SYT10 Gene (Protein Coding)

Synaptotagmin 10

GC12M033374
GIFtS:
35
See more...

Aliases for SYT10 Gene

Aliases for SYT10 Gene

  • Synaptotagmin 10 2 3 5
  • Synaptotagmin X 2 3 4
  • Synaptotagmin-10 3 4
  • SytX 3 4
  • SYT10 5

External Ids for SYT10 Gene

Previous GeneCards Identifiers for SYT10 Gene

  • GC00U906274
  • GC12M033421
  • GC12M033419
  • GC12M033528
  • GC12M033268

Summaries for SYT10 Gene

GeneCards Summary for SYT10 Gene

SYT10 (Synaptotagmin 10) is a Protein Coding gene. Diseases associated with SYT10 include Kaufman Oculocerebrofacial Syndrome and Kagami-Ogata Syndrome. Among its related pathways are Protein-protein interactions at synapses and Transmission across Chemical Synapses. Gene Ontology (GO) annotations related to this gene include calcium ion binding and identical protein binding. An important paralog of this gene is SYT6.

UniProtKB/Swiss-Prot Summary for SYT10 Gene

  • Ca(2+) sensor specifically required for the Ca(2+)-dependent exocytosis of secretory vesicles containing IGF1 in neurons of the olfactory bulb. Exocytosis of IGF1 is required for sensory perception of smell. Not involved in Ca(2+)-dependent synaptic vesicle exocytosis (By similarity). Acts through Ca(2+) and phospholipid binding to the C2 domain: Ca(2+) induces binding of the C2-domains to phospholipid membranes and to assembled SNARE-complexes; both actions contribute to triggering exocytosis (By similarity).

Additional gene information for SYT10 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SYT10 Gene

Genomics for SYT10 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for SYT10 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
GH12J033438 Promoter/Enhancer 1.4 EPDnew Ensembl ENCODE 270.3 +0.4 419 2 CUX1 VEZF1 NONO CTBP1 PRDM10 MAZ NRF1 ZBTB33 TAF1 TFDP1 SYT10 HSALNG0090331 ENSG00000259937 YARS2 PKP2
GH12J033443 Promoter 0.6 Ensembl 250.7 +1.7 1718 0.2 RELA NCOA1 RFX1 BRD4 ATF1 EZH2 HSALNG0090331 SYT10 ENSG00000273853 PKP2
GH12J033534 Enhancer 0.4 Ensembl 22.2 -93.7 -93682 0.2 ZNF140 ZC3H11A ZNF202 ZNF266 ENSG00000257511 ALG10 SYT10 YARS2 piR-61101-128 piR-32023-055
GH12J033533 Enhancer 0.2 Ensembl 22.2 -93.1 -93082 0.6 SYT10 piR-61101-128 piR-32023-055 ALG10
GH12J033020 Enhancer 0.6 ENCODE 4.1 +418.4 418400 1.2 ZNF217 CUX1 CTBP1 SMARCE1 DPF2 FOSL2 ZNF366 GATAD2B NFRKB EP300 piR-43099-106 piR-31432-118 piR-56759-114 piR-45471-107 piR-54764-111 piR-46662-115 piR-56451-031 ENSG00000259937 SYT10 HSALNG0090306
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SYT10 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SYT10

Top Transcription factor binding sites by QIAGEN in the SYT10 gene promoter:
  • c-Myc
  • CUTL1
  • Evi-1
  • FOXD3
  • Max
  • p300
  • Pbx1a
  • SRF
  • SRF (504 AA)
  • YY1

Genomic Locations for SYT10 Gene

Latest Assembly
chr12:33,374,238-33,439,819
(GRCh38/hg38)
Size:
65,582 bases
Orientation:
Minus strand

Previous Assembly
chr12:33,527,173-33,592,754
(GRCh37/hg19 by Entrez Gene)
Size:
65,582 bases
Orientation:
Minus strand

chr12:33,527,173-33,592,754
(GRCh37/hg19 by Ensembl)
Size:
65,582 bases
Orientation:
Minus strand

Genomic View for SYT10 Gene

Genes around SYT10 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SYT10 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SYT10 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for SYT10 Gene

Proteins for SYT10 Gene

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  • Protein details for SYT10 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6XYQ8-SYT10_HUMAN
    Recommended name:
    Synaptotagmin-10
    Protein Accession:
    Q6XYQ8
    Secondary Accessions:
    • Q495U2

    Protein attributes for SYT10 Gene

    Size:
    523 amino acids
    Molecular mass:
    59127 Da
    Cofactor:
    Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
    Quaternary structure:
    • Homodimer; disulfide-linked via the cysteine motif. Can also form heterodimers with SYT3, SYT6, SYT7 and SYT9.

neXtProt entry for SYT10 Gene

Protein Expression for SYT10 Gene

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

Post-translational modifications for SYT10 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SYT10 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SYT10 Gene

Domains & Families for SYT10 Gene

Gene Families for SYT10 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for SYT10 Gene

