U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

SYT6 synaptotagmin 6 [ Homo sapiens (human) ]

Gene ID: 148281, updated on 11-Apr-2024

Summary

Go to the top of the page Help
Official Symbol
SYT6provided by HGNC
Official Full Name
synaptotagmin 6provided by HGNC
Primary source
HGNC:HGNC:18638
See related
Ensembl:ENSG00000134207 MIM:607718; AllianceGenome:HGNC:18638
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
sytVI
Summary
The protein encoded by this gene belongs to the synaptotagmin family. Synaptotagmins share a common domain structure that includes a transmembrane domain and a cytoplasmic region composed of 2 C2 domains, and are involved in calcium-dependent exocytosis of synaptic vesicles. This protein has been shown to be a key component of the secretory machinery involved in acrosomal exocytosis. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2011]
Expression
Biased expression in brain (RPKM 2.6), kidney (RPKM 0.8) and 6 other tissues See more
Orthologs
mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See SYT6 in Genome Data Viewer
Location:
1p13.2
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (114089292..114153869, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (114100938..114165509, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (114631914..114696491, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:114521340-114522173 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:114523841-114524673 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:114525929-114526892 Neighboring gene olfactomedin like 3 Neighboring gene ribosomal protein L13a pseudogene 10 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:114557741-114558940 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:114573243-114573826 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:114574411-114574994 Neighboring gene Sharpr-MPRA regulatory region 7982 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:114579664-114580246 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:114580831-114581413 Neighboring gene NANOG hESC enhancer GRCh37_chr1:114592578-114593255 Neighboring gene NANOG hESC enhancer GRCh37_chr1:114600776-114601630 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:114621064-114621564 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:114634493-114634994 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:114647517-114648164 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1543 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:114667021-114667808 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:114688166-114688878 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:114697666-114698279 Neighboring gene Sharpr-MPRA regulatory region 1115 Neighboring gene uncharacterized LOC107985443 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1544 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:114800040-114800508 Neighboring gene mitochondrial ribosomal protein L57 pseudogene 1

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

Go to the top of the pageHelp

Related articles in PubMed

  1. Calcineurin-mediated dephosphorylation of synaptotagmin VI is necessary for acrosomal exocytosis. Castillo Bennett J, et al. J Biol Chem, 2010 Aug 20. PMID 20551332, Free PMC Article
  2. Protein kinase C-mediated phosphorylation of the two polybasic regions of synaptotagmin VI regulates their function in acrosomal exocytosis. Roggero CM, et al. Dev Biol, 2005 Sep 15. PMID 16111671
  3. Synaptotagmin VI participates in the acrosome reaction of human spermatozoa. Michaut M, et al. Dev Biol, 2001 Jul 15. PMID 11437455
  4. Identification of inherited genetic variations influencing prognosis in early-onset breast cancer. Rafiq S, et al. Cancer Res, 2013 Mar 15. PMID 23319801, Free PMC Article
  5. Identification of novel epigenetic markers for clear cell renal cell carcinoma. Dalgin GS, et al. J Urol, 2008 Sep. PMID 18639284

See all (27) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. synaptotagmin must be dephosphorylated at a specific window of time and phosphorylated synaptotagmin has an active role at early stages of the acrosomal exocytosis.
    Title: Calcineurin-mediated dephosphorylation of synaptotagmin VI is necessary for acrosomal exocytosis.
  2. SYT6 is hypermethylated in renal cell carcinoma.
    Title: Identification of novel epigenetic markers for clear cell renal cell carcinoma.
  3. Acrosomal exocytosis is regulated through the PKC-mediated phosphorylation of conserved threonines in the polybasic regions of synaptotagmin VI.
    Title: Protein kinase C-mediated phosphorylation of the two polybasic regions of synaptotagmin VI regulates their function in acrosomal exocytosis.
Submit: New GeneRIF Correction

Phenotypes

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide association study of behavioral disinhibition.
EBI GWAS Catalog
Identification of inherited genetic variations influencing prognosis in early-onset breast cancer.
EBI GWAS Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
EBI GWAS Catalog

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables SNARE binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables calcium ion binding IBA
Inferred from Biological aspect of Ancestor
more info
  
NOT enables calcium-dependent phospholipid binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables clathrin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables clathrin binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables phosphatidylserine binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein homodimerization activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables syntaxin binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in acrosomal vesicle exocytosis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in calcium-ion regulated exocytosis IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in cytoplasmic side of plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in cytosol ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in exocytic vesicle IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in perinuclear endoplasmic reticulum ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in synaptic vesicle membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

