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    SYNJ2 synaptojanin 2 [ Homo sapiens (human) ]

    Gene ID: 8871, updated on 27-Dec-2024

    Summary

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    Official Symbol
    SYNJ2provided by HGNC
    Official Full Name
    synaptojanin 2provided by HGNC
    Primary source
    HGNC:HGNC:11504
    See related
    Ensembl:ENSG00000078269 MIM:609410; AllianceGenome:HGNC:11504
    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
    INPP5H
    Summary
    The gene is a member of the inositol-polyphosphate 5-phosphatase family. The encoded protein interacts with the ras-related C3 botulinum toxin substrate 1, which causes translocation of the encoded protein to the plasma membrane where it inhibits clathrin-mediated endocytosis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2010]
    Expression
    Ubiquitous expression in brain (RPKM 8.6), colon (RPKM 3.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SYNJ2 in Genome Data Viewer
    Location:
    6q25.3
    Exon count:
    34
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (157981296..158099176)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (159227492..159345318)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (158402895..158520208)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene sorting nexin 9 Neighboring gene NANOG hESC enhancer GRCh37_chr6:158351503-158352004 Neighboring gene heat shock protein family E (Hsp10) member 1 pseudogene 26 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17730 Neighboring gene RNA, U6 small nuclear 786, pseudogene Neighboring gene CRISPRi-validated cis-regulatory element chr6.5510 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158394739-158395292 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158402145-158402660 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158402661-158403176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158420467-158420966 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25345 Neighboring gene SYNJ2 intronic transcript 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158447101-158447788 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158447789-158448476 Neighboring gene Sharpr-MPRA regulatory region 12557 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158458586-158459280 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158461967-158462502 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158470498-158471112 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:158490014-158491213 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158492197-158492760 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158492761-158493322 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17732 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158516915-158517415 Neighboring gene MPRA-validated peak6269 silencer Neighboring gene serine active site containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17733 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17734 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158604236-158604740 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158604741-158605243 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:158615403-158616003 Neighboring gene general transcription factor IIH subunit 5

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. SYNJ2 variant rs9365723 is associated with colorectal cancer risk in Chinese Han population. Du Q, et al. Int J Biol Markers, 2016 May 28. PMID 26616230
    2. Synaptojanin 2 is a druggable mediator of metastasis and the gene is overexpressed and amplified in breast cancer. Ben-Chetrit N, et al. Sci Signal, 2015 Jan 20. PMID 25605973
    3. Synaptojanin 2 functions at an early step of clathrin-mediated endocytosis. Rusk N, et al. Curr Biol, 2003 Apr 15. PMID 12699622
    4. SYNJ2 is a novel and potential biomarker for the prediction and treatment of cancers: from lung squamous cell carcinoma to pan-cancer. Hou W, et al. BMC Med Genomics, 2022 May 17. PMID 35581615, Free PMC Article
    5. Synaptojanin 2 is recognized by HLA class II-restricted hairy cell leukemia-specific T cells. Spaenij-Dekking EH, et al. Leukemia, 2003 Dec. PMID 14562116

    See all (57) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SYNJ2 is a novel and potential biomarker for the prediction and treatment of cancers: from lung squamous cell carcinoma to pan-cancer.
      Title: SYNJ2 is a novel and potential biomarker for the prediction and treatment of cancers: from lung squamous cell carcinoma to pan-cancer.
    2. Identifying the Prognostic Risk Factors of Synaptojanin 2 and Its Underlying Perturbations Pathways in Hepatocellular Carcinoma.
      Title: Identifying the Prognostic Risk Factors of Synaptojanin 2 and Its Underlying Perturbations Pathways in Hepatocellular Carcinoma.
    3. Results, combined with previous studies, suggest that rs9365723, located on SYNJ2, is associated with the risk of CRC in a Chinese population.
      Title: SYNJ2 variant rs9365723 is associated with colorectal cancer risk in Chinese Han population.
    4. Synaptojanin 2 is a druggable mediator of metastasis and the gene is overexpressed and amplified in breast cancer.
      Title: Synaptojanin 2 is a druggable mediator of metastasis and the gene is overexpressed and amplified in breast cancer.
    5. The genetic interactions associated with ILVatrophy rate in this study may be mapping variants inSYNJ2andPI4KAthat interact to decrease synthesisof PIP.
      Title: Genetic interactions within inositol-related pathways are associated with longitudinal changes in ventricle size.
    6. Src-mediated phosphorylation of SYNJ2 contributes to invadopodia formation.
      Title: Regulation of synaptojanin 2 5'-phosphatase activity by Src.
    7. SYNJ2 is a novel gene in which variation is potentially associated with cognitive abilities.
      Title: Evolutionary conserved longevity genes and human cognitive abilities in elderly cohorts.
    8. Single nucleotide polymorphisms in SYNJ2 are associated with personality disorders.
      Title: Longevity candidate genes and their association with personality traits in the elderly.
    9. SYNJ2 is a target gene of the BACH1 transcription factor according to ChIP-seq analysis in HEK 293 cells.
      Title: The BTB and CNC homology 1 (BACH1) target genes are involved in the oxidative stress response and in control of the cell cycle.
    10. Since Syn 2 is a phosphatidylinositol 4,5-biphosphatase involved in cell growth and rearrangement of actin filaments, the increased Syn 2 expression may correlate with the hairy cell leukemia etiology or the characteristic morphologic alterations.
      Title: Synaptojanin 2 is recognized by HLA class II-restricted hairy cell leukemia-specific T cells.
    Submit: New GeneRIF Correction See all GeneRIFs (12)

