U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

SYNJ2 synaptojanin 2 [ Homo sapiens (human) ]

Gene ID: 8871, updated on 3-Apr-2024

Summary

Go to the top of the page Help
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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See SYNJ2 in Genome Data Viewer
Location:
6q25.3
Exon count:
34
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (157981296..158099176)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (159227492..159345318)
105.20220307 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

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

Related articles in PubMed

  1. 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
  2. Identifying the Prognostic Risk Factors of Synaptojanin 2 and Its Underlying Perturbations Pathways in Hepatocellular Carcinoma. Zhang R, et al. Bioengineered, 2021 Dec. PMID 33641617, Free PMC Article
  3. 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
  4. 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
  5. Regulation of synaptojanin 2 5'-phosphatase activity by Src. Chuang Y, et al. Cell Adh Migr, 2012 Nov-Dec. PMID 23076136, Free PMC Article

See all (52) 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

Go to the top of the page Help

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

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

Go to the top of the page

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Markers

Homology

Clone Names

  • KIAA0348, MGC44422

Gene Ontology Provided by GOA

Function Evidence Code Pubs
NOT enables PDZ domain binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA binding IEA
Inferred from Electronic Annotation
more info
  
enables SH3 domain binding 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 IBA
Inferred from Biological aspect of Ancestor
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
  
Component Evidence Code Pubs
located_in cell projection IEA
Inferred from Electronic Annotation
more info
  
located_in cytoskeleton IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol TAS
Traceable Author Statement
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

Go to the top of the page Help
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)

Go to the top of the page Help

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_2023_10

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

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

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

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous