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SYNJ1 synaptojanin 1 [ Homo sapiens (human) ]

Gene ID: 8867, updated on 20-Dec-2019

Summary

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Official Symbol
SYNJ1provided by HGNC
Official Full Name
synaptojanin 1provided by HGNC
Primary source
HGNC:HGNC:11503
See related
Ensembl:ENSG00000159082 MIM:604297
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
EIEE53; INPP5G; PARK20
Summary
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]
Expression
Broad expression in brain (RPKM 21.4), bone marrow (RPKM 6.6) and 22 other tissues See more
Orthologs
mouse all

Genomic context

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See SYNJ1 in Genome Data Viewer
Location:
21q22.11
Exon count:
34
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 21 NC_000021.9 (32628759..32731247, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (33997269..34100351, complement)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene CFAP298-TCP10L readthrough Neighboring gene cilia and flagella associated protein 298 Neighboring gene olfactory receptor family 7 subfamily E member 23 pseudogene Neighboring gene PAXBP1 antisense RNA 1 Neighboring gene PAX3 and PAX7 binding protein 1 Neighboring gene C21orf62 antisense RNA 1 Neighboring gene chromosome 21 open reading frame 62

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. A Novel SYNJ1 Mutation in a Tunisian Family with Juvenile Parkinson's Disease Associated with Epilepsy. Ben Romdhan S, et al. J Mol Neurosci, 2018 Oct. PMID 30187305
  2. Alteration of endosomal trafficking is associated with early-onset parkinsonism caused by SYNJ1 mutations. Fasano D, et al. Cell Death Dis, 2018 Mar 7. PMID 29515184, Free PMC Article
  3. Identification of putative second genetic hits in schizophrenia carriers of high-risk copy number variants and resequencing in additional samples. Rodríguez-López J, et al. Eur Arch Psychiatry Clin Neurosci, 2018 Sep. PMID 28421333
  4. Identification of a novel homozygous mutation Arg459Pro in SYNJ1 gene of an Indian family with autosomal recessive juvenile Parkinsonism. Kirola L, et al. Parkinsonism Relat Disord, 2016 Oct. PMID 27496670
  5. Loss of SYNJ1 dual phosphatase activity leads to early onset refractory seizures and progressive neurological decline. Hardies K, et al. Brain, 2016 Sep. PMID 27435091, Free PMC Article

See all (70) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SYNJ1 contributes to memory deficits in the aging hippocampus in all forms of Alzheimer's disease.
    Title: Excess Synaptojanin 1 Contributes to Place Cell Dysfunction and Memory Deficits in the Aging Hippocampus in Three Types of Alzheimer's Disease.
  2. Data indicate that Synj1 plays a crucial role in regulating the homeostasis and functions of early endosomal compartments in different cell types, and highlight defective cellular pathways in PARK20. In addition, they strengthen the link between endosomal trafficking and Parkinson's disease.
    Title: Alteration of endosomal trafficking is associated with early-onset parkinsonism caused by SYNJ1 mutations.
  3. A novel mutation in the C-terminal domain identified in family members with juvenile PD and epilepsy.
    Title: A Novel SYNJ1 Mutation in a Tunisian Family with Juvenile Parkinson's Disease Associated with Epilepsy.
  4. Excess of rare putative functional variants at SYNJ1 in schizophrenia.
    Title: Identification of putative second genetic hits in schizophrenia carriers of high-risk copy number variants and resequencing in additional samples.
  5. This study identified a novel homozygous missense mutation (c.1376C > G, p.Arg459Pro) in SYNJ1 in an ARJP family from eastern India.
    Title: Identification of a novel homozygous mutation Arg459Pro in SYNJ1 gene of an Indian family with autosomal recessive juvenile Parkinsonism.
  6. Parkinson Sac Domain Mutation in Synaptojanin 1 Impairs Clathrin Uncoating at Synapses
    Title: Parkinson Sac Domain Mutation in Synaptojanin 1 Impairs Clathrin Uncoating at Synapses and Triggers Dystrophic Changes in Dopaminergic Axons.
  7. Thus, synaptojanin is essential for macroautophagy within presynaptic terminals, coupling protein turnover with synaptic vesicle cycling and linking presynaptic-specific autophagy defects to Parkinson's disease.
    Title: The SAC1 domain in synaptojanin is required for autophagosome maturation at presynaptic terminals.
  8. SYNJ1 deficiency leads to early onset refractory seizures and progressive neurological decline.
    Title: Loss of SYNJ1 dual phosphatase activity leads to early onset refractory seizures and progressive neurological decline.
  9. Mutations in SYNJ1 gene do not play a major role in early-onset or familial PD in our population.
    Title: Mutational analysis of SYNJ1 gene (PARK20) in Parkinson's disease in a Taiwanese population.
  10. This study demonstrated that SYNJ1 was significantly higher in Down syndrome and correlated with several measures of Abeta. SYNJ1 was higher in down syndrome with Alzheimer disease and significantly higher than SYNJ1 in sporadic Alzheimer disease.
    Title: Synaptophysin and synaptojanin-1 in Down syndrome are differentially affected by Alzheimer's disease.
Submit: New GeneRIF Correction See all GeneRIFs (23)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Epileptic encephalopathy, early infantile, 53
MedGen: C4479313 OMIM: 617389 GeneReviews: Not available
Compare labs
Parkinson disease 20, early-onset
MedGen: C3809824 OMIM: 615530 GeneReviews: Not available
Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding IEA
Inferred from Electronic Annotation
more info
  
