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Aliases for PGAP1 Gene

Aliases for PGAP1 Gene

  • Post-GPI Attachment To Proteins 1 2 3 5
  • Post-GPI Attachment To Proteins Factor 1 3 4
  • GPI Inositol-Deacylase 2 3
  • EC 3.1.-.- 4
  • ISPD3024 3
  • HPGAP1 4
  • MRT42 3
  • SPG67 3
  • Bst1 3

External Ids for PGAP1 Gene

Previous GeneCards Identifiers for PGAP1 Gene

  • GC02M197914
  • GC02M197525
  • GC02M197405
  • GC02M197697
  • GC02M189550

Summaries for PGAP1 Gene

Entrez Gene Summary for PGAP1 Gene

  • The protein encoded by this gene functions early in the glycosylphosphatidylinositol (GPI) biosynthetic pathway, catalyzing the inositol deacylation of GPI. The encoded protein is required for the production of GPI that can attach to proteins, and this may be an important factor in the transport of GPI-anchored proteins from the endoplasmic reticulum to the Golgi. Defects in this gene are a cause an autosomal recessive form of cognitive impairment. [provided by RefSeq, Jul 2017]

GeneCards Summary for PGAP1 Gene

PGAP1 (Post-GPI Attachment To Proteins 1) is a Protein Coding gene. Diseases associated with PGAP1 include Mental Retardation, Autosomal Recessive 42 and Autosomal Recessive Spastic Paraplegia Type 67. Among its related pathways are Metabolism of proteins and Glycosylphosphatidylinositol (GPI)-anchor biosynthesis. Gene Ontology (GO) annotations related to this gene include hydrolase activity, acting on ester bonds and phosphoric ester hydrolase activity.

UniProtKB/Swiss-Prot for PGAP1 Gene

  • Involved in inositol deacylation of GPI-anchored proteins. GPI inositol deacylation may important for efficient transport of GPI-anchored proteins from the endoplasmic reticulum to the Golgi (By similarity).

Additional gene information for PGAP1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PGAP1 Gene

Genomics for PGAP1 Gene

GeneHancer (GH) Regulatory Elements for PGAP1 Gene

Promoters and enhancers for PGAP1 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
GH02I196924 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 550.8 +1.3 1319 3.8 HDGF PKNOX1 FOXA2 SMAD1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF213 PGAP1 GTF3C3 SF3B1 NPM1P46 LOC101927482 C2orf66 GC02P196852
GH02I196986 Enhancer 1.3 Ensembl ENCODE dbSUPER 11.1 -60.3 -60312 2.3 INSM2 FEZF1 BATF RFX5 ZNF335 ZNF366 RCOR1 ETV6 FOS RUNX3 GC02M196986 ANKRD44 PGAP1 GC02M196966
GH02I196983 Enhancer 0.9 Ensembl dbSUPER 11.2 -56.2 -56205 0.4 FOXA2 MAX CEBPG RAD21 YY1 POLR2A RXRA CEBPB REST EP300 PGAP1 GC02M196986 GC02M196966 ANKRD44
GH02I197012 Enhancer 0.8 ENCODE dbSUPER 10.3 -84.4 -84416 0.2 SMARCA5 ELF3 GATAD2A CTCF PKNOX1 ZNF654 RAD21 YY1 ZNF143 SMC3 PGAP1 ANKRD44 HNRNPA3P15 GC02M196986
GH02I197005 Enhancer 0.7 ENCODE 9.8 -78.0 -78025 0.6 RNF2 RXRA SAP130 L3MBTL2 HLF MAX PPARG DNMT3B YY1 HNF1A ANKRD44 PGAP1 HNRNPA3P15 GC02M196986
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PGAP1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PGAP1 gene promoter:

Genomic Locations for PGAP1 Gene

Genomic Locations for PGAP1 Gene
chr2:196,833,004-196,927,796
(GRCh38/hg38)
Size:
94,793 bases
Orientation:
Minus strand
chr2:197,697,728-197,792,520
(GRCh37/hg19)

Genomic View for PGAP1 Gene

Genes around PGAP1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PGAP1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PGAP1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PGAP1 Gene

Proteins for PGAP1 Gene

  • Protein details for PGAP1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q75T13-PGAP1_HUMAN
    Recommended name:
    GPI inositol-deacylase
    Protein Accession:
    Q75T13
    Secondary Accessions:
    • Q4G0R8
    • Q4ZG47
    • Q53SM0
    • Q6AW92
    • Q6UWV4
    • Q9HA24

