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    SYN1 synapsin I [ Homo sapiens (human) ]

    Gene ID: 6853, updated on 27-Nov-2024

    Summary

    Official Symbol
    SYN1provided by HGNC
    Official Full Name
    synapsin Iprovided by HGNC
    Primary source
    HGNC:HGNC:11494
    See related
    Ensembl:ENSG00000008056 MIM:313440; AllianceGenome:HGNC:11494
    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
    SYNI; EPILX; MRX50; SYN1a; SYN1b; EPILX1
    Summary
    This gene is a member of the synapsin gene family. Synapsins encode neuronal phosphoproteins which associate with the cytoplasmic surface of synaptic vesicles. Family members are characterized by common protein domains, and they are implicated in synaptogenesis and the modulation of neurotransmitter release, suggesting a potential role in several neuropsychiatric diseases. This member of the synapsin family plays a role in regulation of axonogenesis and synaptogenesis. The protein encoded serves as a substrate for several different protein kinases and phosphorylation may function in the regulation of this protein in the nerve terminal. Mutations in this gene may be associated with X-linked disorders with primary neuronal degeneration such as Rett syndrome. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in brain (RPKM 99.5) and adrenal (RPKM 5.6) See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SYN1 in Genome Data Viewer
    Location:
    Xp11.3-p11.23
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (47571901..47619857, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (46981791..47029757, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (47431300..47479256, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905183 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:47372169-47372670 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:47372671-47373170 Neighboring gene MPRA-validated peak7378 silencer Neighboring gene NUS1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20805 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20806 Neighboring gene Sharpr-MPRA regulatory region 9461 Neighboring gene uncharacterized LOC124905184 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:47415445-47415946 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20807 Neighboring gene Sharpr-MPRA regulatory region 4668 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:47434199-47434706 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:47434707-47435213 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:47435306-47435806 Neighboring gene Sharpr-MPRA regulatory region 5152 Neighboring gene A-Raf proto-oncogene, serine/threonine kinase Neighboring gene CRISPRi-FlowFISH-validated HDAC6 regulatory element 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20808 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20809 Neighboring gene Sharpr-MPRA regulatory region 5754 Neighboring gene TIMP metallopeptidase inhibitor 1 Neighboring gene microRNA 4769 Neighboring gene Sharpr-MPRA regulatory region 11481 Neighboring gene complement factor properdin Neighboring gene CRISPRi-FlowFISH-validated PLP2 regulatory element 2 Neighboring gene ETS transcription factor ELK1

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders
    MedGen: C5774177 OMIM: 300491 GeneReviews: Not available
    Compare labs
    Intellectual disability, X-linked 50
    MedGen: C1848087 OMIM: 300115 GeneReviews: Not available
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2022-07-12)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2022-07-12)

    ClinGen Genome Curation PagePubMed

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat Treatment of microglia cells with HIV-1 Tat shows TAU5 and synapsin-1 positive inclusions in cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding TAS
    Traceable Author Statement
    more info
    PubMed 
    enables actin binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables calcium-dependent protein binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables cytoskeletal protein-membrane anchor activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables identical protein binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein kinase binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Process Evidence Code Pubs
    involved_in chemical synaptic transmission TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in neuron development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neurotransmitter secretion IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of neurotransmitter secretion TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in regulation of synaptic vesicle cycle IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of synaptic vesicle exocytosis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of synaptic vesicle exocytosis NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in synapse organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in synaptic vesicle clustering IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    located_in Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
     
    located_in Schaffer collateral - CA1 synapse IEA
    Inferred from Electronic Annotation
    more info
     
    located_in axon IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cell body IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytoskeleton IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in dendrite IEA
    Inferred from Electronic Annotation
    more info
     
    located_in extrinsic component of synaptic vesicle membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in postsynaptic density IEA
    Inferred from Electronic Annotation
    more info
     
    located_in presynapse IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in presynaptic active zone IEA
    Inferred from Electronic Annotation
    more info
     
    located_in synaptic vesicle TAS
    Traceable Author Statement
    more info
    PubMed 
    is_active_in synaptic vesicle membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in synaptonemal complex IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    synapsin-1
    Names
    brain protein 4.1
    synapsin Ib

    NCBI Reference Sequences (RefSeq)

    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_008437.1 RefSeqGene

      Range
      5001..52957
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_006950.3NP_008881.2  synapsin-1 isoform Ia

      See identical proteins and their annotated locations for NP_008881.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (Ia) represents the longer transcript, and encodes the longer isoform (Ia). This isoform (Ia) contains a distinct domain E, as compared to isoform Ib.
      Source sequence(s)
      AI929645, BC036711, BC048799, Z84466
      Consensus CDS
      CCDS14280.1
      UniProtKB/Swiss-Prot
      B1AJQ1, O75825, P17600, Q5H9A9
      Related
      ENSP00000295987.7, ENST00000295987.13
      Conserved Domains (4) summary
      PRK07764
      Location:494686
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      pfam02078
      Location:115212
      Synapsin; N-terminal domain
      pfam10581
      Location:127
      Synapsin_N; Synapsin N-terminal
      cl17255
      Location:214416
      CPSase_L_D2; Carbamoyl-phosphate synthase L chain, ATP binding domain
    2. NM_133499.2NP_598006.1  synapsin-1 isoform Ib

      See identical proteins and their annotated locations for NP_598006.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (Ib) utilizes an alternative splice acceptor site in terminal exon compared to variant Ia, resulting in the lack of an internal segment and a frameshift. This variant encodes isoform Ib, which contains a shorter carboxyl terminus and a distinct domain F, as compared to isoform Ia.
      Source sequence(s)
      AI929645, BC036711, BC048799
      Consensus CDS
      CCDS35233.1
      UniProtKB/Swiss-Prot
      P17600
      Related
      ENSP00000343206.4, ENST00000340666.5
      Conserved Domains (4) summary
      PHA03247
      Location:498669
      PHA03247; large tegument protein UL36; Provisional
      pfam02078
      Location:115212
      Synapsin; N-terminal domain
      pfam10581
      Location:127
      Synapsin_N; Synapsin N-terminal
      cl17255
      Location:214416
      CPSase_L_D2; Carbamoyl-phosphate synthase L chain, ATP binding domain

    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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      47571901..47619857 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      46981791..47029757 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)