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    SNTB1 syntrophin beta 1 [ Homo sapiens (human) ]

    Gene ID: 6641, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SNTB1provided by HGNC
    Official Full Name
    syntrophin beta 1provided by HGNC
    Primary source
    HGNC:HGNC:11168
    See related
    Ensembl:ENSG00000172164 MIM:600026; AllianceGenome:HGNC:11168
    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
    A1B; SNT2; BSYN2; 59-DAP; DAPA1B; SNT2B1; TIP-43
    Summary
    Dystrophin is a large, rod-like cytoskeletal protein found at the inner surface of muscle fibers. Dystrophin is missing in Duchenne Muscular Dystrophy patients and is present in reduced amounts in Becker Muscular Dystrophy patients. The protein encoded by this gene is a peripheral membrane protein found associated with dystrophin and dystrophin-related proteins. This gene is a member of the syntrophin gene family, which contains at least two other structurally-related genes. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in thyroid (RPKM 41.8), adrenal (RPKM 32.7) and 22 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SNTB1 in Genome Data Viewer
    Location:
    8q24.12
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (120535756..120812046, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (121664208..121941521, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (121547996..121824286, complement)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr8:121409422-121409610 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:121409635-121410134 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27849 Neighboring gene mitochondrial ribosomal protein L13 Neighboring gene MDM2 binding protein Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:121567323-121568522 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:121637686-121638215 Neighboring gene NANOG hESC enhancer GRCh37_chr8:121697522-121698069 Neighboring gene non-SMC condensin I complex subunit G pseudogene 1 Neighboring gene uncharacterized LOC101927543 Neighboring gene Sharpr-MPRA regulatory region 2819 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:121910815-121910916 Neighboring gene Sharpr-MPRA regulatory region 15420 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27850 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:122068285-122068786 Neighboring gene VISTA enhancer hs1482 Neighboring gene glucosamine-phosphate N-acetyltransferase 1 pseudogene Neighboring gene uncharacterized LOC124902010

    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. Association of SNTB1 with High Myopia. Cheong KX, et al. Curr Eye Res, 2021 Jan. PMID 32452213
    2. The SNTB1 and ZFHX1B gene have susceptibility in northern Han Chinese populations with high myopia. Yang L, et al. Exp Eye Res, 2023 Dec. PMID 37890754
    3. SNTB1 regulates colorectal cancer cell proliferation and metastasis through YAP1 and the WNT/β-catenin pathway. Zhang H, et al. Cell Cycle, 2023 Sep. PMID 37592763, Free PMC Article
    4. The potential role of human endogenous retrovirus K10 in the pathogenesis of rheumatoid arthritis: a preliminary study. Ejtehadi HD, et al. Ann Rheum Dis, 2006 May. PMID 16192292, Free PMC Article
    5. Genome-wide association study identifies ZFHX1B as a susceptibility locus for severe myopia. Khor CC, et al. Hum Mol Genet, 2013 Dec 20. PMID 23933737