InterPro:
Blocks:
  • C2 domain
ProtoNet:

Suggested Antigen Peptide Sequences for SYT10 Gene

GenScript: Design optimal peptide antigens:
  • SYT10 protein (Q495U1_HUMAN)
  • Synaptotagmin X (SYT10_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q6XYQ8

UniProtKB/Swiss-Prot:

SYT10_HUMAN :
  • The cysteine motif mediates homo- or heterodimer formation via formation of disulfide bonds.
  • Belongs to the synaptotagmin family.
Domain:
  • The cysteine motif mediates homo- or heterodimer formation via formation of disulfide bonds.
  • The first C2 domain mediates Ca(2+)-dependent phospholipid binding.
Family:
  • Belongs to the synaptotagmin family.
genes like me logo Genes that share domains with SYT10: view

Function for SYT10 Gene

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  6. Cell Lines for research

Molecular function for SYT10 Gene

UniProtKB/Swiss-Prot Function:
Ca(2+) sensor specifically required for the Ca(2+)-dependent exocytosis of secretory vesicles containing IGF1 in neurons of the olfactory bulb. Exocytosis of IGF1 is required for sensory perception of smell. Not involved in Ca(2+)-dependent synaptic vesicle exocytosis (By similarity). Acts through Ca(2+) and phospholipid binding to the C2 domain: Ca(2+) induces binding of the C2-domains to phospholipid membranes and to assembled SNARE-complexes; both actions contribute to triggering exocytosis (By similarity).

Phenotypes From GWAS Catalog for SYT10 Gene

Gene Ontology (GO) - Molecular Function for SYT10 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000149 SNARE binding IBA 21873635
GO:0001786 phosphatidylserine binding IBA 21873635
GO:0005509 calcium ion binding IBA,ISS --
GO:0005544 calcium-dependent phospholipid binding IBA 21873635
GO:0019905 syntaxin binding IBA 21873635
genes like me logo Genes that share ontologies with SYT10: view
genes like me logo Genes that share phenotypes with SYT10: view

Animal Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SYT10

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for SYT10 Gene

Localization for SYT10 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SYT10 Gene

Cytoplasmic vesicle, secretory vesicle membrane. Single-pass membrane protein. Note=Localizes to neuronal vesicles containing IGF1 that are not enriched at synapses. Does not colocalize with synaptic vesicles or with the Golgi apparatus. {ECO:0000250 UniProtKB:Q9R0N4}.

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 SYT10 gene
Compartment Confidence
plasma membrane 4
cytosol 3
extracellular 2
cytoskeleton 2
mitochondrion 2
endoplasmic reticulum 2
endosome 2
lysosome 2
golgi apparatus 2
peroxisome 1
nucleus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Vesicles (2)
  • Nucleoplasm (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SYT10 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IBA 21873635
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030658 transport vesicle membrane IEA --
GO:0031410 cytoplasmic vesicle IEA --
genes like me logo Genes that share ontologies with SYT10: view

Pathways & Interactions for SYT10 Gene

genes like me logo Genes that share pathways with SYT10: view

Pathways by source for SYT10 Gene

Gene Ontology (GO) - Biological Process for SYT10 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006887 exocytosis IEA --
GO:0007268 chemical synaptic transmission ISS --
GO:0007608 sensory perception of smell ISS --
GO:0014059 regulation of dopamine secretion IBA 21873635
GO:0016079 NOT synaptic vesicle exocytosis ISS --
genes like me logo Genes that share ontologies with SYT10: view

No data available for SIGNOR curated interactions for SYT10 Gene

Drugs & Compounds for SYT10 Gene

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(1) Drugs for SYT10 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium Nutra 6876
genes like me logo Genes that share compounds with SYT10: view

Transcripts for SYT10 Gene

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mRNA/cDNA for SYT10 Gene

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

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SYT10

Alternative Splicing Database (ASD) splice patterns (SP) for SYT10 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9
SP1:
SP2: - -

Relevant External Links for SYT10 Gene

GeneLoc Exon Structure for
SYT10

Expression for SYT10 Gene

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  1. Primer products for research
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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SYT10 Gene

mRNA expression in normal human tissues for SYT10 Gene
mRNA expression by GTEx for SYT10 GenemRNA expression by BioGPS for SYT10 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SYT10 Gene

This gene is overexpressed in Nerve - Tibial (x8.0), Pituitary (x4.2), and Colon - Sigmoid (x4.1).

Protein differential expression in normal tissues from HIPED for SYT10 Gene

This gene is overexpressed in Pancreatic juice (67.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SYT10 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SYT10

SOURCE GeneReport for Unigene cluster for SYT10 Gene:

Hs.118703

mRNA Expression by UniProt/SwissProt for SYT10 Gene:

Q6XYQ8-SYT10_HUMAN
Tissue specificity: Expressed only in pancreas, lung and kidney.

