAP2 Gene

Molecular function for PGAP2 Gene

UniProtKB/Swiss-Prot Function:
Involved in the lipid remodeling steps of GPI-anchor maturation. Required for stable expression of GPI-anchored proteins at the cell surface.

Gene Ontology (GO) - Molecular Function for PGAP2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with PGAP2: view
genes like me logo Genes that share phenotypes with PGAP2: view

Human Phenotype Ontology for PGAP2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

miRNA for PGAP2 Gene

miRTarBase miRNAs that target PGAP2

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PGAP2

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Animal Models , Transcription Factor Targets and HOMER Transcription for PGAP2 Gene

Localization for PGAP2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PGAP2 Gene

Golgi apparatus membrane. Multi-pass membrane protein. Endoplasmic reticulum membrane. Multi-pass membrane protein.

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 PGAP2 gene
Compartment Confidence
plasma membrane 4
endoplasmic reticulum 4
golgi apparatus 4
cytoskeleton 2
extracellular 1
mitochondrion 1
peroxisome 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PGAP2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IEA,ISS --
GO:0005783 endoplasmic reticulum IEA --
GO:0005789 endoplasmic reticulum membrane IBA,ISS --
GO:0005794 Golgi apparatus IEA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with PGAP2: view

Pathways & Interactions for PGAP2 Gene

PathCards logo

SuperPathways for PGAP2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PGAP2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006506 GPI anchor biosynthetic process IBA,ISS --
genes like me logo Genes that share ontologies with PGAP2: view

No data available for Pathways by source and SIGNOR curated interactions for PGAP2 Gene

Drugs & Compounds for PGAP2 Gene

No Compound Related Data Available

Transcripts for PGAP2 Gene

mRNA/cDNA for PGAP2 Gene

20 REFSEQ mRNAs :
37 NCBI additional mRNA sequence :
37 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 PGAP2

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PGAP2 Gene

ExUns: 1 ^ 2a · 2b · 2c · 2d · 2e ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b · 8c ^ 9a · 9b · 9c · 9d · 9e · 9f · 9g ^ 10 ^ 11a · 11b ·
SP1: - - - - - - - - - -
SP2: - - - - - - - - - - -
SP3: - - - - - - - - - - - - - -
SP4: - - - - - - - - - - -
SP5: - - - - - - - - - - - - -
SP6: - - - - - - - - - - - - -
SP7: - - - - - - - - - - - -
SP8: - - - - -
SP9: - - - - - - - - - - -
SP10: - - - - - - - - - - - -
SP11: - - - - - - - - - -
SP12: - - - - - -
SP13: - - - -
SP14: - - -
SP15: - - - - - - - - - - -
SP16: - - - - - - - - -
SP17: - - - - - - -
SP18: - - - - - - - - - - - - -
SP19: - - - - - - - - - - - -
SP20: - - -
SP21: - - - - -
SP22: - - - - - - - - - - - -
SP23: - - - - - - - -
SP24:

ExUns: 11c ^ 12a · 12b · 12c · 12d · 12e · 12f · 12g · 12h
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:
SP16:
SP17:
SP18:
SP19:
SP20:
SP21:
SP22:
SP23:
SP24:

Relevant External Links for PGAP2 Gene

GeneLoc Exon Structure for
PGAP2

Expression for PGAP2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PGAP2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PGAP2 Gene

This gene is overexpressed in Colon muscle (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PGAP2 Gene



Protein tissue co-expression partners for PGAP2 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PGAP2

SOURCE GeneReport for Unigene cluster for PGAP2 Gene:

Hs.133968

mRNA Expression by UniProt/SwissProt for PGAP2 Gene:

Q9UHJ9-PGAP2_HUMAN
Tissue specificity: Ubiquitously expressed, with highest levels in testis and pancreas.

Evidence on tissue expression from TISSUES for PGAP2 Gene

  • Kidney(4.4)
  • Blood(2.4)
  • Skin(2.3)
  • Nervous system(2.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PGAP2 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 PGAP2: view

No data available for mRNA differential expression in normal tissues for PGAP2 Gene

Orthologs for PGAP2 Gene

This gene was present in the common ancestor of animals.