    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

    EBI GWAS Catalog

    Description
    Genome-wide search for gene-gene interactions in colorectal cancer.
    EBI GWAS Catalog
    The genetic aetiology of cannabis use initiation: a meta-analysis of genome-wide association studies and a SNP-based heritability estimation.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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

    Clone Names

    • KIAA0348, MGC44422

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables inositol-1,4,5-trisphosphate 5-phosphatase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables phosphatidylinositol phosphate 4-phosphatase activity TAS
    Traceable Author Statement
    more info
    		  
    enables phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity TAS
    Traceable Author Statement
    more info
    		  
    enables phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity TAS
    Traceable Author Statement
    more info
    		  
    enables phosphatidylinositol-3-phosphate phosphatase activity TAS
    Traceable Author Statement
    more info
    		  
    enables phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity TAS
    Traceable Author Statement
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in membrane organization TAS
    Traceable Author Statement
    more info
    		  
    involved_in phosphatidylinositol biosynthetic process TAS
    Traceable Author Statement
    more info
    		  
    involved_in phosphatidylinositol dephosphorylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in phosphatidylinositol-3-phosphate biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in synaptic vesicle endocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in synaptic vesicle endocytosis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in synaptic vesicle endocytosis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in synaptic vesicle endocytosis NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cell projection IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoskeleton IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane raft IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in perinuclear region of cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in presynapse IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    synaptojanin-2
    Names
    inositol phosphate 5'-phosphatase 2
    inositol polyphosphate-5-phosphatase H
    phosphoinositide 5-phosphatase
    synaptic inositol 1,4,5-trisphosphate 5-phosphatase 2
    NP_001171559.1
    NP_001397876.1
    NP_003889.1
    XP_005267255.1
    XP_005267257.1
    XP_011534526.1
    XP_011534528.1
    XP_011534529.1
    XP_011534530.1
    XP_047275426.1
    XP_047275428.1
    XP_047275429.1
    XP_047275430.1
    XP_047275431.1
    XP_054212647.1
    XP_054212648.1
    XP_054212649.1
    XP_054212650.1
    XP_054212651.1
    XP_054212652.1
    XP_054212653.1
    XP_054212654.1
    XP_054212655.1
    XP_054212656.1
    XP_054212657.1
    XP_054212658.1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_029907.1 RefSeqGene

      Range
      5008..122321
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001178088.2 → NP_001171559.1  synaptojanin-2 isoform 2

      See identical proteins and their annotated locations for NP_001171559.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The resulting protein (isoform 2) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AF086449, AL139330, BX648749, DA327619
      Consensus CDS
      CCDS87462.1
      UniProtKB/TrEMBL
      A0A1W2PR85
      Related
      ENSP00000492369.1, ENST00000638626.1
      Conserved Domains (3) summary
      pfam02383
      Location:8 → 105
      Syja_N; SacI homology domain
      pfam08952
      Location:635 → 771
      DUF1866; Domain of unknown function (DUF1866)
      cl00490
      Location:293 → 624
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

    2. NM_001410947.1 → NP_001397876.1  synaptojanin-2 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AL139330
      Consensus CDS
      CCDS94025.1
      Related
      ENSP00000492532.1, ENST00000640338.1

