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    STX16 syntaxin 16 [ Homo sapiens (human) ]

    Gene ID: 8675, updated on 10-Dec-2024

    Summary

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    Official Symbol
    STX16provided by HGNC
    Official Full Name
    syntaxin 16provided by HGNC
    Primary source
    HGNC:HGNC:11431
    See related
    Ensembl:ENSG00000124222 MIM:603666; AllianceGenome:HGNC:11431
    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
    SYN16; SYN-16
    Summary
    This gene encodes a protein that is a member of the syntaxin or t-SNARE (target-SNAP receptor) family. These proteins are found on cell membranes and serve as the targets for V-SNARES (vesicle-SNAP receptors) permitting specific synaptic vesicle docking and fusion. A microdeletion in the region of chromosome 20 where this gene is located has been associated with pseudohypoparathyroidism type Ib. Multiple transcript variants have been found for this gene. Read-through transcription also exists between this gene and the neighboring downstream aminopeptidase-like 1 (NPEPL1) gene. [provided by RefSeq, Mar 2011]
    Expression
    Ubiquitous expression in spleen (RPKM 25.9), lymph node (RPKM 25.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See STX16 in Genome Data Viewer
    Location:
    20q13.32
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (58651283..58679526)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (60433347..60461590)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (57226339..57254582)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18175 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18176 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:57212955-57213590 Neighboring gene long intergenic non-protein coding RNA 1711 Neighboring gene uncharacterized LOC107985410 Neighboring gene Sharpr-MPRA regulatory region 5631 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:57223531-57224068 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13074 Neighboring gene STX16-NPEPL1 readthrough (NMD candidate) Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr20:57227205-57227708 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:57236323-57236822 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:57244387-57245042 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:57245043-57245700 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:57245701-57246356 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:57250883-57251408 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:57251409-57251933 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:57267289-57267994 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13077 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13078 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13079 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:57269435-57270042 Neighboring gene aminopeptidase like 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:57276557-57277089 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:57277090-57277621 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:57290235-57291042 Neighboring gene uncharacterized LOC124904942

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Intrafamilial phenotypic heterogeneity in siblings with pseudohypoparathyroidism 1B due to maternal STX16 deletion. Odom J, et al. J Pediatr Endocrinol Metab, 2024 Jan 29. PMID 38095637
    2. Methylation-specific multiplex-ligation-dependent probe amplification as a rapid molecular diagnostic tool for pseudohypoparathyroidism type 1b. Alsum Z, et al. Genet Test Mol Biomarkers, 2010 Feb. PMID 19916794
    3. Growth hormone deficiency in monozygotic twins with autosomal dominant pseudohypoparathyroidism type Ib. Sano S, et al. Endocr J, 2015. PMID 25843330
    4. Syntaxin 16 is a master recruitment factor for cytokinesis. Neto H, et al. Mol Biol Cell, 2013 Dec. PMID 24109596, Free PMC Article
    5. Macrosomia, obesity, and macrocephaly as first clinical presentation of PHP1b caused by STX16 deletion. de Lange IM, et al. Am J Med Genet A, 2016 Sep. PMID 27338644

