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    TNRC6B trinucleotide repeat containing adaptor 6B [ Homo sapiens (human) ]

    Gene ID: 23112, updated on 3-Nov-2024

    Summary

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    Official Symbol
    TNRC6Bprovided by HGNC
    Official Full Name
    trinucleotide repeat containing adaptor 6Bprovided by HGNC
    Primary source
    HGNC:HGNC:29190
    See related
    Ensembl:ENSG00000100354 MIM:610740; AllianceGenome:HGNC:29190
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    GDSBA
    Summary
    Enables RNA binding activity. Involved in positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay; positive regulation of nuclear-transcribed mRNA poly(A) tail shortening; and regulatory ncRNA-mediated gene silencing. Acts upstream of with a positive effect on miRNA-mediated gene silencing by inhibition of translation. Predicted to be located in cytosol. Predicted to be active in P-body and nucleoplasm. Implicated in subserous uterine fibroid and uterine fibroid. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in testis (RPKM 3.9), thyroid (RPKM 2.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TNRC6B in Genome Data Viewer
    Location:
    22q13.1
    Exon count:
    27
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (40044834..40335808)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (40516397..40807210)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (40440838..40731812)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905155 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:40390673-40391306 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr22:40393419-40394024 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr22:40394025-40394630 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:40401347-40401848 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:40401849-40402348 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:40418684-40419184 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:40419185-40419685 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19079 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:40426725-40427244 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:40439529-40440176 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19080 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19081 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13767 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13766 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:40442874-40443092 Neighboring gene family with sequence similarity 83 member F Neighboring gene TNRC6B divergent transcript Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr22:40497428-40497948 Neighboring gene ribosomal protein L7 pseudogene 52 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19082 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:40591286-40591820 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:40591821-40592353 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19083 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:40624195-40624696 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:40633809-40634710 Neighboring gene uncharacterized LOC124905121 Neighboring gene MPRA-validated peak4496 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr22:40740204-40740376 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:40742019-40742532 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:40742533-40743046 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:40743047-40743559 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19084 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13769 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13770 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19086 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19085 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13771 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19087 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19088 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:40812395-40812894 Neighboring gene adenylosuccinate lyase Neighboring gene small G protein signaling modulator 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19089 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19090 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19091 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19092 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:40851734-40851957 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19093 Neighboring gene myocardin related transcription factor A Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:40867879-40868537 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:40894439-40894938 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:40906589-40907133 Neighboring gene MRTFA antisense RNA 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. Pathogenic variants in TNRC6B cause a genetic disorder characterised by developmental delay/intellectual disability and a spectrum of neurobehavioural phenotypes including autism and ADHD. Granadillo JL, et al. J Med Genet, 2020 Oct. PMID 32152250
    2. Replication of GWAS loci revealed the moderate effect of TNRC6B locus on susceptibility of Saudi women to develop uterine leiomyomas. Bondagji NS, et al. J Obstet Gynaecol Res, 2017 Feb. PMID 27987337
    3. Novel variants in TNRC6B cause global developmental delay with speech and behavioral abnormalities, short stature, low body weight, café-au-lait spots, and metabolic abnormality. Yang Q, et al. Mol Genet Genomic Med, 2024 Feb. PMID 38404251, Free PMC Article
    4. Sequence variants at 22q13 are associated with prostate cancer risk. Sun J, et al. Cancer Res, 2009 Jan 1. PMID 19117981, Free PMC Article
    5. Meta-analysis of 2,104 trios provides support for 10 new genes for intellectual disability. Lelieveld SH, et al. Nat Neurosci, 2016 Sep. PMID 27479843

    See all (142) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Novel variants in TNRC6B cause global developmental delay with speech and behavioral abnormalities, short stature, low body weight, cafe-au-lait spots, and metabolic abnormality.
      Title: Novel variants in TNRC6B cause global developmental delay with speech and behavioral abnormalities, short stature, low body weight, café-au-lait spots, and metabolic abnormality.
    2. Impact of scaffolding protein TNRC6 paralogs on gene expression and splicing.
      Title: Impact of scaffolding protein TNRC6 paralogs on gene expression and splicing.
    3. Pathogenic variants in TNRC6B cause a genetic disorder characterised by developmental delay/intellectual disability and a spectrum of neurobehavioural phenotypes including autism and ADHD.
      Title: Pathogenic variants in TNRC6B cause a genetic disorder characterised by developmental delay/intellectual disability and a spectrum of neurobehavioural phenotypes including autism and ADHD.
    4. FOXA1-induced LINC01207 facilitates head and neck squamous cell carcinoma via up-regulation of TNRC6B.
      Title: FOXA1-induced LINC01207 facilitates head and neck squamous cell carcinoma via up-regulation of TNRC6B.
    5. Expression of TNRC6 (GW182) Proteins Is Not Necessary for Gene Silencing by Fully Complementary RNA Duplexes.
      Title: Expression of TNRC6 (GW182) Proteins Is Not Necessary for Gene Silencing by Fully Complementary RNA Duplexes.
    6. The TNRC6 proteins bind to the 5'end of HCV RNA in a miR-122-dependent fashion and contribute functionally to replication of the viral genome by spatially regulating binding of miR-122/Ago2 to the 5'UTR.
      Title: TNRC6 proteins modulate hepatitis C virus replication by spatially regulating the binding of miR-122/Ago2 complexes to viral RNA.
    7. both BET1L and TNRC6B contributed to the risk of UL in Chinese women
      Title: Association of BET1L and TNRC6B with uterine leiomyoma risk and its relevant clinical features in Han Chinese population.
    8. Methylation of three CpGs (DROSHA: cg23230564, TNRC6B: cg06751583, and TNRC6B: cg21034183) was prospectively associated with time to cancer development (positively for cg06751583, inversely for cg23230564 and cg21034183), whereas methylation of one CpG site (DROSHA: cg16131300) was positively associated with cancer prevalence.
      Title: miRNA-Processing Gene Methylation and Cancer Risk.
    9. The rs12484776 significantly contributes to uterine myoma risk among Saudi women, both in single and also in synergistic cooperation with rs2280543, rs7913069, and rs1056836 markers.
      Title: Replication of GWAS loci revealed the moderate effect of TNRC6B locus on susceptibility of Saudi women to develop uterine leiomyomas.
    10. single nucleotide polymorphisms in the TNRC6B gene is associated with uterine fibroid.
      Title: BET1L and TNRC6B associate with uterine fibroid risk among European Americans.
    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
    Global developmental delay with speech and behavioral abnormalities
    MedGen: C5543226 OMIM: 619243 GeneReviews: Not available
    		not available