Orthologs for PGAP2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia PGAP2 30 31
  • 99.37 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia PGAP2 30 31
  • 94.17 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Pgap2 31
  • 94 (a)
OneToOne
Cow
(Bos Taurus)
Mammalia PGAP2 30 31
  • 88.58 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia PGAP2 31
  • 82 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia PGAP2 31
  • 70 (a)
OneToOne
Chicken
(Gallus gallus)
Aves LOC100859632 30
  • 72.18 (n)
PGAP2 31
  • 61 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia PGAP2 31
  • 53 (a)
OneToOne
Zebrafish
(Danio rerio)
Actinopterygii pgap2 30 31
  • 57.52 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta CG3876 30 31
  • 56.29 (n)
OneToMany
CG7990 31
  • 26 (a)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007869 30
  • 53.95 (n)
Worm
(Caenorhabditis elegans)
Secernentea tag-189 30 31
  • 45.66 (n)
OneToOne
Species where no ortholog for PGAP2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • 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)
  • Rat (Rattus norvegicus)
  • Rice (Oryza sativa)
  • 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)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)

Evolution for PGAP2 Gene

ENSEMBL:
Gene Tree for PGAP2 (if available)
TreeFam:
Gene Tree for PGAP2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PGAP2: view image

Paralogs for PGAP2 Gene

Pseudogenes.org Pseudogenes for PGAP2 Gene

genes like me logo Genes that share paralogs with PGAP2: view

No data available for Paralogs for PGAP2 Gene

Variants for PGAP2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PGAP2 Gene

SNP ID Clinical significance and condition Chr 11 pos Variation AA Info Type
694699 Pathogenic: Hyperphosphatasia with mental retardation syndrome 3 3,811,261(+) T/G INITIATIOR_CODON_VARIANT,MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,FIVE_PRIME_UTR_VARIANT,INTRON_VARIANT
714153 Likely Benign: not provided 3,824,069(+) G/A MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,INTRON_VARIANT
723080 Likely Benign: not provided 3,811,409(+) G/T MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT,FIVE_PRIME_UTR_VARIANT,INTRON_VARIANT
724055 Likely Benign: not provided 3,824,274(+) C/T MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
725983 Likely Benign: not provided 3,824,050(+) G/A MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT,INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for PGAP2 Gene

Structural Variations from Database of Genomic Variants (DGV) for PGAP2 Gene

Variant ID Type Subtype PubMed ID
dgv190n67 CNV loss 20364138
esv3353687 CNV insertion 20981092

Variation tolerance for PGAP2 Gene

Residual Variation Intolerance Score: 65.6% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PGAP2 Gene

Human Gene Mutation Database (HGMD)
PGAP2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PGAP2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PGAP2 Gene

Disorders for PGAP2 Gene

MalaCards: The human disease database

(16) MalaCards diseases for PGAP2 Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search PGAP2 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

PGAP2_HUMAN
  • Hyperphosphatasia with mental retardation syndrome 3 (HPMRS3) [MIM:614207]: An autosomal recessive disorder usually characterized by mental retardation, hypotonia with very poor motor development, poor speech, and increased serum alkaline phosphatase. {ECO:0000269 PubMed:23561846, ECO:0000269 PubMed:23561847}. Note=The disease is caused by mutations affecting the gene represented in this entry.
genes like me logo Genes that share disorders with PGAP2: view

No data available for Genatlas for PGAP2 Gene

Publications for PGAP2 Gene

  1. Hypomorphic mutations in PGAP2, encoding a GPI-anchor-remodeling protein, cause autosomal-recessive intellectual disability. (PMID: 23561846) Hansen L … Abou Jamra R (American journal of human genetics 2013) 2 3 4
  2. Human FRAG1 encodes a novel membrane-spanning protein that localizes to chromosome 11p15.5, a region of frequent loss of heterozygosity in cancer. (PMID: 10585768) Lorenzi MV … Miki T (Genomics 1999) 2 3 4
  3. 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
  4. PGAP2 mutations, affecting the GPI-anchor-synthesis pathway, cause hyperphosphatasia with mental retardation syndrome. (PMID: 23561847) Krawitz PM … Horn D (American journal of human genetics 2013) 3 4
  5. PGAP2 is essential for correct processing and stable expression of GPI-anchored proteins. (PMID: 16407401) Tashima Y … Maeda Y (Molecular biology of the cell 2006) 2 3

Products for PGAP2 Gene

Sources for PGAP2 Gene