Go to the top of the page Help
Preferred Names
synaptotagmin-6
Names
synaptotagmin VI

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_050730.1 RefSeqGene

    Range
    4982..69559
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001253772.2 → NP_001240701.1  synaptotagmin-6 isoform a

    Status: REVIEWED

    Source sequence(s)
    AL162594
    Consensus CDS
    CCDS91027.1
    UniProtKB/Swiss-Prot
    B1AMB8, B3KPK1, Q5T7P8
    UniProtKB/TrEMBL
    A0A286YEX2
    Related
    ENSP00000476396.1, ENST00000610222.3
    Conserved Domains (2) summary
    cd08385
    Location:230 → 354
    C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
    cd08403
    Location:363 → 496
    C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10

  2. NM_001270805.2 → NP_001257734.1  synaptotagmin-6 isoform b

    See identical proteins and their annotated locations for NP_001257734.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) represents the longer transcript. Variants 2 and 3 encode the same protein.
    Source sequence(s)
    AL162594, BC044948, N50928
    Consensus CDS
    CCDS871.1
    UniProtKB/TrEMBL
    A0A286YEX2, I6L9C3
    Conserved Domains (2) summary
    cd08385
    Location:145 → 269
    C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
    cd08403
    Location:278 → 411
    C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10

  3. NM_001366223.1 → NP_001353152.1  synaptotagmin-6 isoform b

    Status: REVIEWED

    Source sequence(s)
    AL162594
    Consensus CDS
    CCDS871.1
    UniProtKB/TrEMBL
    A0A286YEX2, I6L9C3
    Related
    ENSP00000477344.1, ENST00000609117.5
    Conserved Domains (2) summary
    cd08385
    Location:145 → 269
    C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
    cd08403
    Location:278 → 411
    C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10

  4. NM_001366224.1 → NP_001353153.1  synaptotagmin-6 isoform c

    Status: REVIEWED

    Source sequence(s)
    AL162594
    Consensus CDS
    CCDS91026.1
    UniProtKB/TrEMBL
    A0A7I2PMW4
    Related
    ENSP00000358560.2, ENST00000369547.6
    Conserved Domains (2) summary
    cd08385
    Location:230 → 354
    C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
    cd08403
    Location:363 → 496
    C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10

  5. NM_001366225.1 → NP_001353154.1  synaptotagmin-6 isoform d

    Status: REVIEWED

    Source sequence(s)
    AL162594
    UniProtKB/TrEMBL
    A0A286YEX2
    Related
    ENSP00000493062.2, ENST00000641643.2
    Conserved Domains (2) summary
    cd08385
    Location:230 → 354
    C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
    cd08403
    Location:363 → 496
    C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10

  6. NM_001366226.1 → NP_001353155.1  synaptotagmin-6 isoform e

    Status: REVIEWED

    Source sequence(s)
    AL162594
    UniProtKB/TrEMBL
    A0A286YEX2
    Conserved Domains (2) summary
    cd08385
    Location:145 → 269
    C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
    cd08403
    Location:278 → 411
    C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10

  7. NM_205848.4 → NP_995320.1  synaptotagmin-6 isoform b

    See identical proteins and their annotated locations for NP_995320.1

    Status: REVIEWED

    Source sequence(s)
    AK056448, AK096744, AL162594, BC044948, BX431128, N50928
    Consensus CDS
    CCDS871.1
    UniProtKB/TrEMBL
    A0A286YEX2, I6L9C3
    Related
    ENSP00000476507.1, ENST00000607941.5
    Conserved Domains (2) summary
    cd08385
    Location:145 → 269
    C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
    cd08403
    Location:278 → 411
    C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    114089292..114153869 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024453337.2 → XP_024309105.1  synaptotagmin-6 isoform X1

    UniProtKB/TrEMBL
    A0A286YEX2
    Conserved Domains (2) summary
    cd08385
    Location:145 → 269
    C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
    cd08403
    Location:278 → 411
    C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10

  2. XM_047446760.1 → XP_047302716.1  synaptotagmin-6 isoform X2

    UniProtKB/Swiss-Prot
    B1AMB8, B3KPK1, Q5T7P8

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    114100938..114165509 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054334548.1 → XP_054190523.1  synaptotagmin-6 isoform X1

  2. XM_054334549.1 → XP_054190524.1  synaptotagmin-6 isoform X2

    UniProtKB/Swiss-Prot
    B1AMB8, B3KPK1, Q5T7P8
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5T7P8.3 GenPept UniProtKB/Swiss-Prot:Q5T7P8

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous