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    STXBP5L syntaxin binding protein 5L [ Homo sapiens (human) ]

    Gene ID: 9515, updated on 10-Dec-2024

    Summary

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    Official Symbol
    STXBP5Lprovided by HGNC
    Official Full Name
    syntaxin binding protein 5Lprovided by HGNC
    Primary source
    HGNC:HGNC:30757
    See related
    Ensembl:ENSG00000145087 MIM:609381; AllianceGenome:HGNC:30757
    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
    LLGL4
    Summary
    The protein encoded by this gene is similar to syntaxin-binding protein 5 and contains ten N-terminal WD40 repeats, four variable region WD40 repeats, and a C-terminal R-SNARE domain. Studies of the orthologous proteins in mouse and rat have shown that the encoded protein may inhibit exocytosis in neurosecretory cells, and may negatively regulate the secretion of insulin. A missense variant in this gene is likely the cause of an infantile-onset neurodegenerative disorder diagnosed in two siblings of consanguineous parents. [provided by RefSeq, Jan 2017]
    Expression
    Biased expression in brain (RPKM 4.6), thyroid (RPKM 3.2) and 5 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See STXBP5L in Genome Data Viewer
    Location:
    3q13.33
    Exon count:
    34
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (120908205..121424761)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (123628071..124144685)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (120627052..121143608)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2049 Neighboring gene uncharacterized LOC105374069 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14637 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:120815644-120816144 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:120816145-120816645 Neighboring gene zinc finger protein 426 pseudogene Neighboring gene microRNA 5682 Neighboring gene MPRA-validated peak4789 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:121090911-121091410 Neighboring gene ARPC1A pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20340 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:121170539-121171040 Neighboring gene DNA polymerase theta Neighboring gene ribosomal protein L7a pseudogene 11 Neighboring gene Sharpr-MPRA regulatory region 30 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20342 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:121279869-121280566 Neighboring gene arginine-fifty homeobox

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Homozygous mutation of STXBP5L explains an autosomal recessive infantile-onset neurodegenerative disorder. Kumar R, et al. Hum Mol Genet, 2015 Apr 1. PMID 25504045
    2. Multiple variants in toll-like receptor 4 gene modulate risk of liver fibrosis in Caucasians with chronic hepatitis C infection. Li Y, et al. J Hepatol, 2009 Oct. PMID 19586676, Free PMC Article
    3. Novel genetic variants linked to prelabor rupture of membranes among Chinese pregnant women. Kan H, et al. Placenta, 2023 Jun. PMID 37054626
    4. Identification and characterization of human LLGL4 gene and mouse Llgl4 gene in silico. Katoh M, et al. Int J Oncol, 2004 Mar. PMID 14767561
    5. A genome-wide association study in Caucasian women points out a putative role of the STXBP5L gene in facial photoaging. Le Clerc S, et al. J Invest Dermatol, 2013 Apr. PMID 23223146

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Novel genetic variants linked to prelabor rupture of membranes among Chinese pregnant women.
      Title: Novel genetic variants linked to prelabor rupture of membranes among Chinese pregnant women.
    2. Homozygous mutation of STXBP5L is associated with autosomal recessive infantile-onset neurodegenerative disorder.
      Title: Homozygous mutation of STXBP5L explains an autosomal recessive infantile-onset neurodegenerative disorder.
    3. A homozygous nonsynonymous mutation in STXBP5L (c.3127G>A, p.Val1043Ile [CCDS43137.1]) was implicated in an infantile-onset neurodegenerative disorder manifesting a predominant sensorimotor axonal neuropathy, optic atrophy and cognitive deficit.
      Title: Homozygous mutation of STXBP5L explains an autosomal recessive infantile-onset neurodegenerative disorder.
    4. In skin aging rs322458, was in linkage disequilibrium (LD) with intronic single nucleotide polymorphisms of the STXBP5L gene, which is expressed in the skin.
      Title: A genome-wide association study in Caucasian women points out a putative role of the STXBP5L gene in facial photoaging.
    5. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    6. Observational study of gene-disease association. (HuGE Navigator)
      Title: Multiple variants in toll-like receptor 4 gene modulate risk of liver fibrosis in Caucasians with chronic hepatitis C infection.
    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 in Caucasian women points out a putative role of the STXBP5L gene in facial photoaging.
    EBI GWAS Catalog
    Genome-wide association study of peripheral neuropathy with D-drug-containing regimens in AIDS Clinical Trials Group protocol 384.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1006

