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Aliases for SYP Gene

Aliases for SYP Gene

  • Synaptophysin 2 3 3 5
  • Major Synaptic Vesicle Protein P38 3 4
  • MRXSYP 3
  • MRX96 3

External Ids for SYP Gene

Previous GeneCards Identifiers for SYP Gene

  • GC0XM047830
  • GC0XM047286
  • GC0XM047850
  • GC0XM048070
  • GC0XM048800
  • GC0XM048931
  • GC0XM049044
  • GC0XM046701

Summaries for SYP Gene

Entrez Gene Summary for SYP Gene

  • This gene encodes an integral membrane protein of small synaptic vesicles in brain and endocrine cells. The protein also binds cholesterol and is thought to direct targeting of vesicle-associated membrane protein 2 (synaptobrevin) to intracellular compartments. Mutations in this gene are associated with an X-linked form of cognitive disability. [provided by RefSeq, Jul 2017]

GeneCards Summary for SYP Gene

SYP (Synaptophysin) is a Protein Coding gene. Diseases associated with SYP include Mental Retardation, X-Linked 96 and X-Linked Non-Specific Intellectual Disability. Among its related pathways are Neural Stem Cell Differentiation Pathways and Lineage-specific Markers and Synaptic vesicle cycle. Gene Ontology (GO) annotations related to this gene include identical protein binding and protein domain specific binding. An important paralog of this gene is SYNPR.

UniProtKB/Swiss-Prot for SYP Gene

  • Possibly involved in structural functions as organizing other membrane components or in targeting the vesicles to the plasma membrane. Involved in the regulation of short-term and long-term synaptic plasticity (By similarity).

Gene Wiki entry for SYP Gene

Additional gene information for SYP Gene

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

Genomics for SYP Gene

GeneHancer (GH) Regulatory Elements for SYP Gene

Promoters and enhancers for SYP Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0XI049199 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 550.8 -0.1 -59 1.2 SMAD1 ZFP64 ARID4B SIN3A YY1 SLC30A9 POLR2B ZNF766 CBX5 ZNF207 SYP SYP-AS1 FTSJ1 RBM3 ENSG00000204620 CACNA1F
GH0XI049198 Enhancer 0.6 ENCODE 550.8 +1.6 1587 1.1 BCOR MAZ ATF1 ZBTB21 ZNF398 NR3C1 ZIC2 ZNF48 ZFHX2 POLR2A SYP SYP-AS1 PRICKLE3
GH0XI048834 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 9.9 +365.1 365078 2.3 ZNF133 ARID4B GLI4 ZNF2 KLF7 SP3 SP5 YY2 MIER2 REST PCSK1N ZNF81 ENSG00000204620 FTSJ1 ENSG00000270012 ZNF182 CCDC120 PRAF2 PQBP1 SYP
GH0XI049183 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 0.4 +14.3 14346 4 PKNOX1 CLOCK ARID4B SIN3A ZNF2 YY1 POLR2B E2F8 ZNF207 ZNF143 PRICKLE3 PRAF2 CACNA1F SYP PLP2
GH0XI049188 Enhancer 1.2 Ensembl ENCODE 0.4 +9.8 9789 4.3 HDGF PKNOX1 ARID4B NEUROD1 SIN3A ZBTB7B POLR2B ZNF143 FOS SP3 PRICKLE3 CACNA1F PLP2 ENSG00000204620 SYP SYP-AS1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SYP on UCSC Golden Path with GeneCards custom track

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

Genomic Locations for SYP Gene

Genomic Locations for SYP Gene
12,456 bases
Minus strand

Genomic View for SYP Gene

Genes around SYP on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for SYP Gene

Proteins for SYP Gene

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

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • B2R7L6
    • B7Z359
    • Q6P2F7

    Protein attributes for SYP Gene

    313 amino acids
    Molecular mass:
    33845 Da
    Quaternary structure:
    • Homohexamer or homotetramer. Interacts with SRCIN1.

    Alternative splice isoforms for SYP Gene


neXtProt entry for SYP Gene

Post-translational modifications for SYP Gene

  • Ubiquitinated; mediated by SIAH1 or SIAH2 and leading to its subsequent proteasomal degradation.
  • Glycosylation at isoforms=59
  • Modification sites at PhosphoSitePlus

Other Protein References for SYP Gene

Antibody Products

No data available for DME Specific Peptides for SYP Gene

Domains & Families for SYP Gene

Gene Families for SYP Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Potential drug targets
  • Predicted membrane proteins
  • Transporters

Protein Domains for SYP Gene

Suggested Antigen Peptide Sequences for SYP Gene

Graphical View of Domain Structure for InterPro Entry



  • The calcium-binding activity is thought to be localized in the cytoplasmic tail of the protein.
  • Belongs to the synaptophysin/synaptobrevin family.
  • The calcium-binding activity is thought to be localized in the cytoplasmic tail of the protein.
  • Belongs to the synaptophysin/synaptobrevin family.
genes like me logo Genes that share domains with SYP: view

Function for SYP Gene

Molecular function for SYP Gene

GENATLAS Biochemistry:
synaptophysin (integral protein of small presynaptic vesicles of neurons)
UniProtKB/Swiss-Prot Function:
Possibly involved in structural functions as organizing other membrane components or in targeting the vesicles to the plasma membrane. Involved in the regulation of short-term and long-term synaptic plasticity (By similarity).

