IFT140 intraflagellar transport 140 [Homo sapiens (human)] - Gene

Summary

Official Symbol: IFT140provided by HGNC
Official Full Name: intraflagellar transport 140provided by HGNC
Primary source: HGNC:HGNC:29077
See related: Ensembl:ENSG00000187535 MIM:614620; AllianceGenome:HGNC:29077
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: RP80; MZSDS; SRTD9; WDTC2; gs114; c305C8.4; c380F5.1
Summary: This gene encodes one of the subunits of the intraflagellar transport (IFT) complex A. Intraflagellar transport is involved in the genesis, resorption and signaling of primary cilia. The primary cilium is a microtubule-based sensory organelle at the surface of most quiescent mammalian cells, that receives signals from its environment, such as the flow of fluid, light or odors, and transduces those signals to the nucleus. Loss of the corresponding protein in mouse results in renal cystic disease. [provided by RefSeq, Jun 2012]
Expression: Broad expression in testis (RPKM 6.4), thyroid (RPKM 4.0) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 16p13.3

Exon count:: 39

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (1510427..1612072, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (1525455..1627919, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (1560428..1662073, complement)

Chromosome 16 - NC_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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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?

Monoallelic IFT140 pathogenic variants are an important cause of the autosomal dominant polycystic kidney-spectrum phenotype.
Title: Monoallelic IFT140 pathogenic variants are an important cause of the autosomal dominant polycystic kidney-spectrum phenotype.
This study for the first time reported IFT140 variants that cause infertility in humans.
Title: Novel IFT140 variants cause spermatogenic dysfunction in humans.
Role of IFT140 in Osteogenesis of Adult Mice Long Bone
Title: The Role of IFT140 in Osteogenesis of Adult Mice Long Bone.
we demonstrated the implication of structural variations in IFT140-related diseases expanding its mutation spectrum. We also provide evidences for a unique genomic event mediated by an Alu-Alu recombination occurring on a shared haplotype.
Title: Whole-genome sequencing in patients with ciliopathies uncovers a novel recurrent tandem duplication in IFT140.
Compound heterozygous variants in IFT140 NM_014714.3: c.4182G>C p.(Thr1394Thr) and c.212C>T p.(Pro71Leu) were identified, and confirmed by Sanger sequencing.
Title: Compound heterozygous variants in IFT140 as a cause of nonsyndromic retinitis pigmentosa.
A maternally inherited homozygous biallelic mutation altering the exon 6 splice donor site in IFT140 gene causes Mainzer-Saldino syndrome.
Title: Partial uniparental isodisomy of chromosome 16 unmasks a deleterious biallelic mutation in IFT140 that causes Mainzer-Saldino syndrome.
We provide the first description of an Opitz trigonocephaly C syndrome (OTCS) phenotype that appears to result from IFT140 mutations. The presentation of this patient is consistent with previous reports showing that OTCS already exhibited skeleletal and nonskeletal features of a ciliopathy
Title: Compound heterozygous mutations in the IFT140 gene cause Opitz trigonocephaly C syndrome in a patient with typical features of a ciliopathy.
Recessive IFT140 mutations cause a severe congenital retinal dystrophy with high hyperopia and often early photophilia. Developmental delay is common but not universal and not all patients have obvious extraocular findings.
Title: The ophthalmic phenotype of IFT140-related ciliopathy ranges from isolated to syndromic congenital retinal dystrophy.
This study highlights the phenotype of nonsyndromic RP due to mutations in IFT140 with milder retinal dystrophy than that associated with the syndromic disease.
Title: Nonsyndromic Retinal Dystrophy due to Bi-Allelic Mutations in the Ciliary Transport Gene IFT140.
Identification of IFT140 variants in multiple unrelated non-syndromic Leber congenital amaurosis and retinitis pigmentosa.
Title: Mutations in human IFT140 cause non-syndromic retinal degeneration.

