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    IFT52 intraflagellar transport 52 [ Homo sapiens (human) ]

    Gene ID: 51098, updated on 2-Nov-2024

    Summary

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    Official Symbol
    IFT52provided by HGNC
    Official Full Name
    intraflagellar transport 52provided by HGNC
    Primary source
    HGNC:HGNC:15901
    See related
    Ensembl:ENSG00000101052 MIM:617094; AllianceGenome:HGNC:15901
    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
    NGD2; NGD5; CGI-53; C20orf9
    Summary
    This gene encodes a conserved proline-rich protein that is a component of the intraflagellar transport-B (IFT-B) core complex. The encoded protein is essential for the integrity of the IFT-B core complex, and for biosynthesis and maintenance of cilia. Mutations in this gene are associated with ciliopathy that affects the skeleton. [provided by RefSeq, Oct 2016]
    Expression
    Ubiquitous expression in testis (RPKM 15.9), thyroid (RPKM 13.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See IFT52 in Genome Data Viewer
    Location:
    20q13.12
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (43590937..43647299)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (45324139..45380495)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (42219577..42275939)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene L3MBTL histone methyl-lysine binding protein 1 Neighboring gene transmembrane protein 14C-like Neighboring gene ReSE screen-validated silencer GRCh37_chr20:42173308-42173524 Neighboring gene serum/glucocorticoid regulated kinase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17904 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:42236005-42236846 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:42266543-42266756 Neighboring gene uncharacterized LOC124904906 Neighboring gene ribosomal protein L27a pseudogene

    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. Molecular basis underlying the ciliary defects caused by IFT52 variations found in skeletal ciliopathies. Ishida Y, et al. Mol Biol Cell, 2022 Aug 1. PMID 35704471, Free PMC Article
    2. The emerging functions of intraflagellar transport 52 in ciliary transport and ciliopathies. Udupa P, et al. Traffic, 2024 Jan. PMID 38272449
    3. IFT52 as a Novel Candidate for Ciliopathies Involving Retinal Degeneration. Chen X, et al. Invest Ophthalmol Vis Sci, 2018 Sep 4. PMID 30242358
    4. A homozygous nonsense variant in IFT52 is associated with a human skeletal ciliopathy. Girisha KM, et al. Clin Genet, 2016 Dec. PMID 26880018
    5. IFT52 mutations destabilize anterograde complex assembly, disrupt ciliogenesis and result in short rib polydactyly syndrome. Zhang W, et al. Hum Mol Genet, 2016 Sep 15. PMID 27466190, Free PMC Article

    See all (31) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The emerging functions of intraflagellar transport 52 in ciliary transport and ciliopathies.
      Title: The emerging functions of intraflagellar transport 52 in ciliary transport and ciliopathies.
    2. The intraflagellar transport protein IFT52 associated with short-rib thoracic dysplasia is essential for ciliary function in osteogenic differentiation in vitro and for sensory perception in Drosophila.
      Title: The intraflagellar transport protein IFT52 associated with short-rib thoracic dysplasia is essential for ciliary function in osteogenic differentiation in vitro and for sensory perception in Drosophila.
    3. Molecular basis underlying the ciliary defects caused by IFT52 variations found in skeletal ciliopathies.
      Title: Molecular basis underlying the ciliary defects caused by IFT52 variations found in skeletal ciliopathies.
    4. our data allowed to have a better comprehensive overview of the genotype/phenotype correlation associated to IFT52 mutations and shed light on a novel function of IFT52 on centriole cohesion via the regulation of microtubule anchorage and dynamics.
      Title: Human IFT52 mutations uncover a novel role for the protein in microtubule dynamics and centrosome cohesion.
    5. This report expands ocular phenotypes of IFT52 mutation-caused ciliopathy to include retinal ciliopathy and demonstrates its deleterious nature in interrupting primary ciliary function.
      Title: IFT52 as a Novel Candidate for Ciliopathies Involving Retinal Degeneration.
    6. The data identify a new locus for short-rib polydactyly syndromes (SRPS) and show that IFT52 mutations result in a ciliopathy with primary effects on the skeleton.
      Title: IFT52 mutations destabilize anterograde complex assembly, disrupt ciliogenesis and result in short rib polydactyly syndrome.
    7. Whole-exome sequencing revealed a homozygous nonsense variant p.R142* in IFT52 encoding an IFT-B core complex protein as the probable cause of her condition. This is the first report of a human disease associated with IFT52
      Title: A homozygous nonsense variant in IFT52 is associated with a human skeletal ciliopathy.
    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

