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    TTC21B tetratricopeptide repeat domain 21B [ Homo sapiens (human) ]

    Gene ID: 79809, updated on 10-Dec-2024

    Summary

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    Official Symbol
    TTC21Bprovided by HGNC
    Official Full Name
    tetratricopeptide repeat domain 21Bprovided by HGNC
    Primary source
    HGNC:HGNC:25660
    See related
    Ensembl:ENSG00000123607 MIM:612014; AllianceGenome:HGNC:25660
    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
    ATD4; THM1; FAP60; FLA17; SRTD4; CFAP60; IFT139; JBTS11; NPHP12; IFT139B; Nbla10696
    Summary
    This gene encodes a member of TTC21 family, containing several tetratricopeptide repeat (TPR) domains. This protein is localized to the cilium axoneme, and may play a role in retrograde intraflagellar transport in cilia. Mutations in this gene are associated with various ciliopathies, nephronophthisis 12, and asphyxiating thoracic dystrophy 4. [provided by RefSeq, Oct 2011]
    Expression
    Ubiquitous expression in prostate (RPKM 1.9), ovary (RPKM 1.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TTC21B in Genome Data Viewer
    Location:
    2q24.3
    Exon count:
    33
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (165873362..165953776, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (166330866..166411321, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (166729872..166810286, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:166649507-166650413 Neighboring gene polypeptide N-acetylgalactosaminyltransferase 3 Neighboring gene uncharacterized LOC124906086 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:166650414-166651319 Neighboring gene NANOG hESC enhancer GRCh37_chr2:166700603-166701418 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:166710405-166710906 Neighboring gene uncharacterized LOC100506124 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16728 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16729 Neighboring gene TTC21B antisense RNA 1 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:166810301-166811050 Neighboring gene uncharacterized LOC102724058 Neighboring gene sodium voltage-gated channel alpha subunit 1 Neighboring gene SCN1A and SCN9A antisense RNA 1 Neighboring gene RN7SK pseudogene 152

    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. Clinical report and genetic analysis of rare premature infant nephronophthisis caused by biallelic TTC21B variants. Li Y, et al. Mol Genet Genomic Med, 2024 Mar. PMID 38439578, Free PMC Article
    2. Retinal dystrophy as part of TTC21B-associated ciliopathy. Ben-Yosef T, et al. Ophthalmic Genet, 2021 Jun. PMID 33599192
    3. A novel heterotaxy gene: Expansion of the phenotype of TTC21B-spectrum disease. Strong A, et al. Am J Med Genet A, 2021 Apr. PMID 33547761, Free PMC Article
    4. A homozygous missense mutation in the ciliary gene TTC21B causes familial FSGS. Huynh Cong E, et al. J Am Soc Nephrol, 2014 Nov. PMID 24876116, Free PMC Article
    5. Contribution of the TTC21B gene to glomerular and cystic kidney diseases. Bullich G, et al. Nephrol Dial Transplant, 2017 Jan 1. PMID 26940125

    See all (35) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Clinical report and genetic analysis of rare premature infant nephronophthisis caused by biallelic TTC21B variants.
      Title: Clinical report and genetic analysis of rare premature infant nephronophthisis caused by biallelic TTC21B variants.
    2. Lethal neonatal respiratory failure due to biallelic variants in BBS1 and monoallelic variant in TTC21B.
      Title: Lethal neonatal respiratory failure due to biallelic variants in BBS1 and monoallelic variant in TTC21B.
    3. Biallelic mutations of TTC12 and TTC21B were identified in Chinese patients with multisystem ciliopathy syndromes.
      Title: Biallelic mutations of TTC12 and TTC21B were identified in Chinese patients with multisystem ciliopathy syndromes.
    4. Retinal dystrophy as part of TTC21B-associated ciliopathy.
      Title: Retinal dystrophy as part of TTC21B-associated ciliopathy.
    5. A novel heterotaxy gene: Expansion of the phenotype of TTC21B-spectrum disease.
      Title: A novel heterotaxy gene: Expansion of the phenotype of TTC21B-spectrum disease.
    6. Case Reports: 3 novel TTC21B mutations in two Chinese pediatric nephronophthisis-related ciliopathies cases that both presented with end-stage renal disease.
      Title: Mutations in TTC21B cause different phenotypes in two childhood cases in China.
    7. TTC21B mutation is associated with glomerular and cystic kidney diseases.
      Title: Contribution of the TTC21B gene to glomerular and cystic kidney diseases.
    8. Exome sequencing and further CRB2 analysis revealed that both siblings are compound heterozygotes for CRB2 mutations p.N800K and p.Gly1036Alafs*43, and heterozygous for a deleterious splice variant in the ciliopathy gene TTCB21
      Title: Expanding the phenotype of CRB2 mutations - A new ciliopathy syndrome?
    9. We demonstrated that the TTC21B gene product IFT139, an intraflagellar transport-A component, mainly localizes at the base of the primary cilium in developing podocytes from human fetal tissue and in undifferentiated cultured podocytes.
      Title: A homozygous missense mutation in the ciliary gene TTC21B causes familial FSGS.
    10. TTC21B contributes pathogenic alleles to approximately 5% of ciliopathy cases. Our data illustrate how genetic lesions can be both causally associated with diverse ciliopathies and interact in trans with other disease-causing genes
      Title: TTC21B contributes both causal and modifying alleles across the ciliopathy spectrum.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    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

