The protein encoded by this gene belongs to a family of peripheral membrane proteins that play a role in vesicular trafficking. This protein binds phospholipids in the presence of calcium ions. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2016] See more...

Aliases for SYTL3 Gene

Aliases for SYTL3 Gene

  • Synaptotagmin Like 3 2 3 5
  • Synaptotagmin-Like Protein 3 3 4
  • Exophilin-6 3 4
  • SLP3 3 4

External Ids for SYTL3 Gene

Previous GeneCards Identifiers for SYTL3 Gene

  • GC06P158521
  • GC06P158944
  • GC06P158980
  • GC06P159041
  • GC06P158991
  • GC06P159071
  • GC06P156541

Summaries for SYTL3 Gene

Entrez Gene Summary for SYTL3 Gene

  • The protein encoded by this gene belongs to a family of peripheral membrane proteins that play a role in vesicular trafficking. This protein binds phospholipids in the presence of calcium ions. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2016]

GeneCards Summary for SYTL3 Gene

SYTL3 (Synaptotagmin Like 3) is a Protein Coding gene. Diseases associated with SYTL3 include Griscelli Syndrome, Type 1 and Griscelli Syndrome, Type 3. Among its related pathways are Deregulation of Rab and Rab Effector Genes in Bladder Cancer. Gene Ontology (GO) annotations related to this gene include calcium ion binding and Rab GTPase binding. An important paralog of this gene is SYTL5.

UniProtKB/Swiss-Prot Summary for SYTL3 Gene

  • May act as Rab effector protein and play a role in vesicle trafficking. Binds phospholipids in the presence of calcium ions (By similarity).

Additional gene information for SYTL3 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SYTL3 Gene

Genomics for SYTL3 Gene

GeneHancer (GH) Regulatory Elements for SYTL3 Gene

Promoters and enhancers for SYTL3 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SYTL3 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SYTL3

Top Transcription factor binding sites by QIAGEN in the SYTL3 gene promoter:
  • aMEF-2
  • Elk-1
  • FAC1
  • LCR-F1
  • MEF-2A
  • Nkx2-5
  • POU3F2
  • POU3F2 (N-Oct-5a)
  • POU3F2 (N-Oct-5b)
  • STAT3

Genomic Locations for SYTL3 Gene

Genomic Locations for SYTL3 Gene
chr6:158,644,899-158,764,876
(GRCh38/hg38)
Size:
119,978 bases
Orientation:
Plus strand
chr6:159,071,046-159,185,908
(GRCh37/hg19)
Size:
114,863 bases
Orientation:
Plus strand

Genomic View for SYTL3 Gene

Genes around SYTL3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SYTL3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SYTL3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SYTL3 Gene

Proteins for SYTL3 Gene

  • Protein details for SYTL3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q4VX76-SYTL3_HUMAN
    Recommended name:
    Synaptotagmin-like protein 3
    Protein Accession:
    Q4VX76
    Secondary Accessions:
    • Q496J4
    • Q496J6
    • Q5U3B9

    Protein attributes for SYTL3 Gene

    Size:
    610 amino acids
    Molecular mass:
    68560 Da
    Quaternary structure:
    • Monomer. Binds NRXN1. Binds RAB27A that has been activated by GTP-binding via its N-terminus (By similarity).

    Alternative splice isoforms for SYTL3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SYTL3 Gene

Post-translational modifications for SYTL3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SYTL3 Gene

Domains & Families for SYTL3 Gene

Gene Families for SYTL3 Gene

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

Protein Domains for SYTL3 Gene

Blocks:
  • C2 domain
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SYTL3 Gene

GenScript: Design optimal peptide antigens:
  • Synaptotagmin-like 3, isoform CRA_d (E1P5A7_HUMAN)
  • Exophilin-6 (SYTL3_HUMAN)
genes like me logo Genes that share domains with SYTL3: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for SYTL3 Gene

Function for SYTL3 Gene

Molecular function for SYTL3 Gene

UniProtKB/Swiss-Prot Function:
May act as Rab effector protein and play a role in vesicle trafficking. Binds phospholipids in the presence of calcium ions (By similarity).