    Associated conditions

    Description Tests
    Short-rib thoracic dysplasia 16 with or without polydactyly
    MedGen: C4310718 OMIM: 617102 GeneReviews: Not available
    		Compare labs

    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

    • FLJ40284

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in cilium assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cilium assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cilium assembly NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in dorsal/ventral pattern formation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in embryonic digit morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in heart looping IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in intraciliary anterograde transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in intraciliary anterograde transport NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in intraciliary transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in keratinocyte proliferation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of keratinocyte proliferation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in neural tube formation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in non-motile cilium assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of protein processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in smoothened signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in centriole IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in centrosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in ciliary basal body IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in ciliary base IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in ciliary tip TAS
    Traceable Author Statement
    more info
    		  
    is_active_in cilium IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cilium NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in cilium TAS
    Traceable Author Statement
    more info
    		  
    located_in dendrite terminus IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of intraciliary transport particle B IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of intraciliary transport particle B IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    part_of intraciliary transport particle B ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in motile cilium ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in photoreceptor connecting cilium IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    intraflagellar transport protein 52 homolog
    Names
    protein NGD5 homolog

    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_051913.1 RefSeqGene

      Range
      5325..61687
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001303458.3 → NP_001290387.1  intraflagellar transport protein 52 homolog isoform 1

      See identical proteins and their annotated locations for NP_001290387.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same isoform (1).
      Source sequence(s)
      AF151811, AI819589, AL121886, BC039831, BP308189, DC358472
      Consensus CDS
      CCDS33470.1
      UniProtKB/Swiss-Prot
      B3KMA1, E1P5W9, Q5H8Z0, Q9H1G3, Q9H1G4, Q9H1H2, Q9Y366
      Related
      ENSP00000362130.4, ENST00000373039.4
      Conserved Domains (1) summary
      cl23805
      Location:2 → 116
      ABC_transp_aux; ABC-type uncharacterized transport system

    2. NM_001303459.3 → NP_001290388.1  intraflagellar transport protein 52 homolog isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site in the 5' UTR and lacks an alternate exon in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (2) has a shorter C-terminus than isoform 1.
      Source sequence(s)
      AI819589, AL121886, Z98752
      Conserved Domains (1) summary
      cl23805
      Location:17 → 116
      ABC_transp_aux; ABC-type uncharacterized transport system

    3. NM_001323578.2 → NP_001310507.1  intraflagellar transport protein 52 homolog isoform 4

      Status: REVIEWED

      Source sequence(s)
      AI819589, AL121886, Z98752

    4. NM_001323579.2 → NP_001310508.1  intraflagellar transport protein 52 homolog isoform 5

      Status: REVIEWED

      Source sequence(s)
      AI819589, AL121886, Z98752

    5. NM_001323580.2 → NP_001310509.1  intraflagellar transport protein 52 homolog isoform 4

      Status: REVIEWED

      Source sequence(s)
      AI819589, AL121886, Z98752

    6. NM_001323581.2 → NP_001310510.1  intraflagellar transport protein 52 homolog isoform 5

      Status: REVIEWED

      Source sequence(s)
      AI819589, AL121886, Z98752

    7. NM_016004.5 → NP_057088.2  intraflagellar transport protein 52 homolog isoform 1

      See identical proteins and their annotated locations for NP_057088.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1). Both variants 1 and 2 encode the same isoform (1).
      Source sequence(s)
      AI819589, AL121886, BC039831, BP308189, DC358472
      Consensus CDS
      CCDS33470.1
      UniProtKB/Swiss-Prot
      B3KMA1, E1P5W9, Q5H8Z0, Q9H1G3, Q9H1G4, Q9H1H2, Q9Y366
      Related
      ENSP00000362121.3, ENST00000373030.8
      Conserved Domains (1) summary
      cl23805
      Location:2 → 116
      ABC_transp_aux; ABC-type uncharacterized transport system

    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_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      43590937..43647299
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      45324139..45380495
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y366.3 GenPept UniProtKB/Swiss-Prot:Q9Y366

    Gene LinkOut

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

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