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2019-06-26)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2019-06-26)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    A genome-wide association study identifies three loci associated with susceptibility to uterine fibroids.
    EBI GWAS Catalog
    A genome-wide association study of northwestern Europeans involves the C-type natriuretic peptide signaling pathway in the etiology of human height variation.
    EBI GWAS Catalog
    A genome-wide search for loci interacting with known prostate cancer risk-associated genetic variants.
    EBI GWAS Catalog
    A meta-analysis of genome-wide association studies to identify prostate cancer susceptibility loci associated with aggressive and non-aggressive disease.
    EBI GWAS Catalog
    Genome-wide association study identifies multiple loci associated with both mammographic density and breast cancer risk.
    EBI GWAS Catalog
    Sequence variants at 22q13 are associated with prostate cancer risk.
    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

    • KIAA1093

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_positive_effect miRNA-mediated gene silencing by inhibition of translation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in miRNA-mediated post-transcriptional gene silencing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of nuclear-transcribed mRNA poly(A) tail shortening IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of nuclear-transcribed mRNA poly(A) tail shortening IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulatory ncRNA-mediated gene silencing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in P-body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    trinucleotide repeat-containing gene 6B protein
    Names
    trinucleotide repeat containing 6B

    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_001024843.2 → NP_001020014.1  trinucleotide repeat-containing gene 6B protein isoform 3

      See identical proteins and their annotated locations for NP_001020014.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate promoter, has a different translation start site, and is missing two in-frame coding exons compared to variant 1. This results in a shorter isoform (3) with a distinct N-terminus and lacking two internal protein segments compared to isoform 1.
      Source sequence(s)
      AL022238, BC028626, BE501815, BX647630, CA312515
      Consensus CDS
      CCDS46712.1
      Related
      ENSP00000306759.9, ENST00000301923.13
      Conserved Domains (3) summary
      cd12712
      Location:843 → 925
      RRM_TNRC6B; RNA recognition motif in vertebrate trinucleotide repeat-containing gene 6B protein (TNRC6B)
      pfam10427
      Location:198 → 308
      Ago_hook; Argonaute hook
      pfam16608
      Location:556 → 841
      TNRC6-PABC_bdg; TNRC6-PABC binding domain

    2. NM_001162501.2 → NP_001155973.1  trinucleotide repeat-containing gene 6B protein isoform 1

      See identical proteins and their annotated locations for NP_001155973.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AK294519, AL022238, AL831862, BQ009349, BU584176, BX537577, BX952326, CA312515, DB147781
      Consensus CDS
      CCDS54533.1
      UniProtKB/Swiss-Prot
      B0QY73, B0QY78, B4DGC0, Q5TH52, Q8TBX2, Q9UPQ9
      Related
      ENSP00000401946.2, ENST00000454349.7
      Conserved Domains (3) summary
      cd12712
      Location:1647 → 1729
      RRM_TNRC6B; RNA recognition motif in vertebrate trinucleotide repeat-containing gene 6B protein (TNRC6B)
      pfam10427
      Location:945 → 1055
      Ago_hook; Argonaute hook
      pfam16608
      Location:1360 → 1645
      TNRC6-PABC_bdg; TNRC6-PABC binding domain

    3. NM_015088.3 → NP_055903.2  trinucleotide repeat-containing gene 6B protein isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) is missing two in-frame coding exons compared to variant 1, resulting in a shorter isoform (2) lacking two internal protein segments compared to isoform 1.
      Source sequence(s)
      AB029016, AL022238, BC028626, BG942870, CA312515
      Consensus CDS
      CCDS46713.1
      Related
      ENSP00000338371.8, ENST00000335727.13
      Conserved Domains (3) summary
      cd12712
      Location:1537 → 1619
      RRM_TNRC6B; RNA recognition motif in vertebrate trinucleotide repeat-containing gene 6B protein (TNRC6B)
      pfam10427
      Location:891 → 1002
      Ago_hook; Argonaute hook
      pfam16608
      Location:1250 → 1535
      TNRC6-PABC_bdg; TNRC6-PABC binding 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_000022.11 Reference GRCh38.p14 Primary Assembly

      Range
      40044834..40335808
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      40516397..40807210
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UPQ9.4 GenPept UniProtKB/Swiss-Prot:Q9UPQ9

    Gene LinkOut

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

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