    3. NM_003898.4 → NP_003889.1  synaptojanin-2 isoform 1

      See identical proteins and their annotated locations for NP_003889.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1). This variant (1) is also known as synaptojanin 2B or 2B2 (SJ2B2).
      Source sequence(s)
      AF086449, AF318616, AK294480, AL139330
      Consensus CDS
      CCDS5254.1
      UniProtKB/Swiss-Prot
      O15056, Q5TA13, Q5TA16, Q5TA19, Q86XK0, Q8IZA8, Q9H226
      Related
      ENSP00000347792.4, ENST00000355585.9
      Conserved Domains (3) summary
      pfam02383
      Location:61 → 342
      Syja_N; SacI homology domain
      pfam08952
      Location:872 → 1008
      DUF1866; Domain of unknown function (DUF1866)
      cl00490
      Location:530 → 861
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      157981296..158099176
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047419472.1 → XP_047275428.1  synaptojanin-2 isoform X3

      UniProtKB/TrEMBL
      A0A1W2PR85

    2. XM_011536224.2 → XP_011534526.1  synaptojanin-2 isoform X1

      Conserved Domains (3) summary
      pfam02383
      Location:61 → 342
      Syja_N; SacI homology domain
      pfam08952
      Location:872 → 1008
      DUF1866; Domain of unknown function (DUF1866)
      cl00490
      Location:530 → 861
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

    3. XM_047419475.1 → XP_047275431.1  synaptojanin-2 isoform X9

    4. XM_011536227.3 → XP_011534529.1  synaptojanin-2 isoform X5

      Conserved Domains (3) summary
      pfam02383
      Location:61 → 342
      Syja_N; SacI homology domain
      pfam08952
      Location:872 → 1008
      DUF1866; Domain of unknown function (DUF1866)
      cl00490
      Location:530 → 861
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

    5. XM_047419474.1 → XP_047275430.1  synaptojanin-2 isoform X8

    6. XM_047419470.1 → XP_047275426.1  synaptojanin-2 isoform X2

    7. XM_047419473.1 → XP_047275429.1  synaptojanin-2 isoform X3

      UniProtKB/TrEMBL
      A0A1W2PR85

    8. XM_005267198.5 → XP_005267255.1  synaptojanin-2 isoform X4

      See identical proteins and their annotated locations for XP_005267255.1

      Conserved Domains (2) summary
      pfam08952
      Location:541 → 677
      DUF1866; Domain of unknown function (DUF1866)
      cl00490
      Location:199 → 530
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

    9. XM_011536226.4 → XP_011534528.1  synaptojanin-2 isoform X4

      See identical proteins and their annotated locations for XP_011534528.1

      Conserved Domains (2) summary
      pfam08952
      Location:541 → 677
      DUF1866; Domain of unknown function (DUF1866)
      cl00490
      Location:199 → 530
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

    10. XM_011536228.4 → XP_011534530.1  synaptojanin-2 isoform X6

      See identical proteins and their annotated locations for XP_011534530.1

      UniProtKB/TrEMBL
      B4DLC4
      Conserved Domains (2) summary
      pfam08952
      Location:489 → 625
      DUF1866; Domain of unknown function (DUF1866)
      cl00490
      Location:147 → 478
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

    11. XM_005267200.2 → XP_005267257.1  synaptojanin-2 isoform X7

      UniProtKB/TrEMBL
      B4DLC4
      Related
      ENSP00000356089.3, ENST00000367122.6
      Conserved Domains (2) summary
      pfam08952
      Location:285 → 421
      DUF1866; Domain of unknown function (DUF1866)
      cl00490
      Location:1 → 274
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      159227492..159345318
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054356674.1 → XP_054212649.1  synaptojanin-2 isoform X3

    2. XM_054356672.1 → XP_054212647.1  synaptojanin-2 isoform X1

    3. XM_054356683.1 → XP_054212658.1  synaptojanin-2 isoform X9

    4. XM_054356678.1 → XP_054212653.1  synaptojanin-2 isoform X5

    5. XM_054356682.1 → XP_054212657.1  synaptojanin-2 isoform X8

    6. XM_054356681.1 → XP_054212656.1  synaptojanin-2 isoform X10

    7. XM_054356673.1 → XP_054212648.1  synaptojanin-2 isoform X2

    8. XM_054356675.1 → XP_054212650.1  synaptojanin-2 isoform X3

    9. XM_054356677.1 → XP_054212652.1  synaptojanin-2 isoform X4

    10. XM_054356676.1 → XP_054212651.1  synaptojanin-2 isoform X4

    11. XM_054356679.1 → XP_054212654.1  synaptojanin-2 isoform X6

      UniProtKB/TrEMBL
      B4DLC4

    12. XM_054356680.1 → XP_054212655.1  synaptojanin-2 isoform X7

      UniProtKB/TrEMBL
      B4DLC4
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O15056.3 GenPept UniProtKB/Swiss-Prot:O15056

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