Submit: New GeneRIF Correction See all GeneRIFs (14)

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
Retinitis pigmentosa 80 MedGen: C4540439 OMIM: 617781 GeneReviews: Not available	Compare labs
Saldino-Mainzer syndrome MedGen: C1849437 OMIM: 266920 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

RH93126 (e-PCR)
- UniSTS:89653

STS-AA025090 (e-PCR)
- UniSTS:27304

D16S3024 (e-PCR)
- UniSTS:8403

Clone Names

FLJ10306, FLJ30571, KIAA0590, DKFZp564L232

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables molecular_function	ND No biological Data available more info
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 determination of left/right symmetry	IEA Inferred from Electronic Annotation more info
involved_in embryonic brain development	IEA Inferred from Electronic Annotation more info
involved_in embryonic camera-type eye development	IEA Inferred from Electronic Annotation more info
involved_in embryonic cranial skeleton morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in embryonic digit morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in heart development	IEA Inferred from Electronic Annotation more info
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
involved_in neural tube patterning	IEA Inferred from Electronic Annotation more info
involved_in non-motile cilium assembly	IEA Inferred from Electronic Annotation more info
involved_in photoreceptor cell outer segment organization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within protein localization to cilium	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein localization to cilium	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of cilium assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of smoothened signaling pathway	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in axoneme	IBA Inferred from Biological aspect of Ancestor more info
located_in axoneme	ISS Inferred from Sequence or Structural Similarity more info
located_in centriole	IEA Inferred from Electronic Annotation more info
located_in centrosome	IDA Inferred from Direct Assay more info	PubMed
is_active_in ciliary basal body	IBA Inferred from Biological aspect of Ancestor more info
located_in ciliary basal body	IDA Inferred from Direct Assay more info	PubMed
located_in ciliary tip	TAS Traceable Author Statement more info
located_in cilium	IDA Inferred from Direct Assay more info	PubMed
located_in cilium	NAS Non-traceable Author Statement more info	PubMed
located_in cilium	TAS Traceable Author Statement more info
located_in cone photoreceptor outer segment	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 photoreceptor connecting cilium	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: intraflagellar transport protein 140 homolog

Names: WD and tetratricopeptide repeats protein 2; intraflagellar transport 140 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_032783.1 RefSeqGene

Range

5037..106682

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_014714.4 → NP_055529.2 intraflagellar transport protein 140 homolog

See identical proteins and their annotated locations for NP_055529.2

Status: REVIEWED

Source sequence(s)

AW245075, BC035577, DC401677

Consensus CDS

CCDS10439.1

UniProtKB/Swiss-Prot

A2A2A8, D3DU75, O60332, Q96RY7, Q9UG52

Related

ENSP00000406012.2, ENST00000426508.7

Conserved Domains (5) summary

COG2319
Location:102 → 434

WD40; WD40 repeat [General function prediction only]

sd00006
Location:957 → 983

TPR; TPR repeat [structural motif]

sd00039
Location:19 → 59

7WD40; WD40 repeat [structural motif]

cl25539
Location:19 → 121

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 ...

cl26002
Location:951 → 1233

TPR_11; TPR repeat

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

NC_000016.10 Reference GRCh38.p14 Primary Assembly

Range

1510427..1612072 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047434970.1 → XP_047290926.1 intraflagellar transport protein 140 homolog isoform X2
XM_006720990.4 → XP_006721053.1 intraflagellar transport protein 140 homolog isoform X1

See identical proteins and their annotated locations for XP_006721053.1

UniProtKB/Swiss-Prot

A2A2A8, D3DU75, O60332, Q96RY7, Q9UG52

Conserved Domains (5) summary

COG2319
Location:102 → 434

WD40; WD40 repeat [General function prediction only]

sd00006
Location:957 → 983

TPR; TPR repeat [structural motif]

sd00039
Location:19 → 59

7WD40; WD40 repeat [structural motif]

cl25539
Location:19 → 121

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 ...

cl26002
Location:951 → 1233

TPR_11; TPR repeat
XM_047434969.1 → XP_047290925.1 intraflagellar transport protein 140 homolog isoform X1

UniProtKB/Swiss-Prot

A2A2A8, D3DU75, O60332, Q96RY7, Q9UG52
XM_047434966.1 → XP_047290922.1 intraflagellar transport protein 140 homolog isoform X1

