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Aliases for IFT52 Gene

Aliases for IFT52 Gene

  • Intraflagellar Transport 52 2 3 5
  • Protein NGD5 Homolog 3 4
  • C20orf9 3 4
  • NGD5 3 4
  • Intraflagellar Transport 52 Homolog (Chlamydomonas) 2
  • Intraflagellar Transport Protein 52 Homolog 3
  • Chromosome 20 Open Reading Frame 9 2
  • CGI-53 3
  • NGD2 3

External Ids for IFT52 Gene

Previous HGNC Symbols for IFT52 Gene

  • C20orf9

Previous GeneCards Identifiers for IFT52 Gene

  • GC20P041653
  • GC20P042219
  • GC20P038955

Summaries for IFT52 Gene

Entrez Gene Summary for IFT52 Gene

  • 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]

GeneCards Summary for IFT52 Gene

IFT52 (Intraflagellar Transport 52) is a Protein Coding gene. Diseases associated with IFT52 include Short-Rib Thoracic Dysplasia 16 With Or Without Polydactyly and Cranioectodermal Dysplasia 1. Among its related pathways are Organelle biogenesis and maintenance and Intraflagellar transport. Gene Ontology (GO) annotations related to this gene include protein C-terminus binding.

UniProtKB/Swiss-Prot for IFT52 Gene

  • Involved in ciliogenesis as part of a complex involved in intraflagellar transport (IFT), the bi-directional movement of particles required for the assembly, maintenance and functioning of primary cilia (PubMed:27466190). Required for the anterograde transport of IFT88 (PubMed:27466190).

Additional gene information for IFT52 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for IFT52 Gene

Genomics for IFT52 Gene

GeneHancer (GH) Regulatory Elements for IFT52 Gene

Promoters and enhancers for IFT52 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH20I043589 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 574.6 +0.2 187 2 HDGF PKNOX1 CLOCK ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B IFT52 ENSG00000282876 MYBL2 SRSF6 GC20P043584 RPL27AP
GH20I043666 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 24 +76.6 76602 2.1 ARID4B SIN3A ZNF48 ZNF121 GLIS2 ZNF213 E2F8 KLF7 ATF7 RUNX3 MYBL2 IFT52 SRSF6 OSER1 GC20M043632
GH20I043656 Enhancer 1.6 FANTOM5 Ensembl ENCODE 28.1 +67.1 67066 2.8 HDGF MLX ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B ZNF207 GC20P043655 IFT52 MYBL2 OSER1 SRSF6 SGK2 L3MBTL1 GC20M043632
GH20I043680 Enhancer 1.2 Ensembl ENCODE dbSUPER 24.1 +91.5 91491 2.8 CTCF BACH1 EBF1 IRF4 ZKSCAN1 RELA POLR2A SCRT2 ZNF143 ATF7 IFT52 MYBL2 GC20M043632
GH20I044173 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 10.9 +591.2 591173 15.7 HDGF PKNOX1 MLX SIN3A YBX1 DMAP1 ZNF48 TCF12 ZNF121 ZNF302 JPH2 SRSF6 OSER1 L3MBTL1 FITM2 IFT52 SGK2 OSER1-AS1 GC20P044130
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around IFT52 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the IFT52 gene promoter:

Genomic Locations for IFT52 Gene

Genomic Locations for IFT52 Gene
chr20:43,590,613-43,647,296
(GRCh38/hg38)
Size:
56,684 bases
Orientation:
Plus strand
chr20:42,219,571-42,275,936
(GRCh37/hg19)

Genomic View for IFT52 Gene

Genes around IFT52 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
IFT52 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for IFT52 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for IFT52 Gene

Proteins for IFT52 Gene

  • Protein details for IFT52 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y366-IFT52_HUMAN
    Recommended name:
    Intraflagellar transport protein 52 homolog
    Protein Accession:
    Q9Y366
    Secondary Accessions:
    • B3KMA1
    • E1P5W9
    • Q5H8Z0
    • Q9H1G3
    • Q9H1G4
    • Q9H1H2

    Protein attributes for IFT52 Gene

    Size:
    437 amino acids
    Molecular mass:
    49706 Da
    Quaternary structure:
    • Component of the IFT complex B, at least composed of IFT20, IFT22, HSPB11/IFT25, IFT27, IFT46, IFT52, TRAF3IP1/IFT54, IFT57, IFT74, IFT80, IFT81, and IFT88. Interacts with IFT88 (By similarity). Interacts with TTC25 (PubMed:25860617).

neXtProt entry for IFT52 Gene

Post-translational modifications for IFT52 Gene

No Post-translational modifications

No data available for DME Specific Peptides for IFT52 Gene

Domains & Families for IFT52 Gene

Gene Families for IFT52 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for IFT52 Gene

Suggested Antigen Peptide Sequences for IFT52 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with IFT52: view

No data available for UniProtKB/Swiss-Prot for IFT52 Gene

Function for IFT52 Gene

Molecular function for IFT52 Gene

UniProtKB/Swiss-Prot Function:
Involved in ciliogenesis as part of a complex involved in intraflagellar transport (IFT), the bi-directional movement of particles required for the assembly, maintenance and functioning of primary cilia (PubMed:27466190). Required for the anterograde transport of IFT88 (PubMed:27466190).

