The protein encoded by this gene is a member of the LAR protein-tyrosine phosphatase-interacting protein (liprin) family. Liprins interact with members of LAR family of transmembrane protein tyrosine phosphatases, which are known to be important for axon guidance and mammary gland development. Liprin family protein has been shown to localize phosphatase LAR to cell focal adhesi... See more...

Aliases for PPFIA3 Gene

Aliases for PPFIA3 Gene

  • PTPRF Interacting Protein Alpha 3 2 3 5
  • Protein Tyrosine Phosphatase, Receptor Type, F Polypeptide (PTPRF), Interacting Protein (Liprin), Alpha 3 2 3
  • Protein Tyrosine Phosphatase Receptor Type F Polypeptide-Interacting Protein Alpha-3 3 4
  • Protein Tyrosine Phosphatase, Receptor Type, F Polypeptide, Alpha 3 2 3
  • Liprin-Alpha-3 3 4
  • KIAA0654 2 4
  • Liprin 2 3
  • LPNA3 2 3
  • PTPRF-Interacting Protein Alpha-3 4
  • Liprin-Alpha 3 2
  • MGC126567 2
  • MGC126569 2
  • PPFIA3 5

External Ids for PPFIA3 Gene

Previous GeneCards Identifiers for PPFIA3 Gene

  • GC19P050280
  • GC19P049990
  • GC19P054299
  • GC19P054314
  • GC19P049622
  • GC19P045998

Summaries for PPFIA3 Gene

Entrez Gene Summary for PPFIA3 Gene

  • The protein encoded by this gene is a member of the LAR protein-tyrosine phosphatase-interacting protein (liprin) family. Liprins interact with members of LAR family of transmembrane protein tyrosine phosphatases, which are known to be important for axon guidance and mammary gland development. Liprin family protein has been shown to localize phosphatase LAR to cell focal adhesions and may be involved in the molecular organization of presynaptic active zones. [provided by RefSeq, Jul 2008]

GeneCards Summary for PPFIA3 Gene

PPFIA3 (PTPRF Interacting Protein Alpha 3) is a Protein Coding gene. Diseases associated with PPFIA3 include Mental Retardation And Microcephaly With Pontine And Cerebellar Hypoplasia and Non-Syndromic X-Linked Intellectual Disability. Among its related pathways are Neurotransmitter Release Cycle and Transmission across Chemical Synapses. An important paralog of this gene is PPFIA1.

UniProtKB/Swiss-Prot Summary for PPFIA3 Gene

  • May regulate the disassembly of focal adhesions. May localize receptor-like tyrosine phosphatases type 2A at specific sites on the plasma membrane, possibly regulating their interaction with the extracellular environment and their association with substrates.

Additional gene information for PPFIA3 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PPFIA3 Gene

Genomics for PPFIA3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PPFIA3 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 PPFIA3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PPFIA3

Top Transcription factor binding sites by QIAGEN in the PPFIA3 gene promoter:
  • GATA-3
  • NF-1
  • NF-1/L
  • NF-kappaB
  • NF-kappaB1
  • Pax-5
  • PPAR-alpha
  • PPAR-gamma1
  • PPAR-gamma2
  • RelA

Genomic Locations for PPFIA3 Gene

Genomic Locations for PPFIA3 Gene
chr19:49,119,389-49,151,030
(GRCh38/hg38)
Size:
31,642 bases
Orientation:
Plus strand
chr19:49,622,646-49,654,283
(GRCh37/hg19)
Size:
31,638 bases
Orientation:
Plus strand

Genomic View for PPFIA3 Gene

Genes around PPFIA3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PPFIA3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PPFIA3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PPFIA3 Gene

Proteins for PPFIA3 Gene

  • Protein details for PPFIA3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O75145-LIPA3_HUMAN
    Recommended name:
    Liprin-alpha-3
    Protein Accession:
    O75145
    Secondary Accessions:
    • A8K142
    • Q3MJA0
    • Q9H8B5
    • Q9UEW4

    Protein attributes for PPFIA3 Gene

    Size:
    1194 amino acids
    Molecular mass:
    133496 Da
    Quaternary structure:
    • Forms homodimers and heterodimers with liprins-alpha and liprins-beta (PubMed:9624153). Interacts with the second PTPase domain of PTPRD, PTPRF and PTPRS (PubMed:9624153). Binds RIMS1, RIMS2, RIMS3 and RIMS4 (By similarity).
    SequenceCaution:
    • Sequence=BAA31629.2; Type=Erroneous initiation; Evidence={ECO:0000305};
    Miscellaneous:
    • [Isoform 2]: May be due to exon skipping.

