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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 61
  • Synaptojanin-1, Polyphosphoinositide Phosphatase 3
  • Inositol 5-Phosphatase (Synaptojanin 1) 3
  • Synaptojanin-1 3
  • KIAA0910 4
  • EC 3.1.3 61
  • EIEE53 3
  • 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 Inositol phosphate metabolism (KEGG) and Vesicle-mediated transport. GO annotations related to this gene include nucleic acid binding and nucleotide binding. An important paralog of this gene is SYNJ2.

UniProtKB/Swiss-Prot for SYNJ1 Gene

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

No data available for CIViC summary , 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 Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH21G032726 1.1 ENCODE 6.9 +0.3 263 2.7 HDGF PKNOX1 CREB3L1 ARNT ZFP64 ARID4B SIN3A YY1 SLC30A9 ZNF143 MIS18A PAXBP1 C21orf62-AS1 EVA1C SYNJ1 PAXBP1-AS1 ENSG00000238220
GH21G033201 1.9 FANTOM5 Ensembl ENCODE dbSUPER 3.3 -475.9 -475914 4.5 HDGF PKNOX1 SIN3A DMAP1 ZNF48 YY1 FOS ZNF548 MCM3 ZNF662 EVA1C IFNAR2 IFNGR2 MIS18A OLIG2 ENSG00000249624 LINC01548 ENSG00000226433 OLIG1 C21orf62-AS1
GH21G032816 1 ENCODE 5.8 -89.3 -89282 2.4 ATF1 PKNOX1 ARNT CREB3L1 TCF12 ZNF766 GATA2 FOS JUNB NCOA1 PAXBP1 C21orf62-AS1 SYNJ1 C21orf62 ENSG00000224427
GH21G032818 0.9 ENCODE 5.4 -91.6 -91581 1.8 ATF1 CBX3 ARNT CREB3L1 TCF12 GATA2 EGR1 FOS EGR2 SMARCA5 C21orf62-AS1 PAXBP1 SYNJ1 C21orf62 ENSG00000224427
GH21G032844 0.9 ENCODE 5.2 -117.1 -117110 0.9 PKNOX1 INSM2 KLF17 FEZF1 ZNF2 ZEB1 GLIS2 ZNF366 ZSCAN5C SCRT2 SYNJ1 GC21M032843 ENSG00000232360 ENSG00000207098
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

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
ENSR00000141463 348 2601 HDGF PKNOX1 CREB3L1 ARNT ZFP64 ARID4B SIN3A YY1 SLC30A9 ZNF143

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

Selected DME Specific Peptides for SYNJ1 Gene


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.
  • 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:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding IEA --
GO:0004438 phosphatidylinositol-3-phosphatase activity TAS --
GO:0004439 phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity TAS --
GO:0008022 protein C-terminus binding IEA --
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:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

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

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 SYNJ1 gene
Compartment Confidence
cytosol 5
plasma membrane 4
cytoskeleton 2
nucleus 2
endosome 2

Gene Ontology (GO) - Cellular Components for SYNJ1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
GO:0005874 colocalizes_with microtubule ISS 9428629
GO:0012506 vesicle membrane ISS --
GO:0030117 membrane coat ISS --
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:0006661 phosphatidylinositol biosynthetic process TAS --
GO:0006836 neurotransmitter transport ISS --
GO:0006897 endocytosis IEA --
GO:0007420 brain development IEA --
GO:0007612 learning IMP 18591654
genes like me logo Genes that share ontologies with SYNJ1: view

Drugs & Compounds for SYNJ1 Gene

(4) Drugs for SYNJ1 Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0

(5) 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-)
genes like me logo Genes that share compounds with SYNJ1: view

Transcripts for SYNJ1 Gene

Unigene Clusters for SYNJ1 Gene

Synaptojanin 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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, MaxQB, and MOPED for SYNJ1 Gene

Protein tissue co-expression partners for SYNJ1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SYNJ1 Gene:


SOURCE GeneReport for Unigene cluster for SYNJ1 Gene:


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.

Evidence on tissue expression from TISSUES for SYNJ1 Gene

  • Nervous system(4.9)
  • Liver(4.1)
  • Eye(2.6)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SYNJ1 Gene

Germ Layers:
  • ectoderm
  • mesoderm
  • integumentary
  • nervous
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • eye
  • eyelid
  • face
  • head
  • lower limb
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal cord
genes like me logo Genes that share expression patterns with SYNJ1: view

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
(Pan troglodytes)
Mammalia SYNJ1 34 35
  • 99.52 (n)
(Canis familiaris)
Mammalia SYNJ1 34 35
  • 91.84 (n)
(Bos Taurus)
Mammalia SYNJ1 34 35
  • 90.35 (n)
(Rattus norvegicus)
Mammalia Synj1 34
  • 88.34 (n)
(Mus musculus)
Mammalia Synj1 34 16 35
  • 86.97 (n)
(Monodelphis domestica)
Mammalia SYNJ1 35
  • 80 (a)
(Ornithorhynchus anatinus)
Mammalia SYNJ1 35
  • 79 (a)
(Gallus gallus)
Aves SYNJ1 34 35
  • 78.39 (n)
(Anolis carolinensis)
Reptilia -- 35
  • 84 (a)
-- 35
  • 81 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia synj1 34
  • 70.03 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.25037 34
(Danio rerio)
Actinopterygii synj1 34 35
  • 66.85 (n)
fruit fly
(Drosophila melanogaster)
Insecta synj 34 35
  • 56.47 (n)
synaptojanin 36
  • 54 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012175 34
  • 54.73 (n)
(Caenorhabditis elegans)
Secernentea unc-26 34 35
  • 54.08 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes INP52 35
  • 30 (a)
INP53 35
  • 30 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 48 (a)
Species where no ortholog for SYNJ1 was found in the sources mined by GeneCards:
  • 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
VAR_070905 Parkinson disease 20, early-onset (PARK20) [MIM:615530]
VAR_070906 Parkinson disease 20, early-onset (PARK20) [MIM:615530]
rs398122403 Pathogenic 32,695,106(-) TGTCC(A/G)GGGAA reference, missense
rs886039732 Pathogenic 32,694,272(-) TTCAT(-/ACAAA)TCCGA reference, frameshift-variant
rs386352368 Uncertain significance 32,639,733(-) CCACG(A/C/T)GCGGG reference, missense

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

Variant ID Type Subtype PubMed ID
dgv2380n106 CNV deletion 24896259
esv3646891 CNV gain 21293372
esv3646892 CNV loss 21293372
nsv1063676 CNV gain 25217958
nsv1131630 CNV deletion 24896259
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)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

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, and GeneCards

Disorder Aliases PubMed IDs
parkinson disease 20, early-onset
  • early-onset parkinson disease 20
atypical juvenile parkinsonism
synj1-related parkinson disease
  • parkinson disease 20 early onset
undetermined early-onset epileptic encephalopathy
  • undetermined eoee
- 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. 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 22 64
  2. Mutation analysis of SYNJ1: a possible candidate gene for chromosome 21q22-linked bipolar disorder. (PMID: 11443522) Saito T. … Lachman H.M. (Mol. Psychiatry 2001) 3 22 46 64
  3. The SH3 domains of endophilin and amphiphysin bind to the proline- rich region of synaptojanin 1 at distinct sites that display an unconventional binding specificity. (PMID: 10542231) Cestra G. … Cesareni G. (J. Biol. Chem. 1999) 3 4 22 64
  4. 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 64
  5. 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 64

Products for SYNJ1 Gene

  • Addgene plasmids for SYNJ1

Sources for SYNJ1 Gene

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