Evidence on tissue expression from TISSUES for SYT10 Gene

  • Nervous system(4.5)
  • Adrenal gland(2.1)
genes like me logo Genes that share expression patterns with SYT10: view

Primer products for research

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for SYT10 Gene

Orthologs for SYT10 Gene

This gene was present in the common ancestor of animals.

Orthologs for SYT10 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia SYT10 30 31
  • 99.11 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia SYT10 30 31
  • 93.3 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia SYT10 30 31
  • 91.33 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Syt10 30
  • 87.19 (n)
Mouse
(Mus musculus)
 Mammalia Syt10 30 17 31
  • 87.19 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia SYT10 31
  • 87 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves SYT10 30 31
  • 81.55 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia SYT10 31
  • 86 (a)
 OneToOne
Zebrafish
(Danio rerio)
 Actinopterygii syt10 30 31
  • 67.88 (n)
 OneToOne
Fruit Fly
(Drosophila melanogaster)
 Insecta Syt1 31
  • 34 (a)
 OneToMany
Worm
(Caenorhabditis elegans)
 Secernentea snt-3 31
  • 45 (a)
 ManyToMany
snt-1 31
  • 35 (a)
 ManyToMany
snt-2 31
  • 35 (a)
 ManyToMany
Species where no ortholog for SYT10 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • 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)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (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)

Evolution for SYT10 Gene

ENSEMBL:
Gene Tree for SYT10 (if available)
TreeFam:
Gene Tree for SYT10 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SYT10: view image

Paralogs for SYT10 Gene

Paralogs for SYT10 Gene

(18) SIMAP similar genes for SYT10 Gene using alignment to 4 proteins:

  • SYT10_HUMAN
  • F5GZB8_HUMAN
  • F5H2A8_HUMAN
  • Q495U1_HUMAN
genes like me logo Genes that share paralogs with SYT10: view

Variants for SYT10 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SYT10 Gene

SNP ID Clinical significance and condition Chr 12 pos Variation AA Info Type
rs11832759 Benign: not provided 33,426,278(-) G/A
NM_198992.4(SYT10):c.369C>T (p.Ala123=) 		SYNONYMOUS
rs34361405 Benign: not provided. - 33,376,888(-) G/Ap.Ala505Val
NM_198992.4(SYT10):c.1514C>T (p.Ala505Val) 		MISSENSE
rs35190376 Benign: not provided. - 33,382,460(-) G/Cp.Thr420Ser
NM_198992.4(SYT10):c.1259C>G (p.Thr420Ser) 		MISSENSE
rs12317722 - p.Ser172Ile
rs34190017 - p.His488Pro

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SYT10 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for SYT10 Gene

Variant ID Type Subtype PubMed ID
dgv1432n100 CNV gain 25217958
dgv1433n100 CNV gain 25217958
dgv2502n54 CNV gain 21841781
dgv2503n54 CNV gain 21841781
dgv267e214 CNV gain 21293372
dgv268e214 CNV loss 21293372
esv2759892 CNV gain+loss 17122850
esv2761043 CNV gain+loss 21179565
esv34883 CNV gain 17911159
esv3581460 CNV gain 25503493
esv3629113 CNV gain 21293372
esv3629115 CNV loss 21293372
nsv1035988 CNV gain 25217958
nsv1036239 CNV gain 25217958
nsv469348 CNV gain 19166990
nsv558248 CNV gain 21841781
nsv558255 CNV loss 21841781
nsv818908 CNV gain 17921354
nsv820253 CNV loss 19587683
nsv832368 CNV gain 17160897

Variation tolerance for SYT10 Gene

Residual Variation Intolerance Score: 29% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.84; 48.05% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SYT10 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SYT10

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SYT10 Gene

Disorders for SYT10 Gene

MalaCards: The human disease database

(3) MalaCards diseases for SYT10 Gene - From: COP

Disorder Aliases PubMed IDs
kaufman oculocerebrofacial syndrome
  • kos
kagami-ogata syndrome
  • uniparental disomy, paternal, chromosome 14
mitochondrial complex i deficiency, nuclear type 1
  • mc1dn1
- elite association - COSMIC cancer census association via MalaCards
Search SYT10 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SYT10

Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with SYT10: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SYT10 Gene

Publications for SYT10 Gene

  1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  2. Cloning and characterization of human synaptotagmin 10 gene. (PMID: 14756426) Zhao E … Mao Y (DNA sequence : the journal of DNA sequencing and mapping 2003) 3 4
  3. The midbody interactome reveals unexpected roles for PP1 phosphatases in cytokinesis. (PMID: 31586073) Capalbo L … D'Avino PP (Nature communications 2019) 3
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3
  5. DEAD-box helicase DDX27 regulates 3' end formation of ribosomal 47S RNA and stably associates with the PeBoW-complex. (PMID: 25825154) Kellner M … Eick D (Experimental cell research 2015) 3

ExternalLinks

View latest publications for SYT10 gene in Mastermind

Products for SYT10 Gene

Sources for SYT10 Gene