Phenotypes From GWAS Catalog for SYTL3 Gene

Gene Ontology (GO) - Molecular Function for SYTL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005544 calcium-dependent phospholipid binding IEA --
GO:0017137 Rab GTPase binding IEA --
GO:0042043 neurexin family protein binding IEA --
genes like me logo Genes that share ontologies with SYTL3: view
genes like me logo Genes that share phenotypes with SYTL3: view

Animal Model Products

CRISPR Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SYTL3 Gene

Localization for SYTL3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SYTL3 Gene

Endomembrane system; Peripheral 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 SYTL3 gene
Compartment Confidence
plasma membrane 3
nucleus 3
cytosol 3
extracellular 1
cytoskeleton 1
mitochondrion 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli fibrillar center (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SYTL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0012505 endomembrane system IEA --
GO:0016020 membrane IEA --
GO:0019897 extrinsic component of plasma membrane IEA --
GO:0070382 exocytic vesicle IBA 21873635
genes like me logo Genes that share ontologies with SYTL3: view

Pathways & Interactions for SYTL3 Gene

genes like me logo Genes that share pathways with SYTL3: view

Pathways by source for SYTL3 Gene

Gene Ontology (GO) - Biological Process for SYTL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006886 intracellular protein transport IEA --
GO:0006887 exocytosis IEA --
genes like me logo Genes that share ontologies with SYTL3: view

No data available for SIGNOR curated interactions for SYTL3 Gene

Drugs & Compounds for SYTL3 Gene

(2) Drugs for SYTL3 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium Approved Nutra 7884
Guanosine triphosphate Experimental Pharma 0
genes like me logo Genes that share compounds with SYTL3: view

Transcripts for SYTL3 Gene

mRNA/cDNA for SYTL3 Gene

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

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SYTL3 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3a · 3b · 3c · 3d ^ 4 ^ 5a · 5b ^ 6a · 6b · 6c ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^
SP1: - - - - - - -
SP2: - - - - - - - - - -
SP3: - -
SP4: - - - - - - - - -
SP5: - - - - - - - -
SP6: - - - - - - -
SP7:
SP8: - - - - - -
SP9: -
SP10: - - -
SP11: - -
SP12:

ExUns: 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22a · 22b · 22c
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7: -
SP8:
SP9:
SP10:
SP11:
SP12:

Relevant External Links for SYTL3 Gene

GeneLoc Exon Structure for
SYTL3

Expression for SYTL3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SYTL3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SYTL3 Gene

This gene is overexpressed in Whole Blood (x16.1).

Protein differential expression in normal tissues from HIPED for SYTL3 Gene

This gene is overexpressed in Urine (65.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SYTL3 Gene



Protein tissue co-expression partners for SYTL3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SYTL3

SOURCE GeneReport for Unigene cluster for SYTL3 Gene:

Hs.436977
genes like me logo Genes that share expression patterns with SYTL3: view

No data available for mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for SYTL3 Gene

Orthologs for SYTL3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SYTL3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SYTL3 31 30
  • 98.69 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SYTL3 31 30
  • 84.92 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SYTL3 31 30
  • 82.38 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Sytl3 17 31 30
  • 82.32 (n)
rat
(Rattus norvegicus)
Mammalia Sytl3 30
  • 80.87 (n)
oppossum
(Monodelphis domestica)
Mammalia SYTL3 31
  • 66 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SYTL3 31
  • 58 (a)
OneToOne
chicken
(Gallus gallus)
Aves SYTL3 31 30
  • 64.46 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SYTL3 31
  • 55 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sytl3 30
  • 61.09 (n)
zebrafish
(Danio rerio)
Actinopterygii sytl3 31
  • 35 (a)
OneToOne
Species where no ortholog for SYTL3 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)
  • 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 SYTL3 Gene