Phenotypes From GWAS Catalog for IFT52 Gene

Gene Ontology (GO) - Molecular Function for IFT52 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008022 protein C-terminus binding ISS --
genes like me logo Genes that share ontologies with IFT52: view
genes like me logo Genes that share phenotypes with IFT52: view

Human Phenotype Ontology for IFT52 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

miRNA for IFT52 Gene

miRTarBase miRNAs that target IFT52

Clone Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for IFT52 Gene

Localization for IFT52 Gene

Subcellular locations from UniProtKB/Swiss-Prot for IFT52 Gene

Cell projection, cilium.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for IFT52 gene
Compartment Confidence
cytosol 4
cytoskeleton 3
peroxisome 2
nucleus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for IFT52 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005813 centrosome IEA --
GO:0005814 centriole IEA --
GO:0005929 cilium TAS --
GO:0030992 intraciliary transport particle B ISS --
GO:0031514 motile cilium ISS --
genes like me logo Genes that share ontologies with IFT52: view

Pathways & Interactions for IFT52 Gene

genes like me logo Genes that share pathways with IFT52: view

Gene Ontology (GO) - Biological Process for IFT52 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001841 neural tube formation IEA --
GO:0001947 heart looping IEA --
GO:0007224 smoothened signaling pathway IEA --
GO:0007368 determination of left/right symmetry IEA --
GO:0009953 dorsal/ventral pattern formation IEA --
genes like me logo Genes that share ontologies with IFT52: view

No data available for SIGNOR curated interactions for IFT52 Gene

Drugs & Compounds for IFT52 Gene

No Compound Related Data Available

Transcripts for IFT52 Gene

Unigene Clusters for IFT52 Gene

Intraflagellar transport 52 homolog (Chlamydomonas):
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for IFT52 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14
SP1: - -
SP2: -
SP3:

Relevant External Links for IFT52 Gene

GeneLoc Exon Structure for
IFT52
ECgene alternative splicing isoforms for
IFT52

Expression for IFT52 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for IFT52 Gene

Protein differential expression in normal tissues from HIPED for IFT52 Gene

This gene is overexpressed in Adipocyte (25.8), Testis (16.5), and Platelet (7.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for IFT52 Gene



NURSA nuclear receptor signaling pathways regulating expression of IFT52 Gene:

IFT52

SOURCE GeneReport for Unigene cluster for IFT52 Gene:

Hs.444332

Evidence on tissue expression from TISSUES for IFT52 Gene

  • Nervous system(2.6)
genes like me logo Genes that share expression patterns with IFT52: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for IFT52 Gene

Orthologs for IFT52 Gene

This gene was present in the common ancestor of animals.

Orthologs for IFT52 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia IFT52 33 34
  • 99.54 (n)
dog
(Canis familiaris)
Mammalia IFT52 33 34
  • 91.69 (n)
cow
(Bos Taurus)
Mammalia IFT52 33 34
  • 89.25 (n)
oppossum
(Monodelphis domestica)
Mammalia IFT52 34
  • 89 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Ift52 33 16 34
  • 88.89 (n)
rat
(Rattus norvegicus)
Mammalia Ift52 33
  • 87.95 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia IFT52 34
  • 84 (a)
OneToOne
chicken
(Gallus gallus)
Aves IFT52 33 34
  • 74.62 (n)
lizard
(Anolis carolinensis)
Reptilia IFT52 34
  • 71 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ift52 33
  • 74.65 (n)
Str.20368 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.26052 33
zebrafish
(Danio rerio)
Actinopterygii ift52 33 34
  • 72.53 (n)
Dr.15827 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.12948 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008725 33
  • 53.33 (n)
fruit fly
(Drosophila melanogaster)
Insecta osm-6 33 34
  • 50.39 (n)
worm
(Caenorhabditis elegans)
Secernentea osm-6 33 34
  • 50.49 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 61 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.200 33
Species where no ortholog for IFT52 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for IFT52 Gene

ENSEMBL:
Gene Tree for IFT52 (if available)
TreeFam:
Gene Tree for IFT52 (if available)

