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 encodi... See more...

Aliases for SNPH Gene

Aliases for SNPH Gene

  • Syntaphilin 2 3 4 5
  • KIAA0374 4

External Ids for SNPH Gene

Previous GeneCards Identifiers for SNPH Gene

  • GC20P001235
  • GC20P001241
  • GC20P001194
  • GC20P001246

Summaries for SNPH Gene

Entrez Gene Summary for SNPH Gene

  • 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]

GeneCards Summary for SNPH Gene

SNPH (Syntaphilin) is a Protein Coding gene. Diseases associated with SNPH include Communicating Hydrocephalus and Spinal Muscular Atrophy, Type Iv. Gene Ontology (GO) annotations related to this gene include syntaxin-1 binding. An important paralog of this gene is SYBU.

UniProtKB/Swiss-Prot Summary for SNPH Gene

Additional gene information for SNPH Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SNPH Gene

Genomics for SNPH Gene

GeneHancer (GH) Regulatory Elements for SNPH Gene

Promoters and enhancers for SNPH Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH20J001264 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 505.6 -0.1 -135 2.9 HNRNPK NRF1 USF1 FOS ZIC2 ZNF423 ZBTB26 REST MYC CTBP1 SNPH NSFL1C piR-61101-386 RAD21L1
GH20J001464 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 11.9 +201.7 201712 6.7 RXRA EP300 FOXK2 HNRNPK ZBTB40 ZNF217 CTCF ZSCAN5C SIN3A TCF12 NSFL1C lnc-SNPH-7 SIRPB2 SDCBP2 SNPH FKBP1A lnc-NSFL1C-1 lnc-NSFL1C-2
GH20J001300 Enhancer 0.8 Ensembl ENCODE 29.1 +34.2 34194 2.5 CTCF JUND NFIC REST FOS FOSL1 RAD21 JUN GABPB1 MAX HSALNG0128101 SNPH SDCBP2 ENSG00000229728 FKBP1A RF00017-3489 SDCBP2-AS1
GH20J001279 Enhancer 1.2 FANTOM5 Ensembl ENCODE dbSUPER 17.3 +17.6 17621 9.4 ZIC2 RFX1 SKI FOXA2 ZNF282 CREB1 MAFF MAFK SPI1 NR2F1 SNPH SDCBP2 RAD21L1 FKBP1A ENSG00000229728 SIRPD ENSG00000242324 SIRPG RF00017-3489 SDCBP2-AS1
GH20J001503 Enhancer 1.3 Ensembl ENCODE dbSUPER 10.1 +237.4 237421 1 CTCF TCF12 ZBTB11 TRIM28 REST ZBTB25 MYC TGIF2 RAD21 CTBP1 NSFL1C FKBP1A SDCBP2 SNPH piR-51070 LOC105372499
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SNPH on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SNPH

Top Transcription factor binding sites by QIAGEN in the SNPH gene promoter:
  • GATA-1
  • GATA-2
  • GATA-3
  • MyoD
  • NF-1
  • NF-1/L
  • Pax-4a
  • POU2F1
  • POU2F1a
  • Spz1

Genomic Locations for SNPH Gene

Genomic Locations for SNPH Gene
chr20:1,266,280-1,309,328
(GRCh38/hg38)
Size:
43,049 bases
Orientation:
Plus strand
chr20:1,246,960-1,289,972
(GRCh37/hg19)
Size:
43,013 bases
Orientation:
Plus strand

Genomic View for SNPH Gene

Genes around SNPH on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SNPH Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SNPH Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SNPH Gene

Proteins for SNPH Gene

  • Protein details for SNPH Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O15079-SNPH_HUMAN
    Recommended name:
    Syntaphilin
    Protein Accession:
    O15079
    Secondary Accessions:
    • Q8IYI3

    Protein attributes for SNPH Gene

    Size:
    494 amino acids
    Molecular mass:
    53537 Da
    Quaternary structure:
    • Binds to syntaxin-1.
    SequenceCaution:
    • Sequence=BAA20829.2; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for SNPH Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SNPH Gene

