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SNPH Gene(Protein Coding)

Syntaphilin

GCID:
GC20P001246
GIFtS:
41
Genes Participants
UDN Logo

Aliases for SNPH Gene

Aliases for SNPH Gene

  • Syntaphilin 2 3 3 5
  • KIAA0374 4

External Ids for SNPH Gene

Previous GeneCards Identifiers for SNPH Gene

  • GC20P001235
  • GC20P001241
  • GC20P001194

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. Gene Ontology (GO) annotations related to this gene include syntaxin-1 binding. An important paralog of this gene is SYBU.

UniProtKB/Swiss-Prot for SNPH Gene

  • Inhibits SNARE complex formation by absorbing free syntaxin-1.

Additional gene information for SNPH Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SNPH Gene

Genomics for SNPH Gene

Products:

  1. Regulatory Element

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 dbSUPER 655.7 -0.2 -220 2.8 HDGF ATF1 PKNOX1 SIN3A TCF12 GLIS2 ZNF143 ZFP91 FOS SP3 SNPH NSFL1C RAD21L1
GH20J001464 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 11.9 +201.7 201695 6.7 MLX IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 NFYC SSRP1 NSFL1C SIRPB2 SDCBP2 SNPH FKBP1A GC20M001435
GH20J001433 Enhancer 1.3 Ensembl ENCODE dbSUPER 10.7 +168.5 168485 2 HDAC1 PKNOX1 ATF1 ZBTB40 YY1 TCF12 ZNF766 ETV6 ATF7 BCLAF1 GC20M001435 NSFL1C FKBP1A SDCBP2 ENSG00000229728 SNPH LOC105372497
GH20J001300 Enhancer 0.7 Ensembl ENCODE 17.6 +34.9 34944 1 FOSL1 JUND GLIS2 JUN GABPB1 REST SNPH SDCBP2 ENSG00000229728 FKBP1A ENSG00000280162 PIR62557
GH20J001503 Enhancer 1.1 ENCODE dbSUPER 10.1 +237.5 237503 0.2 ATF1 ARID4B SIN3A DMAP1 IRF4 YY1 SLC30A9 ARID2 ZNF207 ZNF143 NSFL1C FKBP1A SDCBP2 SNPH PIR45069 LOC105372499
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SNPH on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SNPH gene promoter:

Genomic Locations for SNPH Gene

Genomic Locations for SNPH Gene
chr20:1,266,297-1,309,328
(GRCh38/hg38)
Size:
43,032 bases
Orientation:
Plus strand
chr20:1,246,960-1,289,972
(GRCh37/hg19)

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 Structure • Gene Density

RefSeq DNA sequence for SNPH Gene

Proteins for SNPH Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • 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

Protein Expression for SNPH Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for SNPH Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SNPH Gene

ENSEMBL proteins:
REFSEQ proteins:

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

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SNPH Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SNPH: view

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

Function for SNPH Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

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

Clone Products

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
mitochondrion 3
plasma membrane 2

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:0005739 mitochondrion IEA --
GO:0005881 cytoplasmic microtubule IDA 23264731
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with SNPH: view

Pathways & Interactions for SNPH Gene

SuperPathways for SNPH Gene

PathCards logo More details on SuperPathways for SNPH
No Data Available

Interacting Proteins for SNPH Gene

STRING Interaction Network Preview (showing 1 interactants - click image to see details)
http://version10.5.string-db.org/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000371297%0d%0a9606.ENSP00000222812%0d%0a
Selected Interacting proteins: O15079-SNPH_HUMAN ENSP00000371297 for SNPH Gene via IID STRING

GPS-Prot Interaction Network for SNPH

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

Products:

  1. Drug
No Compound Related Data Available

Transcripts for SNPH Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for SNPH Gene

(79) Selected AceView cDNA sequences:
(3) Additional mRNA sequences :
(6) REFSEQ mRNAs :
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SNPH Gene

Syntaphilin:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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

Clone Products

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
ECgene alternative splicing isoforms for
SNPH

Expression for SNPH Gene

Products:

  1. Primer
  2. Gene Expression Assay

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

mRNA expression in normal human tissues for SNPH Gene
mRNA expression by GTEx for SNPH GenemRNA expression by BioGPS 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

NURSA nuclear receptor signaling pathways regulating expression of SNPH Gene:

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 34 33
  • 99.53 (n)
 OneToOne
cow
(Bos Taurus)
 Mammalia SNPH 34 33
  • 90.28 (n)
 OneToOne
dog
(Canis familiaris)
 Mammalia SNPH 34 33
  • 89.93 (n)
 OneToOne
mouse
(Mus musculus)
 Mammalia Snph 16 34 33
  • 88.05 (n)
rat
(Rattus norvegicus)
 Mammalia Snph 33
  • 87.48 (n)
oppossum
(Monodelphis domestica)
 Mammalia SNPH 34
  • 71 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves SNPH 34
  • 81 (a)
 OneToOne
LOC100858058 33
  • 77.03 (n)
lizard
(Anolis carolinensis)
 Reptilia SNPH 34
  • 68 (a)
 OneToOne
zebrafish
(Danio rerio)
 Actinopterygii LOC569963 33
  • 65.01 (n)
snpha 34
  • 37 (a)
 OneToMany
snphb 34
  • 33 (a)
 OneToMany
rainbow trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.10436 33
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

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for SNPH Gene

SNP ID Clin Chr 20 pos Variation AA Info Type
rs1000034905 -- 1,281,995(+) G/GG intron_variant
rs1000045395 -- 1,276,214(+) C/T intron_variant
rs1000064117 -- 1,295,271(+) G/A intron_variant
rs1000259069 -- 1,306,725(+) TGTCTGTCTGT/TGTCTGT 3_prime_UTR_variant
rs1000323445 -- 1,282,905(+) G/A intron_variant

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 for SNPH Gene

Disorders for SNPH Gene

Additional Disease Information for SNPH

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for SNPH Gene.

No data available for MalaCards , 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 22 58
  2. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 44 58
  3. The DNA sequence and comparative analysis of human chromosome 20. (PMID: 11780052) Deloukas P … Rogers J (Nature 2001) 3 4 58
  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 58
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for SNPH Gene

Sources for SNPH Gene

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