UniProtKB/Swiss-Prot

A2A2A8, D3DU75, O60332, Q96RY7, Q9UG52
XM_006720991.4 → XP_006721054.1 intraflagellar transport protein 140 homolog isoform X1

See identical proteins and their annotated locations for XP_006721054.1

UniProtKB/Swiss-Prot

A2A2A8, D3DU75, O60332, Q96RY7, Q9UG52

Conserved Domains (5) summary

COG2319
Location:102 → 434

WD40; WD40 repeat [General function prediction only]

sd00006
Location:957 → 983

TPR; TPR repeat [structural motif]

sd00039
Location:19 → 59

7WD40; WD40 repeat [structural motif]

cl25539
Location:19 → 121

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 ...

cl26002
Location:951 → 1233

TPR_11; TPR repeat
XM_047434967.1 → XP_047290923.1 intraflagellar transport protein 140 homolog isoform X1

UniProtKB/Swiss-Prot

A2A2A8, D3DU75, O60332, Q96RY7, Q9UG52
XM_047434968.1 → XP_047290924.1 intraflagellar transport protein 140 homolog isoform X1

UniProtKB/Swiss-Prot

A2A2A8, D3DU75, O60332, Q96RY7, Q9UG52
XM_047434965.1 → XP_047290921.1 intraflagellar transport protein 140 homolog isoform X1

UniProtKB/Swiss-Prot

A2A2A8, D3DU75, O60332, Q96RY7, Q9UG52
XM_011522767.2 → XP_011521069.1 intraflagellar transport protein 140 homolog isoform X3

UniProtKB/TrEMBL

B4DR58

Conserved Domains (2) summary

TIGR02917
Location:626 → 908

PEP_TPR_lipo; putative PEP-CTERM system TPR-repeat lipoprotein

sd00006
Location:478 → 512

TPR; TPR repeat [structural motif]
XM_047434971.1 → XP_047290927.1 intraflagellar transport protein 140 homolog isoform X4
XM_006720992.4 → XP_006721055.1 intraflagellar transport protein 140 homolog isoform X11

UniProtKB/TrEMBL

B3KNW3

Related

ENSP00000354895.5, ENST00000361339.9
XM_011522771.4 → XP_011521073.1 intraflagellar transport protein 140 homolog isoform X8

UniProtKB/TrEMBL

B4DQZ8

Conserved Domains (3) summary

COG2319
Location:102 → 434

WD40; WD40 repeat [General function prediction only]

sd00039
Location:21 → 55

7WD40; WD40 repeat [structural motif]

cl02567
Location:15 → 229

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 ...
XM_047434972.1 → XP_047290928.1 intraflagellar transport protein 140 homolog isoform X6
XM_011522772.4 → XP_011521074.1 intraflagellar transport protein 140 homolog isoform X9

UniProtKB/TrEMBL

B4DQZ8

Conserved Domains (3) summary

COG2319
Location:102 → 434

WD40; WD40 repeat [General function prediction only]

sd00039
Location:21 → 55

7WD40; WD40 repeat [structural motif]

cl02567
Location:15 → 229

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 ...
XM_047434975.1 → XP_047290931.1 intraflagellar transport protein 140 homolog isoform X8
XM_047434974.1 → XP_047290930.1 intraflagellar transport protein 140 homolog isoform X8
XM_047434976.1 → XP_047290932.1 intraflagellar transport protein 140 homolog isoform X9
XM_005255725.6 → XP_005255782.1 intraflagellar transport protein 140 homolog isoform X7

UniProtKB/TrEMBL

B4DQZ8

Conserved Domains (3) summary

COG2319
Location:102 → 434

WD40; WD40 repeat [General function prediction only]

sd00039
Location:21 → 55

7WD40; WD40 repeat [structural motif]

cl02567
Location:15 → 229

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 ...
XM_047434973.1 → XP_047290929.1 intraflagellar transport protein 140 homolog isoform X7
XM_005255726.5 → XP_005255783.1 intraflagellar transport protein 140 homolog isoform X10

