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    SYT6 synaptotagmin 6 [ Homo sapiens (human) ]

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

    Summary

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    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
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    Genomic context

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    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

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    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

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    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

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    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

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    Preferred Names
    synaptotagmin-6
    Names
    synaptotagmin VI

    NCBI Reference Sequences (RefSeq)

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    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.

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