This gene is a member of the synaptotagmin gene family and encodes a protein similar to other family members that mediate calcium-dependent regulation of membrane trafficking in synaptic transmission. Studies of the orthologous gene in rat have shown that the encoded protein selectively modulates spontaneous synaptic-vesicle exocytosis and may also be involved in regulating cal... See more...

Aliases for SYT12 Gene

Aliases for SYT12 Gene

  • Synaptotagmin 12 2 3 5
  • Synaptotagmin XII 2 4
  • Synaptotagmin-12 3 4
  • SytXII 3 4
  • Synaptotagmin-XII 3
  • SYT11 3

External Ids for SYT12 Gene

Previous GeneCards Identifiers for SYT12 Gene

  • GC11P069308
  • GC11P068455
  • GC11P066549
  • GC11P066566
  • GC11P066530
  • GC11P066791
  • GC11P063117

Summaries for SYT12 Gene

Entrez Gene Summary for SYT12 Gene

  • This gene is a member of the synaptotagmin gene family and encodes a protein similar to other family members that mediate calcium-dependent regulation of membrane trafficking in synaptic transmission. Studies of the orthologous gene in rat have shown that the encoded protein selectively modulates spontaneous synaptic-vesicle exocytosis and may also be involved in regulating calcium independent secretion in nonneuronal cells. Alternative splicing results in multiple transcript variants. The gene has previously been referred to as synaptotagmin XI but has been renamed synaptotagmin XII to be standard with mouse and rat official nomenclature.[provided by RefSeq, Apr 2010]

GeneCards Summary for SYT12 Gene

SYT12 (Synaptotagmin 12) is a Protein Coding gene. Diseases associated with SYT12 include Parkinson Disease, Late-Onset. 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 calcium-dependent phospholipid binding. An important paralog of this gene is SYT6.

UniProtKB/Swiss-Prot Summary for SYT12 Gene

  • Synaptic vesicle phosphoprotein that enhances spontaneous neurotransmitter release but does not effect induced neurotransmitter release (By similarity). Unlike other synaptotagmins, it does not bind Ca(2+) or phospholipids (By similarity). Essential for mossy-fiber long-term potentiation in the hippocampus (By similarity).

Additional gene information for SYT12 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SYT12 Gene

Genomics for SYT12 Gene

GeneHancer (GH) Regulatory Elements for SYT12 Gene

Promoters and enhancers for SYT12 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
GH11J067021 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE dbSUPER 500.4 +16.8 16819 3.8 EP300 CTCF ZIC2 CLOCK ZNF423 GABPA ZBTB26 REST RFX1 CHD1 SYT12 RHOD PC RNU7-23P CTSF lnc-RHOD-3 lnc-C11orf86-1
GH11J067006 Enhancer 1 Ensembl ENCODE 500.7 +0.1 128 1.8 USF1 AFF1 REST USF2 NR3C1 TOE1 NFRKB NFYB RBM25 RAD51 lnc-C11orf86-1 SYT12 lnc-RHOD-3
GH11J066901 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 10.7 -101.2 -101237 7.8 EP300 FOXK2 TCF12 POLR2G USF1 NCOR1 ZIC2 KDM6A TCF7 ZNF623 PC C11orf80 RHOD ACTN3 CTSF RIN1 C11orf86 LRFN4 SYT12 ENSG00000254510
GH11J066949 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 11.7 -55.3 -55258 4.6 ZNF217 TCF12 POLR2G RBAK JUND FOS ZNF639 ZIC2 TRIM28 TARDBP ACTN3 SYT12 RHOD RPS6KB2 ENSG00000255517 CLCF1 GRK2 LOC105369355 PC piR-44451-003
GH11J066889 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 11.2 -114.7 -114673 4.6 ZNF217 CTCF TCF12 SP1 JUND FOS ZNF639 REST ZBTB11 AFF1 RAD9A LRFN4 CTSF RCE1 RNU7-23P PC SYT12 ACTN3 CDK2AP2 CLCF1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SYT12 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SYT12

Top Transcription factor binding sites by QIAGEN in the SYT12 gene promoter:
  • AML1a
  • AP-2rep
  • Egr-3
  • MIF-1
  • NF-1
  • NF-1/L
  • p300
  • RP58
  • STAT1

