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    YKT6 YKT6 v-SNARE homolog [ Homo sapiens (human) ]

    Gene ID: 10652, updated on 3-Nov-2024

    Summary

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    Official Symbol
    YKT6provided by HGNC
    Official Full Name
    YKT6 v-SNARE homologprovided by HGNC
    Primary source
    HGNC:HGNC:16959
    See related
    Ensembl:ENSG00000106636 MIM:606209; AllianceGenome:HGNC:16959
    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
    Summary
    This gene product is one of the SNARE recognition molecules implicated in vesicular transport between secretory compartments. It is a membrane associated, isoprenylated protein that functions at the endoplasmic reticulum-Golgi transport step. This protein is highly conserved from yeast to human and can functionally complement the loss of the yeast homolog in the yeast secretory pathway. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in brain (RPKM 24.8), colon (RPKM 21.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See YKT6 in Genome Data Viewer
    Location:
    7p13
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (44200978..44214294)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (44359565..44372881)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (44240577..44253893)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105375258 Neighboring gene uncharacterized LOC105375257 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44223563-44224100 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44224101-44224636 Neighboring gene glucokinase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18143 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:44253740-44254655 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:44257065-44257612 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:44257613-44258158 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44260592-44261156 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44261157-44261720 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44275325-44276208 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25933 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25934 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25935 Neighboring gene calcium/calmodulin dependent protein kinase II beta Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44289329-44289847 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25936 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25937 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44301759-44302258 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44302657-44303488 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44303489-44304320 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44307207-44307708 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44307709-44308208 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44311666-44312166 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44322903-44323685 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44328206-44328848 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44329545-44330046 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44333819-44334319 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25938 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:44348485-44349088 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:44349089-44349690 Neighboring gene uncharacterized LOC124901621 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25939 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44389311-44389811 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25940 Neighboring gene NudC domain containing 3 Neighboring gene ribosomal protein L32 pseudogene 18

    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 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. YKT6 expression, exosome release, and survival in non-small cell lung cancer. Ruiz-Martinez M, et al. Oncotarget, 2016 Aug 9. PMID 27285987, Free PMC Article
    2. YKT6, as a potential predictor of prognosis and immunotherapy response for oral squamous cell carcinoma, is related to cell invasion, metastasis, and CD8+ T cell infiltration. Yang Z, et al. Oncoimmunology, 2021 Jun 23. PMID 34221701, Free PMC Article
    3. Localization and activity of the SNARE Ykt6 determined by its regulatory domain and palmitoylation. Fukasawa M, et al. Proc Natl Acad Sci U S A, 2004 Apr 6. PMID 15044687, Free PMC Article
    4. Autophagosomal YKT6 is required for fusion with lysosomes independently of syntaxin 17. Matsui T, et al. J Cell Biol, 2018 Aug 6. PMID 29789439, Free PMC Article
    5. High expression of YKT6 associated with progression and poor prognosis of hepatocellular carcinoma. Xu JZ, et al. Scand J Gastroenterol, 2021 Nov. PMID 34396876

    See all (89) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Homozygous missense variants in YKT6 result in loss of function and are associated with developmental delay, with or without severe infantile liver disease and risk for hepatocellular carcinoma.
      Title: Homozygous missense variants in YKT6 result in loss of function and are associated with developmental delay, with or without severe infantile liver disease and risk for hepatocellular carcinoma.
    2. Human YKT6 forms priming complex with STX17 and SNAP29 to facilitate autophagosome-lysosome fusion.
      Title: Human YKT6 forms priming complex with STX17 and SNAP29 to facilitate autophagosome-lysosome fusion.
    3. A pan-cancer analysis of the oncogenic role of YKT6 in human tumors.
      Title: A pan-cancer analysis of the oncogenic role of YKT6 in human tumors.
    4. High expression of YKT6 associated with progression and poor prognosis of hepatocellular carcinoma.
      Title: High expression of YKT6 associated with progression and poor prognosis of hepatocellular carcinoma.
    5. YKT6, as a potential predictor of prognosis and immunotherapy response for oral squamous cell carcinoma, is related to cell invasion, metastasis, and CD8+ T cell infiltration.
      Title: YKT6, as a potential predictor of prognosis and immunotherapy response for oral squamous cell carcinoma, is related to cell invasion, metastasis, and CD8+ T cell infiltration.
    6. Proinflammatory macrophage-derived microvesicles exhibit tumor tropism dependent on CCL2/CCR2 signaling axis and promote drug delivery via SNARE-mediated membrane fusion.
      Title: Proinflammatory macrophage-derived microvesicles exhibit tumor tropism dependent on CCL2/CCR2 signaling axis and promote drug delivery via SNARE-mediated membrane fusion.
    7. A SNARE geranylgeranyltransferase essential for the organization of the Golgi apparatus.
      Title: A SNARE geranylgeranyltransferase essential for the organization of the Golgi apparatus.
    8. Parkinson's disease alpha-synuclein perturbs the physiological response to lysosomal stress by impeding the SNARE protein ykt6
      Title: Stress-Induced Cellular Clearance Is Mediated by the SNARE Protein ykt6 and Disrupted by α-Synuclein.
    9. The observed anti-migratory activity of Ykt6 is mediated by a unique mechanism involving the expressional upregulation of microRNA 145, which selectively decreases the cellular level of Junctional Adhesion Molecule (JAM) A.
      Title: A membrane fusion protein, Ykt6, regulates epithelial cell migration via microRNA-mediated suppression of Junctional Adhesion Molecule A.
    10. YKT6 forms a SNARE complex with SNAP29 and lysosomal STX7, both of which are required for autophagosomal fusion.
      Title: Autophagosomal YKT6 is required for fusion with lysosomes independently of syntaxin 17.
    Submit: New GeneRIF Correction See all GeneRIFs (15)