    See all (73) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Intrafamilial phenotypic heterogeneity in siblings with pseudohypoparathyroidism 1B due to maternal STX16 deletion.
      Title: Intrafamilial phenotypic heterogeneity in siblings with pseudohypoparathyroidism 1B due to maternal STX16 deletion.
    2. Analysis of defects in GNAS and STX16 genes in a Chinese family with pseudohypoparathyroidism.
      Title: Analysis of defects in GNAS and STX16 genes in a Chinese family with pseudohypoparathyroidism.
    3. Progression of PTH Resistance in Autosomal Dominant Pseudohypoparathyroidism Type Ib Due to Maternal STX16 Deletions.
      Title: Progression of PTH Resistance in Autosomal Dominant Pseudohypoparathyroidism Type Ib Due to Maternal STX16 Deletions.
    4. Preferential Maternal Transmission of STX16-GNAS Mutations Responsible for Autosomal Dominant Pseudohypoparathyroidism Type Ib (PHP1B): Another Example of Transmission Ratio Distortion.
      Title: Preferential Maternal Transmission of STX16-GNAS Mutations Responsible for Autosomal Dominant Pseudohypoparathyroidism Type Ib (PHP1B): Another Example of Transmission Ratio Distortion.
    5. we here present a patient with PHP1b caused by a recurrent STX16 deletion, presenting with macrosomia, early onset obesity, and macrocephaly without other AHO symptoms. we reemphasize STX16 deletions and PHP1b as a rare cause for early onset obesity and macrosomia.
      Title: Macrosomia, obesity, and macrocephaly as first clinical presentation of PHP1b caused by STX16 deletion.
    6. STX16 microdeletion was identified in male monozygotic twins (with pseudohypoparathyroidism type 1B leading to growth hormone deficiency) and mother/grandmother (not father/grandfather or sister [their triplet with separate placenta]). [CASE STUDY]
      Title: Growth hormone deficiency in monozygotic twins with autosomal dominant pseudohypoparathyroidism type Ib.
    7. syntaxin 16 is a key regulator of cytokinesis.
      Title: Syntaxin 16 is a master recruitment factor for cytokinesis.
    8. Data indicate that depletion of VAMP4, syntaxin 6, syntaxin 16, and Vti1a disrupted the Golgi ribbon structure.
      Title: VAMP4 is required to maintain the ribbon structure of the Golgi apparatus.
    9. A patient with familial pseudohypoparathyroidism type Ib and his asymptomatic brother were found to have methylation defect at GNAS (guanine nucleotide-binding protein G) and microdeletion involving exons 4-6 of neighboring gene STX16. [CASE REPORT]
      Title: Neuromuscular symptoms in a patient with familial pseudohypoparathyroidism type Ib diagnosed by methylation-specific multiplex ligation-dependent probe amplification.
    10. De novo 3-kb STX16 deletions, reported only once previously, are infrequent but should be excluded in all cases of Pseudohypoparathyroidism-Ib, even when the family history is negative for an inherited form of this disorder.
      Title: De novo STX16 deletions: an infrequent cause of pseudohypoparathyroidism type Ib that should be excluded in sporadic cases.
    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

    Associated conditions

    Description Tests
    Pseudohypoparathyroidism type 1B
    MedGen: C1864100 OMIM: 603233 GeneReviews: Disorders of GNAS Inactivation
    		not available

    EBI GWAS Catalog

    Description
    Longitudinal genome-wide association of cardiovascular disease risk factors in the Bogalusa heart study.
    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)

    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

    Readthrough STX16-NPEPL1

    Readthrough gene: STX16-NPEPL1, Included gene: NPEPL1

    Homology

    Clone Names

    • MGC90328

    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 SNARE binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables syntaxin binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in endocytic recycling IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in intracellular protein transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in retrograde transport, endosome to Golgi IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in retrograde transport, endosome to Golgi IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in vesicle docking IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in vesicle fusion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in Golgi cisterna IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in Golgi membrane TAS
    Traceable Author Statement
    more info
    		  
    part_of SNARE complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of SNARE complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of SNARE complex TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in endomembrane system IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    colocalizes_with endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in focal adhesion HDA PubMed 
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in synaptic vesicle membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in trans-Golgi network IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in trans-Golgi network membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    syntaxin-16

    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_011831.3 RefSeqGene

      Range
      5002..33245
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001001433.3 → NP_001001433.1  syntaxin-16 isoform a

      See identical proteins and their annotated locations for NP_001001433.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a, also referred to as isoform B).
      Source sequence(s)
      AL050327, AL139349, KF456959
      Consensus CDS
      CCDS13468.1
      UniProtKB/Swiss-Prot
      A6NK32, A6NN69, A8MPP0, B7ZBN1, B7ZBN2, B7ZBN3, E1P5M0, E1P607, O14661, O14662, O14663, O60517, Q5W084, Q5W086, Q5W087, Q5XKI6, Q6GMS8, Q9H0Z0, Q9H1T7, Q9H1T8, Q9UIX5
      UniProtKB/TrEMBL
      B4E3U3
      Related
      ENSP00000360183.4, ENST00000371141.8
      Conserved Domains (2) summary
      COG5325
      Location:75 → 301
      COG5325; t-SNARE complex subunit, syntaxin [Intracellular trafficking and secretion]
      cd15845
      Location:233 → 291
      SNARE_syntaxin16; SNARE motif of syntaxin 16

