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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
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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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