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    SNPH syntaphilin [ Homo sapiens (human) ]

    Gene ID: 9751, updated on 5-Mar-2024

    Summary

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    Official Symbol
    SNPHprovided by HGNC
    Official Full Name
    syntaphilinprovided by HGNC
    Primary source
    HGNC:HGNC:15931
    See related
    Ensembl:ENSG00000101298 MIM:604942; AllianceGenome:HGNC:15931
    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
    Summary
    Syntaxin-1, synaptobrevin/VAMP, and SNAP25 interact to form the SNARE complex, which is required for synaptic vesicle docking and fusion. The protein encoded by this gene is membrane-associated and inhibits SNARE complex formation by binding free syntaxin-1. Expression of this gene appears to be brain-specific. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]
    Expression
    Broad expression in brain (RPKM 12.1), prostate (RPKM 2.0) and 18 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    20p13
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (1266294..1309327)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (1314355..1358530)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (1246938..1289971)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene chromosome 20 open reading frame 202 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12587 Neighboring gene RAD21 cohesin complex component like 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17456 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12588 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12589 Neighboring gene MPRA-validated peak4117 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:1275655-1276546 Neighboring gene FKBP1A-SDCBP2 readthrough (NMD candidate) Neighboring gene uncharacterized LOC124904856 Neighboring gene syndecan binding protein 2 Neighboring gene Sharpr-MPRA regulatory region 67 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17457 Neighboring gene SDCBP2 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 14422 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr20:1358033-1359232 Neighboring gene FKBP prolyl isomerase 1A

    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. Syntaphilin Is a Novel Biphasic Biomarker of Aggressive Prostate Cancer and a Metastasis Predictor. Hwang MJ, et al. Am J Pathol, 2019 Jun. PMID 31079810, Free PMC Article
    2. Syntaphilin controls a mitochondrial rheostat for proliferation-motility decisions in cancer. Caino MC, et al. J Clin Invest, 2017 Oct 2. PMID 28891816, Free PMC Article
    3. Syntaphilin binds to dynamin-1 and inhibits dynamin-dependent endocytosis. Das S, et al. J Biol Chem, 2003 Oct 17. PMID 12896979
    4. Syntaphilin: a syntaxin-1 clamp that controls SNARE assembly. Lao G, et al. Neuron, 2000 Jan. PMID 10707983
    5. Releasing Syntaphilin Removes Stressed Mitochondria from Axons Independent of Mitophagy under Pathophysiological Conditions. Lin MY, et al. Neuron, 2017 May 3. PMID 28472658, Free PMC Article

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. These data suggest that SNPH is a novel marker of high Gleason grade prostate cancer, differentially expressed at the invasive front compared with the central tumor bulk, and is potentially down-regulated in metastatic disease.
      Title: Syntaphilin Is a Novel Biphasic Biomarker of Aggressive Prostate Cancer and a Metastasis Predictor.
    2. By establishing the role of SNPH ubiquitination.
      Title: Syntaphilin Ubiquitination Regulates Mitochondrial Dynamics and Tumor Cell Movements.
    3. SNPH is a stress-regulated mitochondrial switch of the cell proliferation-motility balance in cancer, and its pathway may represent a therapeutic target.
      Title: Syntaphilin controls a mitochondrial rheostat for proliferation-motility decisions in cancer.
    4. Stressed mitochondria are removed from axons triggered by the bulk release of mitochondrial anchoring protein syntaphilin via a new class of mitochondria-derived cargos independent of Parkin, Drp1, and autophagy.
      Title: Releasing Syntaphilin Removes Stressed Mitochondria from Axons Independent of Mitophagy under Pathophysiological Conditions.
    5. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    6. syntaphilin is an inhibitor of both SNARE-based fusion and dynamin-mediated endocytosis
      Title: Syntaphilin binds to dynamin-1 and inhibits dynamin-dependent endocytosis.
    Submit: New GeneRIF Correction

    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
    Discovery of genetic biomarkers contributing to variation in drug response of cytidine analogues using human lymphoblastoid cell lines.
    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)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA0374, MGC46096, bA314N13.5

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables syntaxin-1 binding NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in neuron differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in neurotransmitter secretion NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in synaptic vesicle docking NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in cytoplasmic microtubule IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasmic microtubule IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in neuron projection IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in presynapse IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    syntaphilin

    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.

    mRNA and Protein(s)

    1. NM_001318234.2 → NP_001305163.1  syntaphilin isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AL136531
      Consensus CDS
      CCDS82590.1
      UniProtKB/Swiss-Prot
      O15079
      Related
      ENSP00000371291.1, ENST00000381867.6
      Conserved Domains (1) summary
      pfam15290
      Location:69 → 285
      Syntaphilin; Golgi-localized syntaxin-1-binding clamp

