Free for academic non-profit institutions. Other users need a Commercial license

Aliases for SYNJ1 Gene

Aliases for SYNJ1 Gene

  • Synaptojanin 1 2 3 5
  • Synaptic Inositol 1,4,5-Trisphosphate 5-Phosphatase 1 2 3 4
  • Inositol Polyphosphate-5-Phosphatase G 2 3
  • Phosphoinositide 5-Phosphatase 2 3
  • EC 4 63
  • Synaptic Inositol-1,4,5-Trisphosphate 5-Phosphatase 1 3
  • Synaptojanin-1, Polyphosphoinositide Phosphatase 3
  • Inositol 5-Phosphatase (Synaptojanin 1) 3
  • KIAA0910 4
  • EC 3.1.3 63
  • INPP5G 3
  • PARK20 3

External Ids for SYNJ1 Gene

Previous GeneCards Identifiers for SYNJ1 Gene

  • GC21M030580
  • GC21M030661
  • GC21M032921
  • GC21M032923
  • GC21M032922
  • GC21M033997
  • GC21M019410

Summaries for SYNJ1 Gene

Entrez Gene Summary for SYNJ1 Gene

  • This gene encodes a phosphoinositide phosphatase that regulates levels of membrane phosphatidylinositol-4,5-bisphosphate. As such, expression of this enzyme may affect synaptic transmission and membrane trafficking. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]

GeneCards Summary for SYNJ1 Gene

SYNJ1 (Synaptojanin 1) is a Protein Coding gene. Diseases associated with SYNJ1 include Parkinson Disease 20, Early-Onset and Atypical Juvenile Parkinsonism. Among its related pathways are EPH-Ephrin signaling and Inositol phosphate metabolism (REACTOME). GO annotations related to this gene include nucleic acid binding and nucleotide binding. An important paralog of this gene is INPP5J.

UniProtKB/Swiss-Prot for SYNJ1 Gene

  • Inositol 5-phosphatase which has a role in clathrin-mediated endocytosis.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SYNJ1 Gene

Genomics for SYNJ1 Gene

Regulatory Elements for SYNJ1 Gene

Enhancers for SYNJ1 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around SYNJ1 on UCSC Golden Path with GeneCards custom track

Promoters for SYNJ1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around SYNJ1 on UCSC Golden Path with GeneCards custom track

Genomic Location for SYNJ1 Gene

32,628,759 bp from pter
32,728,048 bp from pter
99,290 bases
Minus strand

Genomic View for SYNJ1 Gene

Genes around SYNJ1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SYNJ1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SYNJ1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SYNJ1 Gene

Proteins for SYNJ1 Gene

  • Protein details for SYNJ1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • O43425
    • O94984
    • Q4KMR1

    Protein attributes for SYNJ1 Gene

    1573 amino acids
    Molecular mass:
    173103 Da
    Quaternary structure:
    • Interacts with ASH/GRB2. Interacts with PACSIN1, PACSIN2 and PACSIN3 (By similarity). Binds AMPH, SH3GL1, SH3GL2 and SH3GL3. Interacts with MYO1E (via SH3 domain).
    • Sequence=BAA74933.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SYNJ1 Gene

    Alternative splice isoforms for SYNJ1 Gene


neXtProt entry for SYNJ1 Gene

Proteomics data for SYNJ1 Gene at MOPED

Post-translational modifications for SYNJ1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for SYNJ1 Gene

Gene Families for SYNJ1 Gene

Graphical View of Domain Structure for InterPro Entry



  • Binds to EPS15 (a clathrin coat-associated protein) via a C-terminal domain containing three Asn-Pro-Phe (NPF) repeats.
  • Belongs to the synaptojanin family.
  • Binds to EPS15 (a clathrin coat-associated protein) via a C-terminal domain containing three Asn-Pro-Phe (NPF) repeats.
  • The C-terminal proline-rich region mediates binding to a variety of SH3 domain-containing proteins including AMPH, SH3GL1, SH3GL2, SH3GL3 and GRB2.
  • Contains 1 RRM (RNA recognition motif) domain.
  • Contains 1 SAC domain.
  • Belongs to the synaptojanin family.
  • In the central section; belongs to the inositol 1,4,5-trisphosphate 5-phosphatase family.
genes like me logo Genes that share domains with SYNJ1: view

Function for SYNJ1 Gene

Molecular function for SYNJ1 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 4-phosphate + phosphate.
UniProtKB/Swiss-Prot Function:
Inositol 5-phosphatase which has a role in clathrin-mediated endocytosis.