Post-translational modifications for SNPH Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

  • Abcam antibodies for SNPH

No data available for DME Specific Peptides for SNPH Gene

Domains & Families for SNPH Gene

Gene Families for SNPH Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for SNPH Gene

Suggested Antigen Peptide Sequences for SNPH Gene

GenScript: Design optimal peptide antigens:
  • Syntaphilin (SNPH_HUMAN)
genes like me logo Genes that share domains with SNPH: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for SNPH Gene

Function for SNPH Gene

Molecular function for SNPH Gene

UniProtKB/Swiss-Prot Function:
Inhibits SNARE complex formation by absorbing free syntaxin-1.

Phenotypes From GWAS Catalog for SNPH Gene

Gene Ontology (GO) - Molecular Function for SNPH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0017075 syntaxin-1 binding NAS 10707983
genes like me logo Genes that share ontologies with SNPH: view
genes like me logo Genes that share phenotypes with SNPH: view

Animal Models for SNPH Gene

MGI Knock Outs for SNPH:
  • Snph Snph<tm1Zhs>
  • Snph Snph<tm1.1(KOMP)Vlcg>

Animal Model Products

CRISPR Products

miRNA for SNPH Gene

miRTarBase miRNAs that target SNPH

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SNPH

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SNPH Gene

Localization for SNPH Gene

Subcellular locations from UniProtKB/Swiss-Prot for SNPH Gene

Membrane; Single-pass membrane protein. Cell junction, synapse, synaptosome.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SNPH gene
Compartment Confidence
cytoskeleton 5
plasma membrane 3
mitochondrion 3
extracellular 1
peroxisome 1
nucleus 1
endoplasmic reticulum 1
endosome 1
cytosol 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytokinetic bridge (1)
  • Mitochondria (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SNPH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IDA 15459722
GO:0005881 cytoplasmic microtubule IDA 23264731
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with SNPH: view

Pathways & Interactions for SNPH Gene

PathCards logo

SuperPathways for SNPH Gene

No Data Available

Interacting Proteins for SNPH Gene

;

Gene Ontology (GO) - Biological Process for SNPH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007269 neurotransmitter secretion NAS 10707983
GO:0007420 brain development IEA --
GO:0016081 synaptic vesicle docking NAS 10707983
GO:0030182 neuron differentiation IEA --
genes like me logo Genes that share ontologies with SNPH: view

No data available for Pathways by source and SIGNOR curated interactions for SNPH Gene

Drugs & Compounds for SNPH Gene

No Compound Related Data Available

Transcripts for SNPH Gene

mRNA/cDNA for SNPH Gene

2 REFSEQ mRNAs :
4 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SNPH

Alternative Splicing Database (ASD) splice patterns (SP) for SNPH Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4a · 4b · 4c ^ 5a · 5b ^ 6 ^ 7a · 7b · 7c
SP1: -
SP2: - - -
SP3: - - -

Relevant External Links for SNPH Gene

GeneLoc Exon Structure for
SNPH

Expression for SNPH Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SNPH Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SNPH Gene

This gene is overexpressed in Brain - Cortex (x5.8), Brain - Frontal Cortex (BA9) (x4.9), Brain - Anterior cingulate cortex (BA24) (x4.5), Brain - Hippocampus (x4.3), and Brain - Amygdala (x4.0).

Protein differential expression in normal tissues from HIPED for SNPH Gene

This gene is overexpressed in Spinal cord (22.5), Retina (17.7), and Frontal cortex (13.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SNPH Gene



Protein tissue co-expression partners for SNPH Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SNPH

SOURCE GeneReport for Unigene cluster for SNPH Gene:

Hs.323833

mRNA Expression by UniProt/SwissProt for SNPH Gene:

O15079-SNPH_HUMAN
Tissue specificity: Brain specific. Found in synapses.

