IFT43 intraflagellar transport 43 [Homo sapiens (human)] - Gene

Summary

Official Symbol: IFT43provided by HGNC
Official Full Name: intraflagellar transport 43provided by HGNC
Primary source: HGNC:HGNC:29669
See related: Ensembl:ENSG00000119650 MIM:614068; AllianceGenome:HGNC:29669
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: CED3; RP81; SRTD18; C14orf179
Summary: This gene encodes a subunit of the intraflagellar transport complex A (IFT-A). IFT-A is a multiprotein complex that plays an important role in cilia assembly and maintenance by mediating retrograde ciliary transport. Mutations in this gene are a cause of cranioectodermal dysplasia-3 (CED3), also known as Sensenbrenner syndrome. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]
Expression: Ubiquitous expression in testis (RPKM 8.4), thyroid (RPKM 6.9) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 14q24.3

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	14	NC_000014.9 (75985763..76084073)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	14	NC_060938.1 (70194954..70293259)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	14	NC_000014.8 (76452106..76550416)

Chromosome 14 - NC_000014.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Studies identified a novel homozygous mutation in the ciliary protein IFT43 as the underlying cause of recessive inherited retinal degeneration. This is the first report demonstrating the involvement of IFT43 in retinal degeneration.
Title: A mutation in IFT43 causes non-syndromic recessive retinal degeneration.
These results suggest that CED-4 forms a complex with ced-3 mRNA and delivers it to ribosomes for translation.
Title: CED-4 is an mRNA-binding protein that delivers ced-3 mRNA to ribosomes.
C14ORF179 encoding IFT43 is mutated in Sensenbrenner syndrome.
Title: C14ORF179 encoding IFT43 is mutated in Sensenbrenner syndrome.

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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
Cranioectodermal dysplasia 3 MedGen: C3279807 OMIM: 614099 GeneReviews: Cranioectodermal Dysplasia	Compare labs
Retinitis pigmentosa 81 MedGen: C4693443 OMIM: 617871 GeneReviews: Not available	Compare labs
Short-rib thoracic dysplasia 18 with polydactyly MedGen: C4693420 OMIM: 617866 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Genome-wide association study in NSAID-induced acute urticaria/angioedema in Spanish and Han Chinese populations. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

A009J27 (e-PCR)
- UniSTS:24072

RH44406 (e-PCR)
- UniSTS:75034

G36086 (e-PCR)
- UniSTS:32809

SHGC-173313 (e-PCR)
- UniSTS:182841

D14S1348 (e-PCR)
- UniSTS:78663

G32751 (e-PCR)
- UniSTS:117332

A009P39 (e-PCR)
- UniSTS:51038

G63027 (e-PCR)
- UniSTS:140152

D14S771 (e-PCR)
- UniSTS:72074

G32586 (e-PCR)
- UniSTS:117169

RH45331 (e-PCR)
- UniSTS:10678

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
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 intraciliary retrograde transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in intraciliary retrograde transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in intraciliary retrograde transport	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in centriolar satellite	IDA Inferred from Direct Assay more info
located_in centriole	IEA Inferred from Electronic Annotation more info
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	IDA Inferred from Direct Assay more info	PubMed
located_in cilium	ISS Inferred from Sequence or Structural Similarity 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
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
located_in microtubule cytoskeleton	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: intraflagellar transport protein 43 homolog

Names: IFT complex A subunit; intraflagellar transport 43 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_031957.1 RefSeqGene

Range

5011..102990

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001102564.3 → NP_001096034.1 intraflagellar transport protein 43 homolog isoform 2

See identical proteins and their annotated locations for NP_001096034.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an exon and contains two alternate exons in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.

Source sequence(s)

AC008015, AF107885

Consensus CDS

CCDS41973.1

UniProtKB/Swiss-Prot

B3KPT6, B4DZI9, G3V385, O95418, Q96FT9, Q9ULA9

UniProtKB/TrEMBL

A0A7I2V6B2

Related

ENSP00000324177.6, ENST00000314067.11

Conserved Domains (1) summary

pfam15305
Location:67 → 193

IFT43; Intraflagellar transport protein 43
NM_001255995.3 → NP_001242924.1 intraflagellar transport protein 43 homolog isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (3) is shorter and has a distinct C-terminus, compared to isoform 1.

Source sequence(s)

AW235031, BC042852, BU627157, DB443802

Consensus CDS

CCDS58330.1

UniProtKB/Swiss-Prot

Q96FT9

Related

ENSP00000451096.1, ENST00000556742.1
NM_052873.3 → NP_443105.2 intraflagellar transport protein 43 homolog isoform 1

See identical proteins and their annotated locations for NP_443105.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

AK056735, BC010436, DB443802

Consensus CDS

CCDS9847.1

Related

ENSP00000238628.6, ENST00000238628.10

Conserved Domains (1) summary

pfam15305
Location:74 → 198

IFT43; Intraflagellar transport protein 43

RNA

NR_045664.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks an internal exon and uses an alternate splice site in the 3' UTR, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK302944, BI821833, DB443802
NR_045665.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (5) lacks an internal exon, contains two alternate internal exons and uses an alternate splice site in the 3' UTR, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK302944, CB853974, DB443802