    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

    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

    Pathways from PubChem

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    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 SNAP receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables SNAP receptor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables cadherin binding HDA PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein-cysteine S-palmitoyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in endoplasmic reticulum to Golgi vesicle-mediated transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in endoplasmic reticulum to Golgi vesicle-mediated transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in membrane fusion IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in retrograde transport, endosome to Golgi IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in vesicle docking involved in exocytosis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in vesicle targeting IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in Golgi apparatus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in Golgi membrane TAS
    Traceable Author Statement
    more info
    		  
    part_of SNARE complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    part_of SNARE complex TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in apical dendrite IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in basal dendrite IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasmic vesicle membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum-Golgi intermediate compartment membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		  
    located_in neuronal cell body IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in transport vesicle TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    synaptobrevin homolog YKT6
    Names
    R-SNARE
    SNARE protein Ykt6
    YKT6 v-SNARE protein
    YKT6, S. cerevisiae, homolog of
    NP_001350607.1
    NP_001397803.1
    NP_006546.1
    XP_054184398.1
    XP_054213078.1

    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.

    mRNA and Protein(s)

    1. NM_001363678.2 → NP_001350607.1  synaptobrevin homolog YKT6 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC006454, AK299158, BC007319
      Consensus CDS
      CCDS87497.1
      UniProtKB/TrEMBL
      B5BU81
      Related
      ENSP00000420805.1, ENST00000496112.5
      Conserved Domains (2) summary
      pfam13774
      Location:44 → 116
      Longin; Regulated-SNARE-like domain
      cl26083
      Location:3 → 155
      Synaptobrevin; Synaptobrevin

    2. NM_001410874.1 → NP_001397803.1  synaptobrevin homolog YKT6 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC006454
      Consensus CDS
      CCDS94093.1
      UniProtKB/TrEMBL
      A0A7I2V4L6
      Related
      ENSP00000504160.1, ENST00000677090.1

    3. NM_006555.4 → NP_006546.1  synaptobrevin homolog YKT6 isoform 1

      See identical proteins and their annotated locations for NP_006546.1

      Status: REVIEWED

      Source sequence(s)
      AC006454, AU130339, BC007319
      Consensus CDS
      CCDS5482.1
      UniProtKB/Swiss-Prot
      B4DR94, O15498, Q53F01, Q6FGU9, Q6IB15
      UniProtKB/TrEMBL
      A4D2J0, B5BU81
      Related
      ENSP00000223369.2, ENST00000223369.3
      Conserved Domains (2) summary
      COG5143
      Location:3 → 198
      SNC1; Synaptobrevin/VAMP-like protein [Intracellular trafficking and secretion]
      cd15867
      Location:136 → 195
      R-SNARE_YKT6; SNARE motif of YKT6

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      44200978..44214294
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054328423.1 → XP_054184398.1  synaptobrevin homolog YKT6 isoform X1

      UniProtKB/TrEMBL
      A0A7I2V4L6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      44359565..44372881
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054357103.1 → XP_054213078.1  synaptobrevin homolog YKT6 isoform X1

      UniProtKB/TrEMBL
      A0A7I2V4L6
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O15498.1 GenPept UniProtKB/Swiss-Prot:O15498

    Gene LinkOut

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

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