    Alternative splice isoforms for PPFIA3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PPFIA3 Gene

Post-translational modifications for PPFIA3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PPFIA3 Gene

No data available for DME Specific Peptides for PPFIA3 Gene

Domains & Families for PPFIA3 Gene

Gene Families for PPFIA3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for PPFIA3 Gene

InterPro:
Blocks:
  • Sterile alpha motif SAM
  • Sterile alpha motif homology 2
ProtoNet:

Suggested Antigen Peptide Sequences for PPFIA3 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ60233, highly similar to Liprin-alpha-3 (B4DEU8_HUMAN)
  • Protein tyrosine phosphatase receptor type f polypeptide-interacting protein alpha-3 (LIPA3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O75145

UniProtKB/Swiss-Prot:

LIPA3_HUMAN :
  • The N-terminal coiled coil regions mediate homodimerization preferentially and heterodimerization type alpha/alpha. The C-terminal, non-coiled coil regions mediate heterodimerization type alpha/beta and interaction with PTPRD, PTPRF and PTPRS.
  • Belongs to the liprin family. Liprin-alpha subfamily.
Domain:
  • The N-terminal coiled coil regions mediate homodimerization preferentially and heterodimerization type alpha/alpha. The C-terminal, non-coiled coil regions mediate heterodimerization type alpha/beta and interaction with PTPRD, PTPRF and PTPRS.
Family:
  • Belongs to the liprin family. Liprin-alpha subfamily.
genes like me logo Genes that share domains with PPFIA3: view

Function for PPFIA3 Gene

Molecular function for PPFIA3 Gene

UniProtKB/Swiss-Prot Function:
May regulate the disassembly of focal adhesions. May localize receptor-like tyrosine phosphatases type 2A at specific sites on the plasma membrane, possibly regulating their interaction with the extracellular environment and their association with substrates.
GENATLAS Biochemistry:
protein tyrosine phosphatase, receptor type,f polypeptide (PTPRF),interacting protein (liprin),alpha 3,expressed in brain,>100kDa,related to LAR-interacting protein LIP1B

Phenotypes From GWAS Catalog for PPFIA3 Gene

Gene Ontology (GO) - Molecular Function for PPFIA3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA,IPI 12923177
genes like me logo Genes that share ontologies with PPFIA3: view
genes like me logo Genes that share phenotypes with PPFIA3: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PPFIA3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PPFIA3 Gene

Localization for PPFIA3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PPFIA3 Gene

Cytoplasm. Cytoplasmic vesicle, secretory vesicle, acrosome. Note=Also detected in epididymosome. {ECO:0000250 UniProtKB:Q91Z79}.

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 PPFIA3 gene
Compartment Confidence
extracellular 4
cytosol 4
nucleus 3
plasma membrane 2
cytoskeleton 2
mitochondrion 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli fibrillar center (1)
  • Vesicles (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PPFIA3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001669 acrosomal vesicle IEA,IDA 23124857
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
GO:0031410 cytoplasmic vesicle IEA --
GO:0045202 synapse IEA --
genes like me logo Genes that share ontologies with PPFIA3: view

Pathways & Interactions for PPFIA3 Gene

genes like me logo Genes that share pathways with PPFIA3: view

Gene Ontology (GO) - Biological Process for PPFIA3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007269 neurotransmitter secretion IEA,TAS --
GO:0014047 glutamate secretion TAS --
GO:0016079 synaptic vesicle exocytosis IEA --
GO:0016081 synaptic vesicle docking IEA --
GO:0048172 regulation of short-term neuronal synaptic plasticity ISS --
genes like me logo Genes that share ontologies with PPFIA3: view

No data available for SIGNOR curated interactions for PPFIA3 Gene

Drugs & Compounds for PPFIA3 Gene

No Compound Related Data Available

Transcripts for PPFIA3 Gene

mRNA/cDNA for PPFIA3 Gene

1 REFSEQ mRNAs :
16 NCBI additional mRNA sequence :
13 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 PPFIA3

Alternative Splicing Database (ASD) splice patterns (SP) for PPFIA3 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b · 4c ^ 5a · 5b · 5c · 5d ^ 6a · 6b ^ 7 ^ 8a · 8b · 8c ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^ 16 ^
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8: - -
SP9: -
SP10:
SP11: -
SP12: - - -
SP13:
SP14: - -
SP15:

ExUns: 17a · 17b ^ 18a · 18b ^ 19 ^ 20 ^ 21 ^ 22 ^ 23a · 23b ^ 24a · 24b ^ 25 ^ 26 ^ 27 ^ 28a · 28b ^ 29a · 29b · 29c
SP1: - -
SP2: - - -
SP3: - -
SP4: - -
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:

Relevant External Links for PPFIA3 Gene

GeneLoc Exon Structure for
PPFIA3

Expression for PPFIA3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PPFIA3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PPFIA3 Gene

This gene is overexpressed in Brain - Cortex (x4.9), Pituitary (x4.2), and Brain - Frontal Cortex (BA9) (x4.0).