    2. NM_014723.4 → NP_055538.2  syntaphilin isoform 2

      See identical proteins and their annotated locations for NP_055538.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains a distinct 5' UTR and lacks an in-frame portion of the 5' coding region, compared to variant 1. The resulting isoform (2) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AL136531
      Consensus CDS
      CCDS13012.1
      UniProtKB/Swiss-Prot
      O15079, Q8IYI3
      Related
      ENSP00000371297.3, ENST00000381873.7
      Conserved Domains (1) summary
      pfam15290
      Location:25 → 241
      Syntaphilin; Golgi-localized syntaxin-1-binding clamp

    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_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      1266294..1309327
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011529404.3 → XP_011527706.1  syntaphilin isoform X3

      See identical proteins and their annotated locations for XP_011527706.1

      UniProtKB/TrEMBL
      A0A3B3IRY9
      Conserved Domains (1) summary
      pfam15290
      Location:51 → 366
      Syntaphilin; Golgi-localized syntaxin-1-binding clamp

    2. XM_047440616.1 → XP_047296572.1  syntaphilin isoform X4

      UniProtKB/Swiss-Prot
      O15079, Q8IYI3

    3. XM_047440614.1 → XP_047296570.1  syntaphilin isoform X4

      UniProtKB/Swiss-Prot
      O15079, Q8IYI3

    4. XM_011529402.3 → XP_011527704.1  syntaphilin isoform X1

      See identical proteins and their annotated locations for XP_011527704.1

      Conserved Domains (1) summary
      pfam15290
      Location:102 → 318
      Syntaphilin; Golgi-localized syntaxin-1-binding clamp

    5. XM_047440612.1 → XP_047296568.1  syntaphilin isoform X3

      UniProtKB/TrEMBL
      A0A3B3IRY9

    6. XM_047440615.1 → XP_047296571.1  syntaphilin isoform X4

      UniProtKB/Swiss-Prot
      O15079, Q8IYI3

    7. XM_047440613.1 → XP_047296569.1  syntaphilin isoform X3

      UniProtKB/TrEMBL
      A0A3B3IRY9

    8. XM_047440617.1 → XP_047296573.1  syntaphilin isoform X4

      UniProtKB/Swiss-Prot
      O15079, Q8IYI3

    9. XM_011529403.3 → XP_011527705.1  syntaphilin isoform X1

      See identical proteins and their annotated locations for XP_011527705.1

      Conserved Domains (1) summary
      pfam15290
      Location:102 → 318
      Syntaphilin; Golgi-localized syntaxin-1-binding clamp

    10. XM_047440611.1 → XP_047296567.1  syntaphilin isoform X2

      Related
      ENSP00000479696.1, ENST00000614659.1

    11. XM_005260889.4 → XP_005260946.1  syntaphilin isoform X3

      See identical proteins and their annotated locations for XP_005260946.1

      UniProtKB/TrEMBL
      A0A3B3IRY9
      Related
      ENSP00000496966.1, ENST00000649598.1
      Conserved Domains (1) summary
      pfam15290
      Location:51 → 366
      Syntaphilin; Golgi-localized syntaxin-1-binding clamp

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      1314355..1358530
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054324266.1 → XP_054180241.1  syntaphilin isoform X3

      UniProtKB/TrEMBL
      A0A3B3IRY9

    2. XM_054324270.1 → XP_054180245.1  syntaphilin isoform X4

      UniProtKB/Swiss-Prot
      O15079, Q8IYI3

    3. XM_054324263.1 → XP_054180238.1  syntaphilin isoform X2

    4. XM_054324268.1 → XP_054180243.1  syntaphilin isoform X4

      UniProtKB/Swiss-Prot
      O15079, Q8IYI3

    5. XM_054324261.1 → XP_054180236.1  syntaphilin isoform X1

    6. XM_054324272.1 → XP_054180247.1  syntaphilin isoform X3

      UniProtKB/TrEMBL
      A0A3B3IRY9

    7. XM_054324269.1 → XP_054180244.1  syntaphilin isoform X4

      UniProtKB/Swiss-Prot
      O15079, Q8IYI3

    8. XM_054324267.1 → XP_054180242.1  syntaphilin isoform X3

      UniProtKB/TrEMBL
      A0A3B3IRY9

    9. XM_054324271.1 → XP_054180246.1  syntaphilin isoform X4

      UniProtKB/Swiss-Prot
      O15079, Q8IYI3

    10. XM_054324262.1 → XP_054180237.1  syntaphilin isoform X1

    11. XM_054324264.1 → XP_054180239.1  syntaphilin isoform X2

    12. XM_054324265.1 → XP_054180240.1  syntaphilin isoform X3

      UniProtKB/TrEMBL
      A0A3B3IRY9
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O15079.2 GenPept UniProtKB/Swiss-Prot:O15079

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