    2. NM_001134772.3 → NP_001128244.1  syntaxin-16 isoform c

      See identical proteins and their annotated locations for NP_001128244.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in a shorter isoform (c), compared to isoform a.
      Source sequence(s)
      AL050327, AL139349, KF456959
      Consensus CDS
      CCDS46619.1
      UniProtKB/TrEMBL
      B4E3U3
      Related
      ENSP00000350723.4, ENST00000358029.8
      Conserved Domains (2) summary
      COG5325
      Location:71 → 297
      COG5325; t-SNARE complex subunit, syntaxin [Intracellular trafficking and secretion]
      cd15845
      Location:229 → 287
      SNARE_syntaxin16; SNARE motif of syntaxin 16

    3. NM_001134773.3 → NP_001128245.1  syntaxin-16 isoform d

      See identical proteins and their annotated locations for NP_001128245.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, resulting in a shorter isoform (d), compared to isoform a.
      Source sequence(s)
      AL050327, AL139349, KF456959
      Consensus CDS
      CCDS46620.1
      UniProtKB/TrEMBL
      B4E3U3
      Related
      ENSP00000348229.5, ENST00000355957.9
      Conserved Domains (2) summary
      COG5325
      Location:58 → 284
      COG5325; t-SNARE complex subunit, syntaxin [Intracellular trafficking and secretion]
      cd15845
      Location:216 → 274
      SNARE_syntaxin16; SNARE motif of syntaxin 16

    4. NM_001204868.2 → NP_001191797.1  syntaxin-16 isoform e

      See identical proteins and their annotated locations for NP_001191797.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, and uses a downstream start codon, compared to variant 1. The encoded isoform (e) is shorter at the N-terminus, compared to isoform a.
      Source sequence(s)
      AL050327, AL139349, KF456959
      Consensus CDS
      CCDS56199.1
      UniProtKB/TrEMBL
      B4E3U3
      Related
      ENSP00000352634.4, ENST00000359617.8
      Conserved Domains (2) summary
      cd15845
      Location:180 → 238
      SNARE_syntaxin16; SNARE motif of syntaxin 16
      cl00143
      Location:29 → 135
      SynN; Syntaxin N-terminus domain; syntaxins are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane; they are a family of receptors for intracellular transport vesicles; each target membrane may ...

    5. NM_003763.6 → NP_003754.2  syntaxin-16 isoform b

      See identical proteins and their annotated locations for NP_003754.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site and lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in a shorter isoform (b, also referred to as isoform A), compared to isoform a.
      Source sequence(s)
      AL050327, AL139349, KF456959
      Consensus CDS
      CCDS13469.1
      UniProtKB/TrEMBL
      B4E3U3
      Related
      ENSP00000360173.4, ENST00000371132.8
      Conserved Domains (2) summary
      COG5325
      Location:54 → 280
      COG5325; t-SNARE complex subunit, syntaxin [Intracellular trafficking and secretion]
      cd15845
      Location:212 → 270
      SNARE_syntaxin16; SNARE motif of syntaxin 16

    RNA

    1. NR_037941.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) uses an alternate splice site in the 5' region and lacks an exon in the central region, compared to variant 1. This variant is represented as non-coding because the use of the supported start codon, as used in variant 1, would render the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL050327, AL139349, KF456959

    2. NR_037942.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) has alternate exon structure in the 5' region and lacks an exon in the central region, compared to variant 1. This variant is represented as non-coding because it lacks the supported start codon, as found in variant 1, and the use of the next available in-frame start codon would render the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL050327, AL139349, KF456959

    3. NR_037943.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) has alternate exon structure in the 5' region and lacks an exon in the central region, compared to variant 1. This variant is represented as non-coding because it lacks the supported start codon, as found in variant 1, and the use of the next available in-frame start codon would render the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL050327, AL139349, KF456959

    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_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      58651283..58679526
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      60433347..60461590
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001001434.1: Suppressed sequence

      Description
      NM_001001434.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O14662.3 GenPept UniProtKB/Swiss-Prot:O14662

    Gene LinkOut

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

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