    Protein attributes for PGAP1 Gene

    Size:
    922 amino acids
    Molecular mass:
    105383 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAQ88987.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=BC040517; Type=Frameshift; Positions=333; Evidence={ECO:0000305};

    Alternative splice isoforms for PGAP1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PGAP1 Gene

Post-translational modifications for PGAP1 Gene

  • Glycosylation at isoforms=2, 3, 4363, isoforms=2, 3, 4402, and Asn558

No data available for DME Specific Peptides for PGAP1 Gene

Domains & Families for PGAP1 Gene

Gene Families for PGAP1 Gene

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

Protein Domains for PGAP1 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for PGAP1 Gene

Graphical View of Domain Structure for InterPro Entry

Q75T13

UniProtKB/Swiss-Prot:

PGAP1_HUMAN :
  • Belongs to the GPI inositol-deacylase family.
Family:
  • Belongs to the GPI inositol-deacylase family.
genes like me logo Genes that share domains with PGAP1: view

Function for PGAP1 Gene

Molecular function for PGAP1 Gene

UniProtKB/Swiss-Prot Function:
Involved in inositol deacylation of GPI-anchored proteins. GPI inositol deacylation may important for efficient transport of GPI-anchored proteins from the endoplasmic reticulum to the Golgi (By similarity).

Enzyme Numbers (IUBMB) for PGAP1 Gene

Phenotypes From GWAS Catalog for PGAP1 Gene

Gene Ontology (GO) - Molecular Function for PGAP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004518 nuclease activity ISS --
GO:0016787 hydrolase activity IEA --
GO:0016788 hydrolase activity, acting on ester bonds IEA,TAS --
GO:0042578 phosphoric ester hydrolase activity ISS --
genes like me logo Genes that share ontologies with PGAP1: view
genes like me logo Genes that share phenotypes with PGAP1: view

Human Phenotype Ontology for PGAP1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PGAP1 Gene

MGI Knock Outs for PGAP1:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Transcription Factor Targets and HOMER Transcription for PGAP1 Gene

Localization for PGAP1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PGAP1 Gene

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 PGAP1 gene
Compartment Confidence
endoplasmic reticulum 5
plasma membrane 3
peroxisome 1

Gene Ontology (GO) - Cellular Components for PGAP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum ISS --
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with PGAP1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PGAP1 Gene

Pathways & Interactions for PGAP1 Gene

genes like me logo Genes that share pathways with PGAP1: view

Interacting Proteins for PGAP1 Gene

Gene Ontology (GO) - Biological Process for PGAP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006506 GPI anchor biosynthetic process IEA --
GO:0006810 transport IEA --
GO:0007605 sensory perception of sound IEA --
GO:0009880 embryonic pattern specification IEA --
GO:0009948 anterior/posterior axis specification IEA --
genes like me logo Genes that share ontologies with PGAP1: view

No data available for SIGNOR curated interactions for PGAP1 Gene

Drugs & Compounds for PGAP1 Gene

No Compound Related Data Available

Transcripts for PGAP1 Gene

Unigene Clusters for PGAP1 Gene

Post-GPI attachment to proteins 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for PGAP1 Gene

No ASD Table

Relevant External Links for PGAP1 Gene

GeneLoc Exon Structure for
PGAP1
ECgene alternative splicing isoforms for
PGAP1

Expression for PGAP1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PGAP1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PGAP1 Gene

This gene is overexpressed in Stomach (68.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PGAP1 Gene



Protein tissue co-expression partners for PGAP1 Gene

NURSA nuclear receptor signaling pathways regulating expression of PGAP1 Gene:

PGAP1

SOURCE GeneReport for Unigene cluster for PGAP1 Gene:

Hs.229988

Evidence on tissue expression from TISSUES for PGAP1 Gene

  • Nervous system(3.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PGAP1 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • integumentary
  • nervous
  • skeletal muscle
Organs:
Head and neck:
  • brain
  • ear
  • head
  • outer ear
General:
  • peripheral nerve
  • peripheral nervous system
  • spinal cord
genes like me logo Genes that share expression patterns with PGAP1: view