Paralogs for IFT52 Gene

No data available for Paralogs for IFT52 Gene

Variants for IFT52 Gene

Sequence variations from dbSNP and Humsavar for IFT52 Gene

SNP ID Clin Chr 20 pos Variation AA Info Type
rs145672738 uncertain-significance, Jeune thoracic dystrophy 43,635,933(+) G/A/C coding_sequence_variant, missense_variant
rs748090019 pathogenic, Short-rib thoracic dysplasia 16 with or without polydactyly 43,605,012(+) C/T 5_prime_UTR_variant, coding_sequence_variant, stop_gained
rs886037869 pathogenic, Short-rib thoracic dysplasia 16 with or without polydactyly, Short-rib thoracic dysplasia 16 with or without polydactyly (SRTD16) [MIM:617102] 43,613,959(+) G/A 5_prime_UTR_variant, coding_sequence_variant, missense_variant
rs886037870 pathogenic, Short-rib thoracic dysplasia 16 with or without polydactyly 43,624,000(+) T/ coding_sequence_variant, frameshift
rs754046046 benign, not specified 43,637,269(+) TTTTTTTTTTT/TTTTTTTTT/TTTTTTTTTT/TTTTTTTTTTTT/TTTTTTTTTTTTT intron_variant

Structural Variations from Database of Genomic Variants (DGV) for IFT52 Gene

Variant ID Type Subtype PubMed ID
nsv821137 CNV deletion 20802225
nsv586035 CNV loss 21841781
nsv586034 CNV loss 21841781
nsv586033 CNV gain 21841781
nsv586032 CNV gain 21841781
nsv514938 CNV gain+loss 21397061
nsv512617 CNV loss 21212237
nsv498971 CNV loss 21111241
nsv3385 CNV deletion 18451855
nsv1114217 CNV deletion 24896259
nsv1111211 CNV tandem duplication 24896259
nsv1073060 CNV deletion 25765185
nsv1057847 CNV loss 25217958
esv3645885 CNV loss 21293372
esv3557104 CNV deletion 23714750
esv3557103 CNV deletion 23714750
esv2677667 CNV deletion 23128226
esv2470167 CNV deletion 19546169
esv23525 CNV gain 19812545
esv1009985 CNV gain 20482838
dgv7581n54 CNV loss 21841781
dgv2253n106 CNV deletion 24896259

Variation tolerance for IFT52 Gene

Residual Variation Intolerance Score: 43.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.74; 33.05% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for IFT52 Gene

Human Gene Mutation Database (HGMD)
IFT52
SNPedia medical, phenotypic, and genealogical associations of SNPs for
IFT52

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for IFT52 Gene

Disorders for IFT52 Gene

MalaCards: The human disease database

(5) MalaCards diseases for IFT52 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
short-rib thoracic dysplasia 16 with or without polydactyly
  • srtd16
cranioectodermal dysplasia 1
  • ced1
ciliopathy
  • ciliopathies
asphyxiating thoracic dystrophy
  • jeune syndrome
cleft lip/palate
  • alveolar cleft lip and palate
- elite association - COSMIC cancer census association via MalaCards
Search IFT52 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

IFT52_HUMAN
  • Short-rib thoracic dysplasia 16 with or without polydactyly (SRTD16) [MIM:617102]: A form of short-rib thoracic dysplasia, a group of autosomal recessive ciliopathies that are characterized by a constricted thoracic cage, short ribs, shortened tubular bones, and a trident appearance of the acetabular roof. Polydactyly is variably present. Non-skeletal involvement can include cleft lip/palate as well as anomalies of major organs such as the brain, eye, heart, kidneys, liver, pancreas, intestines, and genitalia. Some forms of the disease are lethal in the neonatal period due to respiratory insufficiency secondary to a severely restricted thoracic cage, whereas others are compatible with life. Disease spectrum encompasses Ellis-van Creveld syndrome, asphyxiating thoracic dystrophy (Jeune syndrome), Mainzer-Saldino syndrome, and short rib-polydactyly syndrome. {ECO:0000269 PubMed:26880018, ECO:0000269 PubMed:27466190}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for IFT52

genes like me logo Genes that share disorders with IFT52: view

No data available for Genatlas for IFT52 Gene

Publications for IFT52 Gene

  1. Identification of novel human genes evolutionarily conserved in Caenorhabditis elegans by comparative proteomics. (PMID: 10810093) Lai CH … Lin W (Genome research 2000) 2 3 4 58
  2. IFT52 mutations destabilize anterograde complex assembly, disrupt ciliogenesis and result in short rib polydactyly syndrome. (PMID: 27466190) Zhang W … Cohn DH (Human molecular genetics 2016) 3 4 58
  3. A homozygous nonsense variant in IFT52 is associated with a human skeletal ciliopathy. (PMID: 26880018) Girisha KM … Rolfs A (Clinical genetics 2016) 3 4 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for IFT52 Gene

Sources for IFT52 Gene

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