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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
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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 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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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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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
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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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