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

Gene ID: 79809, updated on 16-Apr-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
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Genomic context

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Location:
2q24.3
Exon count:
33
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (165873362..165953776, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (166330866..166411321, complement)
105.20220307 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: 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. Retinal dystrophy as part of TTC21B-associated ciliopathy. Ben-Yosef T, et al. Ophthalmic Genet, 2021 Jun. PMID 33599192
  2. 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
  3. Mutations in TTC21B cause different phenotypes in two childhood cases in China. Zhang H, et al. Nephrology (Carlton), 2018 Apr. PMID 28124483
  4. Contribution of the TTC21B gene to glomerular and cystic kidney diseases. Bullich G, et al. Nephrol Dial Transplant, 2017 Jan 1. PMID 26940125
  5. 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

See all (34) 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)

Genotypes

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_2023_10

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

  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

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

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

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

Gene LinkOut

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