Free for academic non-profit institutions. Other users need a Commercial license

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. Diseases associated with SNPH include Communicating Hydrocephalus. 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.

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

Genomics for SNPH Gene

Regulatory Elements for SNPH Gene

Enhancers for SNPH Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH20F001433 1.4 Ensembl ENCODE 10.7 +168.5 168502 2.0 PKNOX1 ARNT MLX ARID4B SIN3A DMAP1 YY1 FOS SP3 JUNB NSFL1C MIR6869 FKBP1A SDCBP2 ENSG00000229728 SNPH GC20M001435 LOC105372497
GH20F001300 0.8 Ensembl ENCODE 17.6 +34.8 34777 1.3 ESRRA GLIS2 JUND JUN REST MAFK SNPH SDCBP2 ENSG00000229728 FKBP1A MIR6869 ENSG00000280162 PIR62557
GH20F001286 1 FANTOM5 ENCODE 12.4 +20.7 20691 1.0 ZNF263 SP3 ZIC2 ZKSCAN1 ZNF335 ATF3 ZBTB48 ZNF366 ZNF600 ZBTB20 SNPH RAD21L1 SDCBP2 FKBP1A MIR6869 ENSG00000242324 SIRPD SIRPG PIR62557 ENSG00000280162
GH20F001503 1.2 Ensembl ENCODE 10.1 +237.5 237456 0.3 ATF1 WRNIP1 ARID4B FEZF1 DMAP1 SLC30A9 ZNF143 ZNF207 MXD4 MIER2 NSFL1C FKBP1A MIR6869 SDCBP2 SNPH PIR45069 LOC105372499
GH20F001869 1.6 FANTOM5 Ensembl ENCODE 5.6 +607.1 607105 7.2 HDGF PKNOX1 ZFP64 SIN3A ARID4B DMAP1 ZNF48 YY1 ZNF207 MXD4 SIRPA SIRPB2 SNPH LOC100289473 SIRPB1 NSFL1C PIR58932 ENSG00000230839
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SNPH on UCSC Golden Path with GeneCards custom track

Promoters for SNPH Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000396407 303 1601 INSM2 ZNF76 KLF17 SIN3A NFXL1 RAD21 GLIS2 GATA2 ZNF366 FOS

Genomic Location for SNPH Gene

1,266,297 bp from pter
1,309,328 bp from pter
43,032 bases
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:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • Q8IYI3

    Protein attributes for SNPH Gene

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

    Alternative splice isoforms for SNPH Gene


neXtProt entry for SNPH Gene

Post-translational modifications for SNPH Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SNPH Gene

Antibody Products

  • Abcam antibodies for SNPH

No data available for DME Specific Peptides for SNPH Gene

Domains & Families for SNPH Gene

Protein Domains for SNPH Gene

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 Gene Families 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.

Gene Ontology (GO) - Molecular Function for SNPH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0017075 syntaxin-1 binding IEA,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:

Animal Model Products

miRNA for SNPH Gene

miRTarBase miRNAs that target SNPH

Inhibitory RNA Products

Flow Cytometry 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

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
endoplasmic reticulum 1

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

No Data Available

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

Transcripts for SNPH Gene

Unigene Clusters for SNPH Gene

Representative Sequences:

Inhibitory RNA Products

Flow Cytometry 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
ECgene alternative splicing isoforms for

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, PaxDb, 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:


SOURCE GeneReport for Unigene cluster for SNPH Gene:


mRNA Expression by UniProt/SwissProt for SNPH Gene:

Tissue specificity: Brain specific. Found in synapses.
genes like me logo Genes that share expression patterns with SNPH: view

Primer Products

Orthologs for SNPH Gene

This gene was present in the common ancestor of chordates.

Orthologs for SNPH Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SNPH 34 35
  • 99.53 (n)
(Bos Taurus)
Mammalia SNPH 34 35
  • 90.28 (n)
(Canis familiaris)
Mammalia SNPH 34 35
  • 89.93 (n)
(Mus musculus)
Mammalia Snph 34 16 35
  • 88.05 (n)
(Rattus norvegicus)
Mammalia Snph 34
  • 87.48 (n)
(Monodelphis domestica)
Mammalia SNPH 35
  • 71 (a)
(Gallus gallus)
Aves SNPH 35
  • 81 (a)
LOC100858058 34
  • 77.03 (n)
(Anolis carolinensis)
Reptilia SNPH 35
  • 68 (a)
(Danio rerio)
Actinopterygii LOC569963 34
  • 65.01 (n)
snpha 35
  • 37 (a)
snphb 35
  • 33 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10436 34
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

Gene Tree for SNPH (if available)
Gene Tree for SNPH (if available)

Paralogs for SNPH Gene

Paralogs for SNPH Gene

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

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

Variants for SNPH Gene

Sequence variations from dbSNP and Humsavar for SNPH Gene

SNP ID Clin Chr 20 pos Sequence Context AA Info Type
rs1008918 -- 1,288,627(+) TTTTT(C/T)TTTTT intron-variant
rs1010870 -- 1,291,242(-) CACAG(C/T)GGCAA intron-variant
rs1040974 -- 1,287,606(-) AGAAT(A/G)GAAAG intron-variant
rs10485822 -- 1,265,768(+) TGATT(C/G)ACCTT upstream-variant-2KB
rs10668153 -- 1,278,063(+) TCTGT(-/TT/TTGT)GTGTG intron-variant

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

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

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)

Relevant External Links for SNPH Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SNPH Gene

Disorders for SNPH Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
communicating hydrocephalus
- elite association - COSMIC cancer census association via MalaCards
Search SNPH in MalaCards View complete list of genes associated with diseases

Relevant External Links for SNPH

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
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 Z.-H. (Neuron 2000) 2 3 4 22 64
  2. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson S.L. … O'Brien S.J. (PLoS ONE 2010) 3 46 64
  3. The DNA sequence and comparative analysis of human chromosome 20. (PMID: 11780052) Deloukas P. … Rogers J. (Nature 2001) 3 4 64
  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 Res. 1997) 3 4 64
  5. Discovery of genetic biomarkers contributing to variation in drug response of cytidine analogues using human lymphoblastoid cell lines. (PMID: 24483146) Li L. … Wang L. (BMC Genomics 2014) 3 64

Products for SNPH Gene

Sources for SNPH Gene

Loading form....