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GTPase activator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables myosin II binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables syntaxin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in Golgi to plasma membrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in exocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of SNARE complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    syntaxin-binding protein 5-like
    Names
    lethal(2) giant larvae protein homolog 4
    syntaxin binding protein 5 like
    tomosyn-2
    tomosyn-like

    NCBI Reference Sequences (RefSeq)

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    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_052890.1 RefSeqGene

      Range
      5003..521559
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001308330.2 → NP_001295259.1  syntaxin-binding protein 5-like isoform 2

      See identical proteins and their annotated locations for NP_001295259.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. It encodes isoform 2 which is shorter compared to isoform 1. Variants 2, 4, and 5 all encode the same isoform (2).
      Source sequence(s)
      AC078854, AC079841, AI279148, AK296544
      Consensus CDS
      CCDS77799.1
      UniProtKB/TrEMBL
      B4DKF6, E9PFI2
      Related
      ENSP00000420019.1, ENST00000471454.6
      Conserved Domains (5) summary
      COG2319
      Location:249 → 552
      WD40; WD40 repeat [General function prediction only]
      cd15893
      Location:1095 → 1155
      R-SNARE_STXBP5; SNARE domain of STXBP5
      sd00039
      Location:74 → 107
      7WD40; WD40 repeat [structural motif]
      pfam08366
      Location:288 → 396
      LLGL; LLGL2
      cl29593
      Location:74 → 281
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    2. NM_001348343.2 → NP_001335272.1  syntaxin-binding protein 5-like isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same isoform (1).
      Source sequence(s)
      AC072026, AC078854, AC078857, AC079841, AC128659
      Consensus CDS
      CCDS43137.1
      UniProtKB/Swiss-Prot
      Q4G1B4, Q6PIC3, Q9Y2K9
      UniProtKB/TrEMBL
      B4DKF6
      Related
      ENSP00000516710.1, ENST00000707001.1
      Conserved Domains (5) summary
      COG2319
      Location:249 → 552
      WD40; WD40 repeat [General function prediction only]
      cd15893
      Location:1119 → 1179
      R-SNARE_STXBP5; SNARE domain of STXBP5
      sd00039
      Location:74 → 107
      7WD40; WD40 repeat [structural motif]
      pfam08366
      Location:288 → 396
      LLGL; LLGL2
      cl29593
      Location:74 → 281
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    3. NM_001348344.2 → NP_001335273.1  syntaxin-binding protein 5-like isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. It encodes isoform 2 which is shorter compared to isoform 1. Variants 2, 4, and 5 all encode the same isoform (2).
      Source sequence(s)
      AC072026, AC078854, AC078857, AC079841, AC128659
      Consensus CDS
      CCDS77799.1
      UniProtKB/TrEMBL
      B4DKF6, E9PFI2
      Conserved Domains (5) summary
      COG2319
      Location:249 → 552
      WD40; WD40 repeat [General function prediction only]
      cd15893
      Location:1095 → 1155
      R-SNARE_STXBP5; SNARE domain of STXBP5
      sd00039
      Location:74 → 107
      7WD40; WD40 repeat [structural motif]
      pfam08366
      Location:288 → 396
      LLGL; LLGL2
      cl29593
      Location:74 → 281
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    4. NM_001348345.2 → NP_001335274.1  syntaxin-binding protein 5-like isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR and lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. It encodes isoform 2 which is shorter compared to isoform 1. Variants 2, 4, and 5 all encode the same isoform (2).
      Source sequence(s)
      AC072026, AC078854, AC078857, AC079841, AC128659
      Consensus CDS
      CCDS77799.1
      UniProtKB/TrEMBL
      B4DKF6, E9PFI2
      Conserved Domains (5) summary
      COG2319
      Location:249 → 552
      WD40; WD40 repeat [General function prediction only]
      cd15893
      Location:1095 → 1155
      R-SNARE_STXBP5; SNARE domain of STXBP5
      sd00039
      Location:74 → 107
      7WD40; WD40 repeat [structural motif]
      pfam08366
      Location:288 → 396
      LLGL; LLGL2
      cl29593
      Location:74 → 281
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    5. NM_014980.3 → NP_055795.1  syntaxin-binding protein 5-like isoform 1