ENSEMBL:
Gene Tree for SYTL3 (if available)
TreeFam:
Gene Tree for SYTL3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SYTL3: view image

Paralogs for SYTL3 Gene

(7) SIMAP similar genes for SYTL3 Gene using alignment to 3 proteins:

  • SYTL3_HUMAN
  • F8W7H4_HUMAN
  • H0UI19_HUMAN
genes like me logo Genes that share paralogs with SYTL3: view

Variants for SYTL3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SYTL3 Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
rs2291388 - p.Val540Ile
rs3123101 - p.Leu587Gln
rs901363 - p.Pro414Ser

Additional dbSNP identifiers (rs#s) for SYTL3 Gene

Structural Variations from Database of Genomic Variants (DGV) for SYTL3 Gene

Variant ID Type Subtype PubMed ID
dgv1028e201 CNV deletion 23290073
dgv1029e201 CNV deletion 23290073
esv2134507 CNV deletion 18987734
esv24318 CNV loss 19812545
esv2587253 CNV insertion 19546169
esv2663267 CNV deletion 23128226
esv2678909 CNV deletion 23128226
esv2733001 CNV deletion 23290073
esv2733002 CNV deletion 23290073
esv2733003 CNV deletion 23290073
esv2733013 CNV deletion 23290073
esv2733014 CNV deletion 23290073
esv3339618 CNV insertion 20981092
esv3395272 CNV insertion 20981092
esv3540747 CNV deletion 23714750
esv3540748 CNV deletion 23714750
esv3611400 CNV loss 21293372
esv3611402 CNV loss 21293372
esv3611403 CNV loss 21293372
nsv1121659 CNV deletion 24896259
nsv1133387 CNV tandem duplication 24896259
nsv1152331 CNV deletion 26484159
nsv1153026 CNV deletion 26484159
nsv349192 CNV deletion 16902084
nsv478339 CNV novel sequence insertion 20440878
nsv523641 CNV gain 19592680
nsv528373 CNV loss 19592680
nsv528709 CNV loss 19592680
nsv5562 CNV insertion 18451855
nsv823893 CNV loss 20364138
nsv823894 CNV loss 20364138
nsv949875 CNV duplication 24416366

Variation tolerance for SYTL3 Gene

Residual Variation Intolerance Score: 89.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 14.33; 96.31% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SYTL3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SYTL3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SYTL3 Gene

Disorders for SYTL3 Gene

MalaCards: The human disease database

(3) MalaCards diseases for SYTL3 Gene - From: DISEASES

Disorder Aliases PubMed IDs
griscelli syndrome, type 1
  • gs1
griscelli syndrome, type 3
  • gs3
griscelli syndrome
  • ch��diak-higashi-like syndrome
- elite association - COSMIC cancer census association via MalaCards
Search SYTL3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SYTL3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SYTL3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SYTL3 Gene

Publications for SYTL3 Gene

  1. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 41 54
  2. The Slp homology domain of synaptotagmin-like proteins 1-4 and Slac2 functions as a novel Rab27A binding domain. (PMID: 11773082) Kuroda TS … Mikoshiba K (The Journal of biological chemistry 2002) 2 3 54
  3. The C2A domain of synaptotagmin-like protein 3 (Slp3) is an atypical calcium-dependent phospholipid-binding machine: comparison with the C2A domain of synaptotagmin I. (PMID: 12049610) Fukuda M (The Biochemical journal 2002) 3 23 54
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 54
  5. Rab27a controls HIV-1 assembly by regulating plasma membrane levels of phosphatidylinositol 4,5-bisphosphate. (PMID: 25940347) Gerber PP … Ostrowski M (The Journal of cell biology 2015) 3 54

Products for SYTL3 Gene

Sources for SYTL3 Gene