    See all (67) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The SNTB1 and ZFHX1B gene have susceptibility in northern Han Chinese populations with high myopia.
      Title: The SNTB1 and ZFHX1B gene have susceptibility in northern Han Chinese populations with high myopia.
    2. SNTB1 regulates colorectal cancer cell proliferation and metastasis through YAP1 and the WNT/beta-catenin pathway.
      Title: SNTB1 regulates colorectal cancer cell proliferation and metastasis through YAP1 and the WNT/β-catenin pathway.
    3. Association of SNTB1 with High Myopia.
      Title: Association of SNTB1 with High Myopia.
    4. Association of the ZC3H11B, ZFHX1B and SNTB1 genes with myopia of different severities.
      Title: Association of the ZC3H11B, ZFHX1B and SNTB1 genes with myopia of different severities.
    5. Our study confirms that the two susceptibility loci ZFHX1B and SNTB1 are associated with moderate to high myopia in a Han Chinese population, as well as in a European population, when both SNPs are combined.
      Title: Association and interaction of myopia with SNP markers rs13382811 and rs6469937 at ZFHX1B and SNTB1 in Han Chinese and European populations.
    6. SNPs within the SNTB1 gene are associated with increased risk of oral cancer.
      Title: Single nucleotide polymorphisms in an Indian cohort and association of CNTN4, MMP2 and SNTB1 variants with oral cancer.
    7. SNTB1 and MCPH1 are located on chromosome 8, which may be involved in neuroticism, avoidant personality and depression.
      Title: Association of microcephalin 1, syntrophin-beta 1, and other genes with automatic thoughts in the Japanese population.
    8. beta1-syntrophin acts through a class-I PDZ interaction with the C terminus of ABCA1 to regulate the cellular distribution and activity of the transporter
      Title: Purification of ATP-binding cassette transporter A1 and associated binding proteins reveals the importance of beta1-syntrophin in cholesterol efflux.
    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 meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder.
    EBI GWAS Catalog
    A genome-wide meta-analysis identifies two novel loci associated with high myopia in the Han Chinese population.
    EBI GWAS Catalog
    Common variants at 5q22 associate with pediatric eosinophilic esophagitis.
    EBI GWAS Catalog
    Genome-wide association study identifies ZFHX1B as a susceptibility locus for severe myopia.
    EBI GWAS Catalog
    Genome-wide association study of chronic periodontitis in a general German 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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Nef nef Yeast two hybrid assay identifies the HIV-1 Nef-interacting protein syntrophin PubMed

    Go to the HIV-1, Human Interaction Database

    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

    Clone Names

    • FLJ22442, MGC111389

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables PDZ domain binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables actin binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables calmodulin binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables structural molecule activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in muscle contraction TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoskeleton IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of dystrophin-associated glycoprotein complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in focal adhesion HDA PubMed 
    is_active_in intracellular anatomical structure IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in sarcolemma IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in synapse IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    beta-1-syntrophin
    Names
    59 kDa dystrophin-associated protein A1 basic component 1
    dystrophin-associated protein A1, 59kD, basic component 1
    syntrophin, beta 1 (dystrophin-associated protein A1, 59kDa, basic component 1)
    syntrophin-2
    tax interaction protein 43

    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.

    mRNA and Protein(s)

    1. NM_021021.4 → NP_066301.1  beta-1-syntrophin

      See identical proteins and their annotated locations for NP_066301.1

      Status: REVIEWED

      Source sequence(s)
      AC105142, AK292655, BC098573
      Consensus CDS
      CCDS6334.1
      UniProtKB/Swiss-Prot
      A8K9E0, O14912, Q13884, Q4KMG8
      Related
      ENSP00000431124.1, ENST00000517992.2
      Conserved Domains (4) summary
      smart00233
      Location:323 → 433
      PH; Pleckstrin homology domain
      cd00992
      Location:111 → 192
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      cd01258
      Location:242 → 299
      PHsplit_syntrophin; Syntrophin Split Pleckstrin homology (PH) domain
      pfam00169
      Location:323 → 433
      PH; PH domain

    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_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      120535756..120812046 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047422126.1 → XP_047278082.1  beta-1-syntrophin isoform X2

    2. XM_047422127.1 → XP_047278083.1  beta-1-syntrophin isoform X2

    3. XM_011517239.3 → XP_011515541.1  beta-1-syntrophin isoform X1

      UniProtKB/TrEMBL
      A0A3B3ITC2
      Related
      ENSP00000497707.1, ENST00000648490.1
      Conserved Domains (4) summary
      smart00233
      Location:323 → 375
      PH; Pleckstrin homology domain
      cd00992
      Location:111 → 192
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      cd01258
      Location:242 → 299
      PHsplit_syntrophin; Syntrophin Split Pleckstrin homology (PH) domain
      pfam00169
      Location:323 → 375
      PH; PH domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      121664208..121941521 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054361060.1 → XP_054217035.1  beta-1-syntrophin isoform X3

    2. XM_054361062.1 → XP_054217037.1  beta-1-syntrophin isoform X2

    3. XM_054361061.1 → XP_054217036.1  beta-1-syntrophin isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q13884.3 GenPept UniProtKB/Swiss-Prot:Q13884

    Gene LinkOut

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

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