IFT80 intraflagellar transport 80 [Homo sapiens (human)] - Gene

Summary

Official Symbol: IFT80provided by HGNC
Official Full Name: intraflagellar transport 80provided by HGNC
Primary source: HGNC:HGNC:29262
See related: Ensembl:ENSG00000068885 MIM:611177; AllianceGenome:HGNC:29262
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: ATD2; SRTD2; WDR56; FAP167; CFAP167
Summary: The protein encoded by this gene is part of the intraflagellar transport complex B and is necessary for the function of motile and sensory cilia. Defects in this gene are a cause of asphyxiating thoracic dystrophy 2 (ATD2). Three transcript variants encoding two different isoforms have been found for this gene.[provided by RefSeq, Jun 2010]
Expression: Ubiquitous expression in testis (RPKM 12.7), brain (RPKM 10.4) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3q25.33

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (160256986..160399225, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (163031586..163173837, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (159974774..160117013, complement)

Chromosome 3 - NC_000003.12 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?

Mutations in IFT80 cause Short rib-polydactyly syndrome, Beemer type.
Title: Mutations in IFT80 cause SRPS Type IV. Report of two families and review.
IFT80 plays an important role in invasion of gastric cancer.
Title: IFT80 Improves Invasion Ability in Gastric Cancer Cell Line via ift80/p75NGFR/MMP9 Signaling.
Mutations in IFT80 can be responsible for a lethal form of short-rib polydactyly and provide the molecular basis for the Jeune-Verma-Naumoff dysplasia spectrum.
Title: Mutation in IFT80 in a fetus with the phenotype of Verma-Naumoff provides molecular evidence for Jeune-Verma-Naumoff dysplasia spectrum.
Identification and characterization of a human IFT80 long isoform (namely IFT80-L), the carboxyl terminus of which shares the protein sequence of IFT80, is reported.
Title: Identification and characterization of a long isoform of human IFT80, IFT80-L.
Mutations in IFT80 is associated with Jeune asphyxiating thoracic dystrophy
Title: IFT80, which encodes a conserved intraflagellar transport protein, is mutated in Jeune asphyxiating thoracic dystrophy.

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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
Asphyxiating thoracic dystrophy 2 MedGen: C1970005 OMIM: 611263 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

D8S2279 (e-PCR)
- UniSTS:473907

RH121371 (e-PCR)
- UniSTS:134217

SHGC-145195 (e-PCR)
- UniSTS:174438

D11S3114 (e-PCR)
- UniSTS:152207

D16S325 (e-PCR)
- UniSTS:147089

SHGC-37245 (e-PCR)
- UniSTS:15013

D3S4120 (e-PCR)
- UniSTS:25049

STS-N68628 (e-PCR)
- UniSTS:67290

Readthrough TRIM59-IFT80

Readthrough gene: TRIM59-IFT80, Included gene: TRIM59

Gene Ontology Provided by GOA

Process	Evidence Code	Pubs
involved_in articular cartilage development	IEA Inferred from Electronic Annotation more info
involved_in bone mineralization involved in bone maturation	IEA Inferred from Electronic Annotation more info
involved_in cilium assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in cilium assembly	NAS Non-traceable Author Statement more info	PubMed
involved_in endochondral ossification	IEA Inferred from Electronic Annotation more info
involved_in growth plate cartilage chondrocyte differentiation	IEA Inferred from Electronic Annotation more info
involved_in intraciliary anterograde transport	NAS Non-traceable Author Statement more info	PubMed
involved_in keratinocyte proliferation	IEA Inferred from Electronic Annotation more info
involved_in limb development	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of keratinocyte proliferation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of non-canonical Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in non-canonical Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in non-motile cilium assembly	IEA Inferred from Electronic Annotation more info
involved_in osteoblast differentiation	IEA Inferred from Electronic Annotation more info
involved_in osteoblast proliferation	IEA Inferred from Electronic Annotation more info
involved_in receptor localization to non-motile cilium	IEA Inferred from Electronic Annotation more info
involved_in smoothened signaling pathway	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in 9+0 non-motile cilium	IEA Inferred from Electronic Annotation more info
is_active_in centrosome	IBA Inferred from Biological aspect of Ancestor more info
located_in ciliary basal body	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	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 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

General protein information

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Preferred Names: intraflagellar transport protein 80 homolog

Names: WD repeat domain 56; WD repeat-containing protein 56; intraflagellar transport 80 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_022932.2 RefSeqGene

Range

5000..147239

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001190241.2 → NP_001177170.1 intraflagellar transport protein 80 homolog isoform b

See identical proteins and their annotated locations for NP_001177170.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2 and 3 both encode the same isoform.

Source sequence(s)

AB037795, AK125342, BC030774, CA421514

Consensus CDS

CCDS54668.1

UniProtKB/Swiss-Prot

Q9P2H3

Related

ENSP00000420646.1, ENST00000496589.5

Conserved Domains (3) summary

COG2319
Location:3 → 423

WD40; WD40 repeat [General function prediction only]

sd00039
Location:13 → 49

7WD40; WD40 repeat [structural motif]

cl02567
Location:12 → 176

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001190242.2 → NP_001177171.1 intraflagellar transport protein 80 homolog isoform b

See identical proteins and their annotated locations for NP_001177171.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2 and 3 both encode the same isoform.

Source sequence(s)

AB037795, CA421514, DR000297

Consensus CDS

CCDS54668.1

UniProtKB/Swiss-Prot

Q9P2H3

Related

ENSP00000418196.1, ENST00000483465.5

Conserved Domains (3) summary

COG2319
Location:3 → 423

WD40; WD40 repeat [General function prediction only]

sd00039
Location:13 → 49

7WD40; WD40 repeat [structural motif]

cl02567
Location:12 → 176

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_020800.3 → NP_065851.1 intraflagellar transport protein 80 homolog isoform a

See identical proteins and their annotated locations for NP_065851.1

Status: REVIEWED

Description

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

Source sequence(s)

AB037795, AK125342, CA421514

Consensus CDS

CCDS3188.1

UniProtKB/Swiss-Prot

B4E0K1, C9J8I0, Q3MJC4, Q86YF4, Q9P2H3, Q9UIX1

Related

ENSP00000312778.7, ENST00000326448.12

Conserved Domains (2) summary

sd00039
Location:110 → 145

7WD40; WD40 repeat [structural motif]

cl25539
Location:17 → 254

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...