Protein differential expression in normal tissues from HIPED for PPFIA3 Gene

This gene is overexpressed in Brain (28.4), Frontal cortex (21.3), and Fetal Brain (8.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PPFIA3 Gene



Protein tissue co-expression partners for PPFIA3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PPFIA3

SOURCE GeneReport for Unigene cluster for PPFIA3 Gene:

Hs.413748

mRNA Expression by UniProt/SwissProt for PPFIA3 Gene:

O75145-LIPA3_HUMAN
Tissue specificity: Predominantly expressed in brain (PubMed:9624153). Also detected in sperm (at protein level) (PubMed:23124857).

Evidence on tissue expression from TISSUES for PPFIA3 Gene

  • Nervous system(4.8)
  • Muscle(4.3)
  • Skin(2.4)
genes like me logo Genes that share expression patterns with PPFIA3: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for PPFIA3 Gene

Orthologs for PPFIA3 Gene

This gene was present in the common ancestor of animals.

Orthologs for PPFIA3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia PPFIA3 30 31
  • 96.43 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia PPFIA3 30 31
  • 92.77 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia PPFIA3 30 31
  • 92.45 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Ppfia3 30 17 31
  • 89.17 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Ppfia3 30
  • 88.62 (n)
Oppossum
(Monodelphis domestica)
Mammalia PPFIA3 31
  • 80 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia PPFIA3 31
  • 77 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia PPFIA3 31
  • 83 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia ppfia3 30
  • 72.08 (n)
Zebrafish
(Danio rerio)
Actinopterygii ppfia3 30 31
  • 70.65 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta Liprin-alpha 31
  • 49 (a)
OneToMany
CG11206 32
  • 38 (a)
Worm
(Caenorhabditis elegans)
Secernentea syd-2 31 32
  • 45 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 47 (a)
OneToMany
Species where no ortholog for PPFIA3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • Chicken (Gallus gallus)
  • 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)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • 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 PPFIA3 Gene

ENSEMBL:
Gene Tree for PPFIA3 (if available)
TreeFam:
Gene Tree for PPFIA3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PPFIA3: view image

Paralogs for PPFIA3 Gene

Paralogs for PPFIA3 Gene

(4) SIMAP similar genes for PPFIA3 Gene using alignment to 3 proteins:

  • LIPA3_HUMAN
  • R4GN36_HUMAN
  • R4GNF1_HUMAN
genes like me logo Genes that share paralogs with PPFIA3: view

Variants for PPFIA3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PPFIA3 Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
916246 Likely Benign: not provided 49,148,154(+) A/G NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
rs2303053 - p.Ala563Ser

Additional dbSNP identifiers (rs#s) for PPFIA3 Gene

Structural Variations from Database of Genomic Variants (DGV) for PPFIA3 Gene

Variant ID Type Subtype PubMed ID
dgv3619n100 CNV gain 25217958
dgv3620n100 CNV gain 25217958
dgv3621n100 CNV gain 25217958
dgv667e214 CNV gain 21293372
esv2760526 CNV gain 21179565
esv3644616 CNV gain 21293372
nsv1060108 CNV gain 25217958
nsv470149 CNV loss 18288195
nsv524235 CNV gain 19592680
nsv819445 CNV gain 19587683
nsv833857 CNV loss 17160897
nsv833859 CNV loss 17160897
nsv9739 CNV gain+loss 18304495

Variation tolerance for PPFIA3 Gene

Residual Variation Intolerance Score: 2.51% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.73; 91.54% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PPFIA3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PPFIA3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PPFIA3 Gene

Disorders for PPFIA3 Gene

MalaCards: The human disease database

(2) MalaCards diseases for PPFIA3 Gene - From: DISEASES

- elite association - COSMIC cancer census association via MalaCards
genes like me logo Genes that share disorders with PPFIA3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PPFIA3 Gene

Publications for PPFIA3 Gene

  1. Prediction of the coding sequences of unidentified human genes. X. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. (PMID: 9734811) Ishikawa K … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1998) 2 3 4
  2. Liprins, a family of LAR transmembrane protein-tyrosine phosphatase-interacting proteins. (PMID: 9624153) Serra-Pagès C … Streuli M (The Journal of biological chemistry 1998) 2 3 4
  3. Liprin α3: a putative estrogen regulated acrosomal protein. (PMID: 23124857) Joshi CS … Khole VV (Histochemistry and cell biology 2013) 3 4
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4

Products for PPFIA3 Gene

Sources for PPFIA3 Gene