IFT52 intraflagellar transport 52 [Homo sapiens (human)] - Gene

Summary

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

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_000020.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.

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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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AL023481 (e-PCR)
- UniSTS:79146

SHGC-141781 (e-PCR)
- UniSTS:171079

SHGC-36858 (e-PCR)
- UniSTS:7821

AL031488 (e-PCR)
- UniSTS:51144

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

NG_051913.1 RefSeqGene

Range

5325..61687

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Status: REVIEWED

Source sequence(s)

AI819589, AL121886, Z98752
NM_001323579.2 → NP_001310508.1 intraflagellar transport protein 52 homolog isoform 5

Status: REVIEWED

Source sequence(s)

AI819589, AL121886, Z98752
NM_001323580.2 → NP_001310509.1 intraflagellar transport protein 52 homolog isoform 4

Status: REVIEWED

Source sequence(s)

AI819589, AL121886, Z98752
NM_001323581.2 → NP_001310510.1 intraflagellar transport protein 52 homolog isoform 5

Status: REVIEWED

Source sequence(s)

AI819589, AL121886, Z98752
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