Enzyme Numbers (IUBMB) for SYNJ1 Gene

Gene Ontology (GO) - Molecular Function for SYNJ1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding IEA --
GO:0004439 phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity ISS,TAS --
GO:0004445 inositol-polyphosphate 5-phosphatase activity TAS 9428629
genes like me logo Genes that share ontologies with SYNJ1: view
genes like me logo Genes that share phenotypes with SYNJ1: view

Human Phenotype Ontology for SYNJ1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SYNJ1 Gene

MGI Knock Outs for SYNJ1:

No data available for Transcription Factor Targets and HOMER Transcription for SYNJ1 Gene

Localization for SYNJ1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SYNJ1 Gene


Subcellular locations from

Jensen Localization Image for SYNJ1 Gene COMPARTMENTS Subcellular localization image for SYNJ1 gene
Compartment Confidence
cytosol 5
cytoskeleton 2
endosome 2
nucleus 2
plasma membrane 1

Gene Ontology (GO) - Cellular Components for SYNJ1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030117 membrane coat ISS --
GO:0097060 synaptic membrane ISS 9428629
genes like me logo Genes that share ontologies with SYNJ1: view

Pathways & Interactions for SYNJ1 Gene

genes like me logo Genes that share pathways with SYNJ1: view

SIGNOR curated interactions for SYNJ1 Gene

Is inactivated by:

Gene Ontology (GO) - Biological Process for SYNJ1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006644 phospholipid metabolic process TAS --
GO:0006796 phosphate-containing compound metabolic process TAS 9428629
GO:0007612 learning IMP 18591654
GO:0014015 positive regulation of gliogenesis IEA --
GO:0016191 synaptic vesicle uncoating ISS --
genes like me logo Genes that share ontologies with SYNJ1: view

Drugs & Compounds for SYNJ1 Gene

(2) Drugs for SYNJ1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(7) Additional Compounds for SYNJ1 Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • (3-Phosphatidyl)-1-D-inositol
  • 1,2-Diacyl-sn-glycero-3-phosphoinositol
  • 1-Phosphatidyl-1D-myo-inositol
  • 1-Phosphatidyl-myo-inositol
  • Phosphatidyl-1D-myo-inositol
  • NFB Orthophosphate
  • O-Phosphoric acid
  • Ortho-phosphate
  • Orthophosphate (PO43-)
  • Orthophosphate(3-)
phosphoric acid
  • Acide phosphorique (FRENCH)
  • Acido fosforico [Italian]
  • Acidum phosphoricum
  • Diphosphate tetrasodium
  • Fosforzuuroplossingen [Dutch]
  • Dihydrogen oxide
  • Steam
genes like me logo Genes that share compounds with SYNJ1: view

Transcripts for SYNJ1 Gene

Unigene Clusters for SYNJ1 Gene

Synaptojanin 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for SYNJ1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13a · 13b ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23 ^
SP1: -
SP4: -
SP7: -

ExUns: 24a · 24b ^ 25 ^ 26 ^ 27 ^ 28 ^ 29 ^ 30a · 30b ^ 31 ^ 32 ^ 33
SP1: - - -
SP2: -
SP5: -

Relevant External Links for SYNJ1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SYNJ1 Gene

mRNA expression in normal human tissues for SYNJ1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SYNJ1 Gene

This gene is overexpressed in Brain - Frontal Cortex (BA9) (x4.5) and Brain - Anterior cingulate cortex (BA24) (x4.1).

Protein differential expression in normal tissues from HIPED for SYNJ1 Gene

This gene is overexpressed in Frontal cortex (30.4), Brain (20.1), and Spinal cord (8.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for SYNJ1 Gene

SOURCE GeneReport for Unigene cluster for SYNJ1 Gene Hs.473632

mRNA Expression by UniProt/SwissProt for SYNJ1 Gene

Tissue specificity: Concentrated at clathrin-coated endocytic intermediates in nerve terminals. Isoform 1 is more enriched than isoform 2 in developing brain as well as non-neuronal cells. Isoform 2 is very abundant in nerve terminals.
genes like me logo Genes that share expression patterns with SYNJ1: view

Protein tissue co-expression partners for SYNJ1 Gene

- Elite partner

Primer Products

Orthologs for SYNJ1 Gene

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

Orthologs for SYNJ1 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia SYNJ1 35
  • 90.35 (n)
  • 94.46 (a)
SYNJ1 36
  • 94 (a)
(Canis familiaris)
Mammalia SYNJ1 35
  • 91.84 (n)
  • 93.12 (a)
SYNJ1 36
  • 94 (a)
(Mus musculus)
Mammalia Synj1 35
  • 86.97 (n)
  • 90.26 (a)
Synj1 16
Synj1 36
  • 90 (a)
(Pan troglodytes)
Mammalia SYNJ1 35
  • 99.52 (n)
  • 99.69 (a)
SYNJ1 36
  • 100 (a)
(Rattus norvegicus)
Mammalia Synj1 35
  • 88.34 (n)
  • 94.17 (a)
(Monodelphis domestica)
Mammalia SYNJ1 36
  • 80 (a)
(Ornithorhynchus anatinus)
Mammalia SYNJ1 36
  • 79 (a)
(Gallus gallus)
Aves SYNJ1 35
  • 78.39 (n)
  • 80.95 (a)
SYNJ1 36
  • 81 (a)
(Anolis carolinensis)
Reptilia -- 36
  • 84 (a)
-- 36
  • 81 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia synj1 35
  • 70.03 (n)
  • 72.85 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.25037 35
(Danio rerio)
Actinopterygii synj1 35
  • 66.85 (n)
  • 72.91 (a)
synj1 36
  • 65 (a)
fruit fly
(Drosophila melanogaster)
Insecta synaptojanin 37
  • 54 (a)
synj 35
  • 56.47 (n)
  • 57.72 (a)
synj 36
  • 50 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012175 35
  • 54.73 (n)
  • 58.77 (a)
(Caenorhabditis elegans)
Secernentea unc-26 35
  • 54.08 (n)
  • 47.3 (a)
unc-26 36
  • 42 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes INP52 36
  • 30 (a)
INP53 36
  • 30 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 48 (a)
Species with no ortholog for SYNJ1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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 SYNJ1 Gene