Gene Ontology (GO) - Molecular Function for SYP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0015485 cholesterol binding IDA 10620806
GO:0042169 SH2 domain binding IEA --
GO:0042802 identical protein binding IEA --
GO:0043621 protein self-association TAS 15217342
genes like me logo Genes that share ontologies with SYP: view
genes like me logo Genes that share phenotypes with SYP: view

Human Phenotype Ontology for SYP Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SYP Gene

MGI Knock Outs for SYP:

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Transcription Factor Targets and HOMER Transcription for SYP Gene

Localization for SYP Gene

Subcellular locations from UniProtKB/Swiss-Prot for SYP Gene

Cytoplasmic vesicle, secretory vesicle, synaptic vesicle membrane; Multi-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 SYP gene
Compartment Confidence
plasma membrane 5
cytoskeleton 3
extracellular 2
mitochondrion 2
nucleus 2
endoplasmic reticulum 2
cytosol 2
lysosome 2
golgi apparatus 2
endosome 1

Gene Ontology (GO) - Cellular Components for SYP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008021 synaptic vesicle IEA,ISS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030054 cell junction IEA --
GO:0030285 integral component of synaptic vesicle membrane NAS 1975480
genes like me logo Genes that share ontologies with SYP: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SYP Gene

Pathways & Interactions for SYP Gene

genes like me logo Genes that share pathways with SYP: view

Pathways by source for SYP Gene

1 BioSystems pathway for SYP Gene
1 Cell Signaling Technology pathway for SYP Gene

Gene Ontology (GO) - Biological Process for SYP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006897 endocytosis ISS --
GO:0016188 synaptic vesicle maturation NAS 10620806
GO:0048168 regulation of neuronal synaptic plasticity IBA,IEA --
GO:0048169 regulation of long-term neuronal synaptic plasticity ISS --
GO:0048172 regulation of short-term neuronal synaptic plasticity ISS --
genes like me logo Genes that share ontologies with SYP: view

No data available for SIGNOR curated interactions for SYP Gene

Drugs & Compounds for SYP Gene

(44) Drugs for SYP Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Approved Nutra 0

(35) Additional Compounds for SYP Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with SYP: view

Transcripts for SYP Gene

Unigene Clusters for SYP Gene

Representative Sequences:

Clone Products

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

ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4a · 4b · 4c ^ 5a · 5b · 5c ^ 6a · 6b ^ 7a · 7b ^ 8a · 8b
SP1: - - - -
SP2: - - - - - -
SP3: - -
SP4: - - - - -
SP5: - - - - - - - -
SP6: -
SP7: - -

Relevant External Links for SYP Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SYP Gene

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

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

This gene is overexpressed in Brain - Frontal Cortex (BA9) (x7.5), Brain - Anterior cingulate cortex (BA24) (x6.7), Brain - Cortex (x6.3), Brain - Hippocampus (x4.6), and Brain - Hypothalamus (x4.1).

Protein differential expression in normal tissues from HIPED for SYP Gene

This gene is overexpressed in Frontal cortex (30.4), Brain (19.0), and Retina (13.5).

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

Protein tissue co-expression partners for SYP Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SYP Gene:


SOURCE GeneReport for Unigene cluster for SYP Gene:


mRNA Expression by UniProt/SwissProt for SYP Gene:

Tissue specificity: Characteristic of a type of small (30-80 nm) neurosecretory vesicles, including presynaptic vesicles, but also vesicles of various neuroendocrine cells of both neuronal and epithelial phenotype.

Evidence on tissue expression from TISSUES for SYP Gene

  • Nervous system(5)
  • Eye(3.2)
  • Adrenal gland(3.1)
  • Intestine(3)
  • Pancreas(3)
  • Lung(2.4)
  • Stomach(2.4)
  • Muscle(2.3)
  • Lymph node(2.1)
  • Skin(2.1)
  • Gall bladder(2)
  • Kidney(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SYP Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • digestive
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Head and neck:
  • brain
  • cerebellum
  • cheek
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • nose
  • outer ear
  • salivary gland
  • skull
  • tooth
  • lung
  • rib
  • rib cage
  • pelvis
  • testicle
  • urinary bladder
  • ankle
  • digit
  • elbow
  • finger
  • foot
  • hand
  • hip
  • knee
  • lower limb
  • shoulder
  • toe
  • upper limb
  • wrist
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with SYP: view

Orthologs for SYP Gene

This gene was present in the common ancestor of animals.