Genomic Locations for SYT12 Gene

Genomic Locations for SYT12 Gene
chr11:67,006,773-67,050,863
(GRCh38/hg38)
Size:
44,091 bases
Orientation:
Plus strand
chr11:66,774,249-66,818,334
(GRCh37/hg19)
Size:
44,086 bases
Orientation:
Plus strand

Genomic View for SYT12 Gene

Genes around SYT12 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SYT12 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SYT12 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SYT12 Gene

Proteins for SYT12 Gene

  • Protein details for SYT12 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8IV01-SYT12_HUMAN
    Recommended name:
    Synaptotagmin-12
    Protein Accession:
    Q8IV01

    Protein attributes for SYT12 Gene

    Size:
    421 amino acids
    Molecular mass:
    46537 Da
    Quaternary structure:
    • Homodimer (By similarity). Can also form heterodimers (By similarity). Interacts with SYT1 (By similarity).

neXtProt entry for SYT12 Gene

Post-translational modifications for SYT12 Gene

  • Phosphorylation of Ser-97 is required for mossy-fiber long-term potentiation.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SYT12 Gene

Domains & Families for SYT12 Gene

Gene Families for SYT12 Gene

Protein Domains for SYT12 Gene

Blocks:
  • C2 domain
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SYT12 Gene

GenScript: Design optimal peptide antigens:
  • Synaptotagmin XII (SYT12_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8IV01

UniProtKB/Swiss-Prot:

SYT12_HUMAN :
  • Belongs to the synaptotagmin family.
Family:
  • Belongs to the synaptotagmin family.
genes like me logo Genes that share domains with SYT12: view

Function for SYT12 Gene

Molecular function for SYT12 Gene

UniProtKB/Swiss-Prot Function:
Synaptic vesicle phosphoprotein that enhances spontaneous neurotransmitter release but does not effect induced neurotransmitter release (By similarity). Unlike other synaptotagmins, it does not bind Ca(2+) or phospholipids (By similarity). Essential for mossy-fiber long-term potentiation in the hippocampus (By similarity).

Phenotypes From GWAS Catalog for SYT12 Gene

Gene Ontology (GO) - Molecular Function for SYT12 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 21873635
GO:0005544 calcium-dependent phospholipid binding IBA 21873635
GO:0019905 syntaxin binding IBA 21873635
genes like me logo Genes that share ontologies with SYT12: view
genes like me logo Genes that share phenotypes with SYT12: view

Animal Model Products

  • Taconic Biosciences Mouse Models for SYT12

CRISPR Products

miRNA for SYT12 Gene

miRTarBase miRNAs that target SYT12

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SYT12

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SYT12 Gene

Localization for SYT12 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SYT12 Gene

Cytoplasmic vesicle, secretory vesicle, synaptic vesicle membrane; Single-pass membrane protein.

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 SYT12 gene
Compartment Confidence
plasma membrane 4
extracellular 2
cytoskeleton 2
nucleus 2
endoplasmic reticulum 2
endosome 2
cytosol 2
lysosome 2
golgi apparatus 2
mitochondrion 1
peroxisome 0

Gene Ontology (GO) - Cellular Components for SYT12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IBA 21873635
GO:0008021 synaptic vesicle IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030054 cell junction IEA --
genes like me logo Genes that share ontologies with SYT12: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SYT12 Gene

Pathways & Interactions for SYT12 Gene

genes like me logo Genes that share pathways with SYT12: view

Pathways by source for SYT12 Gene

Gene Ontology (GO) - Biological Process for SYT12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0014059 regulation of dopamine secretion IBA 21873635
GO:0016192 vesicle-mediated transport IBA 21873635
GO:0017156 calcium ion regulated exocytosis IBA 21873635
GO:0017158 regulation of calcium ion-dependent exocytosis IBA 21873635
GO:0046928 regulation of neurotransmitter secretion IEA --
genes like me logo Genes that share ontologies with SYT12: view

No data available for SIGNOR curated interactions for SYT12 Gene

Drugs & Compounds for SYT12 Gene

No Compound Related Data Available

Transcripts for SYT12 Gene

mRNA/cDNA for SYT12 Gene

4 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
7 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 SYT12