SH3 domain binding IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
phosphatidylinositol phosphate 5-phosphatase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
phosphatidylinositol-3-phosphatase activity IDA
Inferred from Direct Assay
more info
 PubMed 
phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity IDA
Inferred from Direct Assay
more info
 PubMed 
phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity TAS
Traceable Author Statement
more info
  
phosphatidylinositol-4-phosphate phosphatase activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
brain development IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
inositol phosphate dephosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
inositol phosphate dephosphorylation ISS
Inferred from Sequence or Structural Similarity
more info
  
inositol phosphate metabolic process TAS
Traceable Author Statement
more info
  
learning IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
learning IMP
Inferred from Mutant Phenotype
more info
 PubMed 
membrane organization TAS
Traceable Author Statement
more info
  
neurotransmitter transport ISS
Inferred from Sequence or Structural Similarity
more info
  
phosphatidylinositol biosynthetic process TAS
Traceable Author Statement
more info
  
phosphatidylinositol dephosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
phosphatidylinositol dephosphorylation IDA
Inferred from Direct Assay
more info
 PubMed 
phosphatidylinositol dephosphorylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
phosphatidylinositol dephosphorylation ISS
Inferred from Sequence or Structural Similarity
more info
  
phosphatidylinositol metabolic process ISS
Inferred from Sequence or Structural Similarity
more info
  
positive regulation of endosome organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
synaptic vesicle endocytosis IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
synaptic vesicle endocytosis IGI
Inferred from Genetic Interaction
more info
 PubMed 
synaptic vesicle endocytosis ISS
Inferred from Sequence or Structural Similarity
more info
  
synaptic vesicle priming ISS
Inferred from Sequence or Structural Similarity
more info
  
synaptic vesicle transport ISS
Inferred from Sequence or Structural Similarity
more info
  
synaptic vesicle uncoating ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
cell IEA
Inferred from Electronic Annotation
more info
  
clathrin coat of coated pit ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
cytosol TAS
Traceable Author Statement
more info
  
membrane coat ISS
Inferred from Sequence or Structural Similarity
more info
  
colocalizes_with microtubule ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
perinuclear region of cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
perinuclear region of cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
  
presynapse IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
presynapse IDA
Inferred from Direct Assay
more info
 PubMed 
synaptic membrane ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
terminal bouton ISS
Inferred from Sequence or Structural Similarity
more info
  
vesicle membrane ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
synaptojanin-1
Names
inositol 5'-phosphatase (synaptojanin 1)
inositol polyphosphate-5-phosphatase G
phosphoinositide 5-phosphatase
synaptic inositol 1,4,5-trisphosphate 5-phosphatase 1
synaptojanin-1, polyphosphoinositide phosphatase
NP_001153774.1
NP_001153778.1
NP_003886.3
NP_982271.3
XP_016883983.1
XP_016883984.1
XP_016883985.1
XP_016883986.1
XP_016883987.1
XP_016883988.1
XP_016883989.1
XP_016883990.1
XP_016883991.1
XP_016883992.1
XP_016883993.1
XP_016883994.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_030017.1 RefSeqGene

    Range
    5001..104283
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001160302.1 → NP_001153774.1  synaptojanin-1 isoform c

