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IFT52 intraflagellar transport 52 [ Homo sapiens (human) ]

Gene ID: 51098, updated on 5-Mar-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (43590937..43647299)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (45324139..45380495)
105.20220307 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
  • 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. IFT52 as a Novel Candidate for Ciliopathies Involving Retinal Degeneration. Chen X, et al. Invest Ophthalmol Vis Sci, 2018 Sep 4. PMID 30242358
  3. A homozygous nonsense variant in IFT52 is associated with a human skeletal ciliopathy. Girisha KM, et al. Clin Genet, 2016 Dec. PMID 26880018
  4. 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
  5. 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. Guleria VS, et al. Exp Cell Res, 2022 Sep 15. PMID 35839863

See all (30) 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
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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_2023_10

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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