Gene Tree for SYNJ1 (if available)
Gene Tree for SYNJ1 (if available)

Paralogs for SYNJ1 Gene

Paralogs for SYNJ1 Gene

genes like me logo Genes that share paralogs with SYNJ1: view

Variants for SYNJ1 Gene

Sequence variations from dbSNP and Humsavar for SYNJ1 Gene

SNP ID Clin Chr 21 pos Sequence Context AA Info Type
rs2254562 - 32,687,042(+) TTTGT(C/T)TACCA reference, missense
rs9980589 - 32,631,620(+) TCAAA(A/G)CATTA reference, missense, utr-variant-3-prime
rs2230767 -, -, - 32,631,077(-) GCTCC(C/T)GCCCG reference, missense, utr-variant-3-prime
VAR_070905 Parkinson disease 20, early-onset (PARK20)
VAR_070906 -

Structural Variations from Database of Genomic Variants (DGV) for SYNJ1 Gene

Variant ID Type Subtype PubMed ID
dgv4731n71 CNV Gain 21882294
dgv4732n71 CNV Gain 21882294
nsv834086 CNV Loss 17160897

Variation tolerance for SYNJ1 Gene

Residual Variation Intolerance Score: 20.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 12.31; 94.12% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SYNJ1 Gene

Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SYNJ1 Gene

Disorders for SYNJ1 Gene

MalaCards: The human disease database

(4) MalaCards diseases for SYNJ1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
parkinson disease 20, early-onset
  • parkinson disease 20 early onset
atypical juvenile parkinsonism
synj1-related parkinson disease
  • parkinson disease 20 early onset
oculocerebrorenal syndrome
  • lowe syndrome
- elite association - COSMIC cancer census association via MalaCards
Search SYNJ1 in MalaCards View complete list of genes associated with diseases


  • Parkinson disease 20, early-onset (PARK20) [MIM:615530]: An early-onset form of Parkinson disease, a complex neurodegenerative disorder characterized by bradykinesia, resting tremor, muscular rigidity and postural instability, as well as by a clinically significant response to treatment with levodopa. The pathology involves the loss of dopaminergic neurons in the substantia nigra and the presence of Lewy bodies (intraneuronal accumulations of aggregated proteins), in surviving neurons in various areas of the brain. PARK20 is characterized by young adult-onset of parkinsonism. Additional features may include seizures, cognitive decline, abnormal eye movements, and dystonia. {ECO:0000269 PubMed:23804563, ECO:0000269 PubMed:23804577}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for SYNJ1

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with SYNJ1: view

No data available for Genatlas for SYNJ1 Gene

Publications for SYNJ1 Gene

  1. Synaptojanin 1: localization on coated endocytic intermediates in nerve terminals and interaction of its 170 kDa isoform with Eps15. (PMID: 9428629) Haffner C. … De Camilli P. (FEBS Lett. 1997) 2 3 4 67
  2. Regulation of synaptojanin 1 by cyclin-dependent kinase 5 at synapses. (PMID: 14704270) Lee S.Y. … De Camilli P. (Proc. Natl. Acad. Sci. U.S.A. 2004) 2 3 23
  3. The recurrent mutation Arg258Gln in SYNJ1 (PARK20) is not a common cause of Parkinson's disease. (PMID: 24609975) Winkler S. … Lohmann K. (J. Neurol. 2014) 2 3
  4. Alternative splicing affecting the SH3A domain controls the binding properties of intersectin 1 in neurons. (PMID: 18539136) Tsyba L. … Rynditch A. (Biochem. Biophys. Res. Commun. 2008) 3 23
  5. Synaptojanin 1-linked phosphoinositide dyshomeostasis and cognitive deficits in mouse models of Down's syndrome. (PMID: 18591654) Voronov S.V. … Di Paolo G. (Proc. Natl. Acad. Sci. U.S.A. 2008) 3 23

Products for SYNJ1 Gene

Sources for SYNJ1 Gene