    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

    Homology

    Clone Names

    • FLJ11457

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables chromatin binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in Bergmann glial cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cerebellar Purkinje cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cilium assembly NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in forebrain dorsal/ventral pattern formation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in intraciliary retrograde transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in intraciliary retrograde transport NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of eating behavior IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of canonical Wnt signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein localization to cilium IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within protein localization to cilium IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein localization to non-motile cilium IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of intraciliary retrograde transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of smoothened signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in smoothened signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in ventricular system development IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in ciliary tip TAS
    Traceable Author Statement
    more info
    		  
    located_in cilium NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in cilium TAS
    Traceable Author Statement
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoskeleton IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of intraciliary transport particle A IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of intraciliary transport particle A IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of intraciliary transport particle A IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    tetratricopeptide repeat protein 21B
    Names
    Nephronophthisis type12
    TPR repeat protein 21B
    intraflagellar transport 139 homolog
    putative protein product of Nbla10696
    tetratricopeptide repeat-containing hedgehog modulator-1

    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_030345.1 RefSeqGene

      Range
      5063..85477
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_024753.5 → NP_079029.3  tetratricopeptide repeat protein 21B

      See identical proteins and their annotated locations for NP_079029.3

      Status: REVIEWED

      Source sequence(s)
      AC011241, AK292942, BC035767, BC055424, BX114229, CK905149
      Consensus CDS
      CCDS33315.1
      UniProtKB/Swiss-Prot
      A8MUZ3, Q3LIE4, Q53T84, Q6P4A1, Q6PIF5, Q7Z4L5, Q8NCN3, Q96MA4, Q9HAK8
      UniProtKB/TrEMBL
      A0A7P0TAJ8
      Related
      ENSP00000243344.7, ENST00000243344.8
      Conserved Domains (4) summary
      TIGR02917
      Location:48 → 550
      PEP_TPR_lipo; putative PEP-CTERM system TPR-repeat lipoprotein
      sd00006
      Location:722 → 750
      TPR; TPR repeat [structural motif]
      pfam13414
      Location:721 → 784
      TPR_11; TPR repeat
      pfam14559
      Location:895 → 961
      TPR_19; Tetratricopeptide repeat

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      165873362..165953776 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047445870.1 → XP_047301826.1  tetratricopeptide repeat protein 21B isoform X2

      UniProtKB/TrEMBL
      A0A7P0T962

    2. XM_011511871.4 → XP_011510173.1  tetratricopeptide repeat protein 21B isoform X3

      UniProtKB/TrEMBL
      A0A7P0T962
      Conserved Domains (3) summary
      sd00006
      Location:472 → 500
      TPR; TPR repeat [structural motif]
      pfam13414
      Location:471 → 534
      TPR_11; TPR repeat
      pfam14559
      Location:645 → 711
      TPR_19; Tetratricopeptide repeat

    3. XM_017004967.2 → XP_016860456.1  tetratricopeptide repeat protein 21B isoform X1

      UniProtKB/TrEMBL
      A0A494C0N4, A0A7P0TB61
      Related
      ENSP00000506449.1, ENST00000681024.1

    4. XM_006712761.2 → XP_006712824.1  tetratricopeptide repeat protein 21B isoform X4

      UniProtKB/TrEMBL
      A0A7P0TA66, A0A7P0Z487
      Related
      ENSP00000505921.1, ENST00000680448.1
      Conserved Domains (5) summary
      COG0457
      Location:90 → 355
      TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
      sd00006
      Location:722 → 750
      TPR; TPR repeat [structural motif]
      pfam12895
      Location:770 → 857
      ANAPC3; Anaphase-promoting complex, cyclosome, subunit 3
      pfam13414
      Location:721 → 784
      TPR_11; TPR repeat
      pfam14559
      Location:895 → 961
      TPR_19; Tetratricopeptide repeat

    5. XM_011511872.3 → XP_011510174.1  tetratricopeptide repeat protein 21B isoform X5

      UniProtKB/TrEMBL
      A0A7P0Z487
      Related
      ENSP00000505499.1, ENST00000681483.1
      Conserved Domains (5) summary
      TIGR02917
      Location:48 → 550
      PEP_TPR_lipo; putative PEP-CTERM system TPR-repeat lipoprotein
      sd00006
      Location:722 → 750
      TPR; TPR repeat [structural motif]
      pfam12895
      Location:770 → 857
      ANAPC3; Anaphase-promoting complex, cyclosome, subunit 3
      pfam13414
      Location:721 → 784
      TPR_11; TPR repeat
      pfam14559
      Location:505 → 571
      TPR_19; Tetratricopeptide repeat

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      166330866..166411321 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054343984.1 → XP_054199959.1  tetratricopeptide repeat protein 21B isoform X1

      UniProtKB/TrEMBL
      A0A494C0N4

    2. XM_054343985.1 → XP_054199960.1  tetratricopeptide repeat protein 21B isoform X4

      UniProtKB/TrEMBL
      A0A7P0Z487

    3. XM_054343986.1 → XP_054199961.1  tetratricopeptide repeat protein 21B isoform X5

      UniProtKB/TrEMBL
      A0A7P0Z487
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7Z4L5.2 GenPept UniProtKB/Swiss-Prot:Q7Z4L5

    Gene LinkOut

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

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