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SYT12 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b · 12c · 12d · 12e ^ 13 ^ 14 ^ 15 ^ 16
SP1: - - - - - - -
SP2: - -
SP3: - - -
SP4: - - - - -
SP5: - - - -
SP6: -
SP7: - - -

Relevant External Links for SYT12 Gene

GeneLoc Exon Structure for
SYT12

Expression for SYT12 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SYT12 Gene

mRNA differential expression in normal tissues according to GTEx for SYT12 Gene

This gene is overexpressed in Brain - Cerebellum (x7.8), Brain - Cerebellar Hemisphere (x7.4), Brain - Cortex (x4.9), and Brain - Frontal Cortex (BA9) (x4.0).

Protein differential expression in normal tissues from HIPED for SYT12 Gene

This gene is overexpressed in Frontal cortex (36.7) and Cervix (32.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SYT12 Gene



Protein tissue co-expression partners for SYT12 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SYT12

SOURCE GeneReport for Unigene cluster for SYT12 Gene:

Hs.287636

Evidence on tissue expression from TISSUES for SYT12 Gene

  • Nervous system(4.5)
  • Liver(4.1)
genes like me logo Genes that share expression patterns with SYT12: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SYT12 Gene

Orthologs for SYT12 Gene

This gene was present in the common ancestor of animals.

Orthologs for SYT12 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SYT12 31 30
  • 99.27 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SYT12 31 30
  • 90.89 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SYT12 31 30
  • 90.82 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SYT12 31
  • 89 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Syt12 30
  • 88.12 (n)
mouse
(Mus musculus)
Mammalia Syt12 17 31 30
  • 87.97 (n)
oppossum
(Monodelphis domestica)
Mammalia SYT12 31
  • 78 (a)
OneToOne
chicken
(Gallus gallus)
Aves SYT12 31 30
  • 76.38 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SYT12 31
  • 74 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia syt12 30
  • 68.56 (n)
zebrafish
(Danio rerio)
Actinopterygii syt12 31 30
  • 68.04 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Syt12 31
  • 16 (a)
OneToOne
Species where no ortholog for SYT12 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)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for SYT12 Gene

ENSEMBL:
Gene Tree for SYT12 (if available)
TreeFam:
Gene Tree for SYT12 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SYT12: view image

Paralogs for SYT12 Gene

(6) SIMAP similar genes for SYT12 Gene using alignment to 2 proteins:

  • SYT12_HUMAN
  • E9PNM5_HUMAN
genes like me logo Genes that share paralogs with SYT12: view

Variants for SYT12 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SYT12 Gene

SNP ID Clinical significance and condition Chr 11 pos Variation AA Info Type
rs201856506 Not Provided: not provided 67,043,807(+) C/T MISSENSE_VARIANT
rs11227664 - p.Asn170His

Additional dbSNP identifiers (rs#s) for SYT12 Gene

Structural Variations from Database of Genomic Variants (DGV) for SYT12 Gene

Variant ID Type Subtype PubMed ID
dgv1973n54 CNV loss 21841781
nsv1134147 CNV deletion 24896259
nsv555226 CNV gain 21841781
nsv832194 CNV gain+loss 17160897

Variation tolerance for SYT12 Gene

Residual Variation Intolerance Score: 82.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.86; 67.35% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SYT12 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SYT12

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SYT12 Gene

Disorders for SYT12 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SYT12 Gene - From: DISEASES

Disorder Aliases PubMed IDs
parkinson disease, late-onset
  • pd
- elite association - COSMIC cancer census association via MalaCards
Search SYT12 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SYT12

genes like me logo Genes that share disorders with SYT12: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SYT12 Gene

Publications for SYT12 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 54
  2. Agrin has a pathological role in the progression of oral cancer. (PMID: 29872149) Rivera C … Paes Leme AF (British journal of cancer 2018) 3 54
  3. LuTHy: a double-readout bioluminescence-based two-hybrid technology for quantitative mapping of protein-protein interactions in mammalian cells. (PMID: 29997244) Trepte P … Wanker EE (Molecular systems biology 2018) 3 54
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 54
  5. An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome. (PMID: 24275569) Bian Y … Zou H (Journal of proteomics 2014) 4 54

Products for SYT12 Gene

Sources for SYT12 Gene