      See identical proteins and their annotated locations for NP_055795.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1). Variants 1 and 3 both encode the same isoform (1).
      Source sequence(s)
      AB023223, AC079841, AI279148, DC324331
      Consensus CDS
      CCDS43137.1
      UniProtKB/Swiss-Prot
      Q4G1B4, Q6PIC3, Q9Y2K9
      UniProtKB/TrEMBL
      B4DKF6
      Related
      ENSP00000273666.6, ENST00000273666.10
      Conserved Domains (5) summary
      COG2319
      Location:249 → 552
      WD40; WD40 repeat [General function prediction only]
      cd15893
      Location:1119 → 1179
      R-SNARE_STXBP5; SNARE domain of STXBP5
      sd00039
      Location:74 → 107
      7WD40; WD40 repeat [structural motif]
      pfam08366
      Location:288 → 396
      LLGL; LLGL2
      cl29593
      Location:74 → 281
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    RNA

    1. NR_145516.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) contains an alternate exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC072026, AC078854, AC078857, AC079841, AC128659

    2. NR_145517.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) is shorter at the 3' end compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC072026, AC078857, AC128659
      Related
      ENST00000461772.5

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      120908205..121424761
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017007534.2 → XP_016863023.1  syntaxin-binding protein 5-like isoform X3

    2. XM_011513331.3 → XP_011511633.1  syntaxin-binding protein 5-like isoform X4

      Conserved Domains (4) summary
      COG2319
      Location:109 → 494
      WD40; WD40 repeat [General function prediction only]
      pfam08366
      Location:289 → 396
      LLGL; LLGL2
      sd00039
      Location:74 → 107
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:74 → 281
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    3. XM_011513333.4 → XP_011511635.1  syntaxin-binding protein 5-like isoform X6

      Conserved Domains (4) summary
      COG2319
      Location:109 → 494
      WD40; WD40 repeat [General function prediction only]
      pfam08366
      Location:289 → 396
      LLGL; LLGL2
      sd00039
      Location:74 → 107
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:74 → 281
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    4. XM_006713825.4 → XP_006713888.1  syntaxin-binding protein 5-like isoform X1

      See identical proteins and their annotated locations for XP_006713888.1

      UniProtKB/Swiss-Prot
      Q4G1B4, Q6PIC3, Q9Y2K9
      UniProtKB/TrEMBL
      B4DKF6
      Conserved Domains (5) summary
      COG2319
      Location:249 → 552
      WD40; WD40 repeat [General function prediction only]
      cd15893
      Location:1119 → 1179
      R-SNARE_STXBP5; SNARE domain of STXBP5
      sd00039
      Location:74 → 107
      7WD40; WD40 repeat [structural motif]
      pfam08366
      Location:288 → 396
      LLGL; LLGL2
      cl29593
      Location:74 → 281
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    5. XM_017007535.3 → XP_016863024.1  syntaxin-binding protein 5-like isoform X6

      Conserved Domains (4) summary
      COG2319
      Location:109 → 494
      WD40; WD40 repeat [General function prediction only]
      pfam08366
      Location:289 → 396
      LLGL; LLGL2
      sd00039
      Location:74 → 107
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:74 → 281
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    6. XM_047449249.1 → XP_047305205.1  syntaxin-binding protein 5-like isoform X2

      UniProtKB/TrEMBL
      B4DKF6

    7. XM_011513332.2 → XP_011511634.1  syntaxin-binding protein 5-like isoform X5

      Conserved Domains (1) summary
      cd15893
      Location:635 → 695
      R-SNARE_STXBP5; SNARE domain of STXBP5

    RNA

    1. XR_924217.3 RNA Sequence

    2. XR_001740373.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      123628071..124144685
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054348472.1 → XP_054204447.1  syntaxin-binding protein 5-like isoform X3

    2. XM_054348473.1 → XP_054204448.1  syntaxin-binding protein 5-like isoform X4

    3. XM_054348475.1 → XP_054204450.1  syntaxin-binding protein 5-like isoform X6

    4. XM_054348470.1 → XP_054204445.1  syntaxin-binding protein 5-like isoform X1

      UniProtKB/Swiss-Prot
      Q4G1B4, Q6PIC3, Q9Y2K9
      UniProtKB/TrEMBL
      B4DKF6

    5. XM_054348476.1 → XP_054204451.1  syntaxin-binding protein 5-like isoform X6

    6. XM_054348471.1 → XP_054204446.1  syntaxin-binding protein 5-like isoform X2

      UniProtKB/TrEMBL
      B4DKF6

    7. XM_054348474.1 → XP_054204449.1  syntaxin-binding protein 5-like isoform X5

    RNA

    1. XR_008486853.1 RNA Sequence

    2. XR_008486854.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y2K9.2 GenPept UniProtKB/Swiss-Prot:Q9Y2K9

    Gene LinkOut

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