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for PGAP1 Gene

Orthologs for PGAP1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for PGAP1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PGAP1 33 34
  • 99.49 (n)
cow
(Bos Taurus)
Mammalia PGAP1 33 34
  • 93.31 (n)
dog
(Canis familiaris)
Mammalia PGAP1 33 34
  • 92.7 (n)
mouse
(Mus musculus)
Mammalia Pgap1 33 16 34
  • 88.83 (n)
rat
(Rattus norvegicus)
Mammalia Pgap1 33
  • 86.88 (n)
oppossum
(Monodelphis domestica)
Mammalia PGAP1 34
  • 69 (a)
OneToOne
chicken
(Gallus gallus)
Aves PGAP1 33 34
  • 70.01 (n)
lizard
(Anolis carolinensis)
Reptilia PGAP1 34
  • 61 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC101732527 33
  • 74.15 (n)
zebrafish
(Danio rerio)
Actinopterygii pgap1 33 34
  • 51.93 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG3160 33 34
  • 40.49 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011299 33
  • 40.34 (n)
worm
(Caenorhabditis elegans)
Secernentea T19B10.8 34
  • 20 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes BST1 34 36
  • 18 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 42 (a)
OneToMany
-- 34
  • 30 (a)
OneToMany
Species where no ortholog for PGAP1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • 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)
  • 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)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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)
  • wheat (Triticum aestivum)

Evolution for PGAP1 Gene

ENSEMBL:
Gene Tree for PGAP1 (if available)
TreeFam:
Gene Tree for PGAP1 (if available)

Paralogs for PGAP1 Gene

No data available for Paralogs for PGAP1 Gene

Variants for PGAP1 Gene

Sequence variations from dbSNP and Humsavar for PGAP1 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs138525017 likely-benign, benign, not specified, Mental retardation, autosomal recessive 42 196,897,152(-) A/G 5_prime_UTR_variant, coding_sequence_variant, non_coding_transcript_variant, synonymous_variant
rs143038880 pathogenic, Mental retardation, autosomal recessive 42 196,875,776(-) G/A coding_sequence_variant, non_coding_transcript_variant, stop_gained
rs149815494 benign, Mental retardation, autosomal recessive 42 196,847,146(-) G/A coding_sequence_variant, genic_downstream_transcript_variant, non_coding_transcript_variant, synonymous_variant
rs150893861 likely-benign, Mental retardation, autosomal recessive 42 196,848,023(-) A/G coding_sequence_variant, genic_downstream_transcript_variant, missense_variant, non_coding_transcript_variant
rs201002323 uncertain-significance, Mental retardation, autosomal recessive 42 196,873,021(-) T/C coding_sequence_variant, genic_downstream_transcript_variant, missense_variant, non_coding_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for PGAP1 Gene

Variant ID Type Subtype PubMed ID
esv3575323 CNV gain 25503493
esv3593895 CNV loss 21293372
nsv584153 CNV loss 21841781

Variation tolerance for PGAP1 Gene

Residual Variation Intolerance Score: 4.64% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.53; 29.73% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PGAP1 Gene

Human Gene Mutation Database (HGMD)
PGAP1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PGAP1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PGAP1 Gene

Disorders for PGAP1 Gene

MalaCards: The human disease database

(5) MalaCards diseases for PGAP1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search PGAP1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

PGAP1_HUMAN
  • Mental retardation, autosomal recessive 42 (MRT42) [MIM:615802]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. {ECO:0000269 PubMed:24482476, ECO:0000269 PubMed:24784135}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for PGAP1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PGAP1: view

No data available for Genatlas for PGAP1 Gene

Publications for PGAP1 Gene

  1. Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. (PMID: 24482476) Novarino G … Gleeson JG (Science (New York, N.Y.) 2014) 2 3 4 58
  2. Inositol deacylation of glycosylphosphatidylinositol-anchored proteins is mediated by mammalian PGAP1 and yeast Bst1p. (PMID: 14734546) Tanaka S … Kinoshita T (The Journal of biological chemistry 2004) 2 3 4 58
  3. Null mutation in PGAP1 impairing Gpi-anchor maturation in patients with intellectual disability and encephalopathy. (PMID: 24784135) Murakami Y … Jamra RA (PLoS genetics 2014) 3 4 58
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  5. PGAP1 knock-out mice show otocephaly and male infertility. (PMID: 17711852) Ueda Y … Kinoshita T (The Journal of biological chemistry 2007) 2 3 58

Products for PGAP1 Gene

Sources for PGAP1 Gene

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