    See identical proteins and their annotated locations for NP_001153774.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in its 5' UTR, 5' coding region and 3' coding region, and uses a downstream translational start codon, compared to variant 1. The encoded isoform (c) has a shorter N-terminus, a distinct C-terminus, and is shorter than isoform a.
    Source sequence(s)
    AB020717, AP000275, BP350252, CA944966
    Consensus CDS
    CCDS54483.1
    UniProtKB/Swiss-Prot
    O43426
    Related
    ENSP00000349903.3, ENST00000357345.7
    Conserved Domains (5) summary
    cd09098
    Location:533 → 868
    INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
    PRK05641
    Location:1017 → 1097
    PRK05641; putative acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated
    pfam02383
    Location:60 → 340
    Syja_N; SacI homology domain
    pfam08952
    Location:867 → 1008
    DUF1866; Domain of unknown function (DUF1866)
    pfam11235
    Location:1078 → 1262
    Med25_SD1; Mediator complex subunit 25 synapsin 1

  2. NM_001160306.2 → NP_001153778.1  synaptojanin-1 isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, uses a downstream translational start codon, and has multiple differences in the coding region, compared to variant 1. The encoded isoform (d) has a shorter N-terminus, a distinct C-terminus, and is shorter than isoform a.
    Source sequence(s)
    AB020717, BC098395, BC136603, BP350252, CA944966
    Consensus CDS
    CCDS54484.1
    UniProtKB/Swiss-Prot
    O43426
    UniProtKB/TrEMBL
    A0A0D9SGJ6, B9EGN3
    Related
    ENSP00000487560.1, ENST00000630077.2
    Conserved Domains (4) summary
    cd09098
    Location:528 → 863
    INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
    pfam02383
    Location:60 → 340
    Syja_N; SacI homology domain
    pfam08952
    Location:862 → 1003
    DUF1866; Domain of unknown function (DUF1866)
    pfam11235
    Location:1054 → 1231
    Med25_SD1; Mediator complex subunit 25 synapsin 1

  3. NM_003895.3 → NP_003886.3  synaptojanin-1 isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AB020717, AF009040, AP000279, BC019630, CA944966, DB071394
    Consensus CDS
    CCDS33539.2
    UniProtKB/Swiss-Prot
    O43426
    UniProtKB/TrEMBL
    J3KQV8, Q05CZ1
    Related
    ENSP00000409667.2, ENST00000433931.6
    Conserved Domains (3) summary
    cd09098
    Location:572 → 907
    INPP5c_Synj1; Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1
    pfam02383
    Location:99 → 379
    Syja_N; SacI homology domain
    pfam08952
    Location:906 → 1047
    DUF1866; Domain of unknown function (DUF1866)

  4. NM_203446.3 → NP_982271.3  synaptojanin-1 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) includes an alternate exon in the 3' coding region that causes a frameshift, compared to variant 1. The encoded isoform (b) has a distinct and shorter C-terminus, compared to isoform a.
    Source sequence(s)
    AB020717, AF009039, AF009040, AP000275, AP000279, BC019630
    Consensus CDS
    CCDS33540.2
    Related
    ENSP00000371939.2, ENST00000382499.6

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000021.9 Reference GRCh38.p13 Primary Assembly

    Range
    32628759..32731247 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017028497.2 → XP_016883986.1  synaptojanin-1 isoform X4

  2. XM_017028499.2 → XP_016883988.1  synaptojanin-1 isoform X6

  3. XM_017028505.2 → XP_016883994.1  synaptojanin-1 isoform X12

    Related
    ENSP00000371931.4, ENST00000382491.7

  4. XM_017028495.2 → XP_016883984.1  synaptojanin-1 isoform X2

  5. XM_017028498.1 → XP_016883987.1  synaptojanin-1 isoform X5

  6. XM_017028504.1 → XP_016883993.1  synaptojanin-1 isoform X11

  7. XM_017028496.1 → XP_016883985.1  synaptojanin-1 isoform X3

  8. XM_017028503.1 → XP_016883992.1  synaptojanin-1 isoform X10

  9. XM_017028494.1 → XP_016883983.1  synaptojanin-1 isoform X1

  10. XM_017028502.1 → XP_016883991.1  synaptojanin-1 isoform X9

  11. XM_017028501.1 → XP_016883990.1  synaptojanin-1 isoform X8

  12. XM_017028500.1 → XP_016883989.1  synaptojanin-1 isoform X7

    UniProtKB/Swiss-Prot
    O43426
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O43426.2 GenPept UniProtKB/Swiss-Prot:O43426

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