Orthologs for SYP Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SYP 33 34
  • 99.72 (n)
(Bos Taurus)
Mammalia SYP 33 34
  • 91.97 (n)
(Mus musculus)
Mammalia Syp 33 16 34
  • 90.52 (n)
(Rattus norvegicus)
Mammalia Syp 33
  • 90.41 (n)
(Canis familiaris)
Mammalia SYP 33 34
  • 90.29 (n)
(Monodelphis domestica)
Mammalia SYP 34
  • 83 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 64 (a)
(Anolis carolinensis)
Reptilia SYP 34
  • 69 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia syp 33
  • 70.45 (n)
African clawed frog
(Xenopus laevis)
Amphibia syp-B 33
(Danio rerio)
Actinopterygii sypa 33 34
  • 68.49 (n)
sypb 34
  • 67 (a)
Dr.11716 33
(Caenorhabditis elegans)
Secernentea sph-1 34
  • 26 (a)
Species where no ortholog for SYP was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • chicken (Gallus gallus)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • 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)
  • wheat (Triticum aestivum)

Evolution for SYP Gene

Gene Tree for SYP (if available)
Gene Tree for SYP (if available)

Paralogs for SYP Gene

Paralogs for SYP Gene

(4) SIMAP similar genes for SYP Gene using alignment to 5 proteins:

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

Variants for SYP Gene

Sequence variations from dbSNP and Humsavar for SYP Gene

SNP ID Clin Chr 0X pos Variation AA Info Type
rs1057515926 uncertain-significance, Non-syndromic X-linked intellectual disability 49,191,602(-) G/A coding_sequence_variant, synonymous_variant
rs1057515927 uncertain-significance, Non-syndromic X-linked intellectual disability 49,200,194(-) G/A/T 5_prime_UTR_variant
rs137852561 pathogenic, Mental retardation, X-linked 96, Mental retardation, X-linked 96 (MRX96) [MIM:300802] 49,191,730(-) C/G/T coding_sequence_variant, missense_variant
rs139475570 likely-benign, Non-syndromic X-linked intellectual disability, Mental retardation, X-linked 96 (MRX96) [MIM:300802] 49,191,502(-) C/T coding_sequence_variant, missense_variant
rs17144222 benign, Non-syndromic X-linked intellectual disability 49,188,232(-) G/A 3_prime_UTR_variant

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

Variant ID Type Subtype PubMed ID
esv32909 CNV gain+loss 17666407
nsv205 OTHER inversion 15895083
nsv528292 CNV gain 19592680
nsv7442 OTHER inversion 18451855

Variation tolerance for SYP Gene

Residual Variation Intolerance Score: 61.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.27; 6.00% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SYP Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

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

Disorders for SYP Gene

MalaCards: The human disease database

(212) MalaCards diseases for SYP Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
mental retardation, x-linked 96
  • mrx96
x-linked non-specific intellectual disability
  • x-linked non-syndromic intellectual disability
central neurocytoma
  • neurolipocytoma
neuroendocrine tumor
  • neuroendocrine neoplasm
large cell carcinoma
  • carcinoma large cell
- elite association - COSMIC cancer census association via MalaCards
Search SYP in MalaCards View complete list of genes associated with diseases


  • Mental retardation, X-linked 96 (MRX96) [MIM:300802]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. {ECO:0000269 PubMed:19377476}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for SYP

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

No data available for Genatlas for SYP Gene

Publications for SYP Gene

  1. A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardation. (PMID: 19377476) Tarpey PS … Stratton MR (Nature genetics 2009) 2 3 4 58
  2. Sequence-based exon prediction around the synaptophysin locus reveals a gene-rich area containing novel genes in human proximal Xp. (PMID: 9344658) Fisher SE … Craig IW (Genomics 1997) 3 4 22 58
  3. Synaptophysin: structure of the human gene and assignment to the X chromosome in man and mouse. (PMID: 1975480) Ozçelik T … Südhof TC (American journal of human genetics 1990) 3 4 22 58
  4. The cDNA and derived amino acid sequences for rat and human synaptophysin. (PMID: 3120152) Südhof TC … Jahn R (Nucleic acids research 1987) 2 3 4 58
  5. Characterization of a multidomain adaptor protein, p140Cap, as part of a pre-synaptic complex. (PMID: 18662323) Ito H … Nagata K (Journal of neurochemistry 2008) 3 4 58

Products for SYP Gene

Sources for SYP Gene

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