Evidence on tissue expression from TISSUES for SNPH Gene

  • Nervous system(4.7)
genes like me logo Genes that share expression patterns with SNPH: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for SNPH Gene

Orthologs for SNPH Gene

This gene was present in the common ancestor of chordates.

Orthologs for SNPH Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SNPH 31 30
  • 99.53 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SNPH 31 30
  • 90.28 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SNPH 31 30
  • 89.93 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Snph 17 31 30
  • 88.05 (n)
rat
(Rattus norvegicus)
Mammalia Snph 30
  • 87.48 (n)
oppossum
(Monodelphis domestica)
Mammalia SNPH 31
  • 71 (a)
OneToOne
chicken
(Gallus gallus)
Aves SNPH 31
  • 81 (a)
OneToOne
LOC100858058 30
  • 77.03 (n)
lizard
(Anolis carolinensis)
Reptilia SNPH 31
  • 68 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii LOC569963 30
  • 65.01 (n)
snpha 31
  • 37 (a)
OneToMany
snphb 31
  • 33 (a)
OneToMany
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10436 30
Species where no ortholog for SNPH was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SNPH Gene

ENSEMBL:
Gene Tree for SNPH (if available)
TreeFam:
Gene Tree for SNPH (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SNPH: view image

Paralogs for SNPH Gene

Paralogs for SNPH Gene

(1) SIMAP similar genes for SNPH Gene using alignment to 1 proteins:

  • SNPH_HUMAN
genes like me logo Genes that share paralogs with SNPH: view

Variants for SNPH Gene

Additional dbSNP identifiers (rs#s) for SNPH Gene

Structural Variations from Database of Genomic Variants (DGV) for SNPH Gene

Variant ID Type Subtype PubMed ID
dgv2383e59 CNV duplication 20981092
dgv2384e59 CNV duplication 20981092
esv1588736 CNV deletion 17803354
esv1774028 CNV deletion 17803354
esv24525 CNV gain+loss 19812545
esv2722063 CNV deletion 23290073
esv2722064 CNV deletion 23290073
esv2722065 CNV deletion 23290073
esv2722066 CNV deletion 23290073
esv2722067 CNV deletion 23290073
esv2722068 CNV deletion 23290073
esv2722069 CNV deletion 23290073
esv3584406 CNV loss 25503493
nsv1057097 CNV gain 25217958
nsv1142983 CNV tandem duplication 24896259
nsv1150964 CNV duplication 26484159
nsv518957 CNV gain 19592680
nsv821480 CNV deletion 20802225

Variation tolerance for SNPH Gene

Residual Variation Intolerance Score: 71.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.00; 36.88% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SNPH Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SNPH

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SNPH Gene

Disorders for SNPH Gene

MalaCards: The human disease database

(3) MalaCards diseases for SNPH Gene - From: DISEASES

Disorder Aliases PubMed IDs
communicating hydrocephalus
spinal muscular atrophy, type iv
  • sma4
charcot-marie-tooth disease
  • peroneal muscular atrophy
- elite association - COSMIC cancer census association via MalaCards
Search SNPH in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SNPH

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SNPH: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SNPH Gene

Publications for SNPH Gene

  1. Syntaphilin: a syntaxin-1 clamp that controls SNARE assembly. (PMID: 10707983) Lao G … Sheng ZH (Neuron 2000) 2 3 4 23 54
  2. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 41 54
  3. The DNA sequence and comparative analysis of human chromosome 20. (PMID: 11780052) Deloukas P … Rogers J (Nature 2001) 3 4 54
  4. Prediction of the coding sequences of unidentified human genes. VII. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. (PMID: 9205841) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1997) 3 4 54
  5. VIRMA mediates preferential m6A mRNA methylation in 3'UTR and near stop codon and associates with alternative polyadenylation. (PMID: 29507755) Yue Y … Liu J (Cell discovery 2018) 3 54

Products for SNPH Gene

Sources for SNPH Gene