UniProtKB/TrEMBL

B4DQZ8

Conserved Domains (3) summary

COG2319
Location:102 → 434

WD40; WD40 repeat [General function prediction only]

sd00039
Location:21 → 55

7WD40; WD40 repeat [structural motif]

cl02567
Location:15 → 229

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 ...
XM_047434978.1 → XP_047290934.1 intraflagellar transport protein 140 homolog isoform X10
XM_047434977.1 → XP_047290933.1 intraflagellar transport protein 140 homolog isoform X10
XM_047434980.1 → XP_047290936.1 intraflagellar transport protein 140 homolog isoform X10
XM_047434979.1 → XP_047290935.1 intraflagellar transport protein 140 homolog isoform X10
XM_011522769.4 → XP_011521071.1 intraflagellar transport protein 140 homolog isoform X5

UniProtKB/TrEMBL

B4DQZ8

Conserved Domains (3) summary

COG2319
Location:102 → 434

WD40; WD40 repeat [General function prediction only]

sd00039
Location:21 → 55

7WD40; WD40 repeat [structural motif]

cl02567
Location:15 → 229

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 ...

Alternate T2T-CHM13v2.0

Genomic

NC_060940.1 Alternate T2T-CHM13v2.0

Range

1525455..1627919 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054314518.1 → XP_054170493.1 intraflagellar transport protein 140 homolog isoform X2
XM_054314512.1 → XP_054170487.1 intraflagellar transport protein 140 homolog isoform X1

UniProtKB/Swiss-Prot

A2A2A8, D3DU75, O60332, Q96RY7, Q9UG52
XM_054314515.1 → XP_054170490.1 intraflagellar transport protein 140 homolog isoform X1

UniProtKB/Swiss-Prot

A2A2A8, D3DU75, O60332, Q96RY7, Q9UG52
XM_054314514.1 → XP_054170489.1 intraflagellar transport protein 140 homolog isoform X1

UniProtKB/Swiss-Prot

A2A2A8, D3DU75, O60332, Q96RY7, Q9UG52
XM_054314516.1 → XP_054170491.1 intraflagellar transport protein 140 homolog isoform X1

UniProtKB/Swiss-Prot

A2A2A8, D3DU75, O60332, Q96RY7, Q9UG52
XM_054314513.1 → XP_054170488.1 intraflagellar transport protein 140 homolog isoform X1

UniProtKB/Swiss-Prot

A2A2A8, D3DU75, O60332, Q96RY7, Q9UG52
XM_054314517.1 → XP_054170492.1 intraflagellar transport protein 140 homolog isoform X1

UniProtKB/Swiss-Prot

A2A2A8, D3DU75, O60332, Q96RY7, Q9UG52
XM_054314511.1 → XP_054170486.1 intraflagellar transport protein 140 homolog isoform X1

UniProtKB/Swiss-Prot

A2A2A8, D3DU75, O60332, Q96RY7, Q9UG52
XM_054314519.1 → XP_054170494.1 intraflagellar transport protein 140 homolog isoform X3
XM_054314520.1 → XP_054170495.1 intraflagellar transport protein 140 homolog isoform X4
XM_054314535.1 → XP_054170510.1 intraflagellar transport protein 140 homolog isoform X11
XM_054314525.1 → XP_054170500.1 intraflagellar transport protein 140 homolog isoform X8
XM_054314527.1 → XP_054170502.1 intraflagellar transport protein 140 homolog isoform X8
XM_054314522.1 → XP_054170497.1 intraflagellar transport protein 140 homolog isoform X6
XM_054314528.1 → XP_054170503.1 intraflagellar transport protein 140 homolog isoform X9
XM_054314526.1 → XP_054170501.1 intraflagellar transport protein 140 homolog isoform X8
XM_054314529.1 → XP_054170504.1 intraflagellar transport protein 140 homolog isoform X9
XM_054314523.1 → XP_054170498.1 intraflagellar transport protein 140 homolog isoform X7
XM_054314524.1 → XP_054170499.1 intraflagellar transport protein 140 homolog isoform X7
XM_054314530.1 → XP_054170505.1 intraflagellar transport protein 140 homolog isoform X10
XM_054314534.1 → XP_054170509.1 intraflagellar transport protein 140 homolog isoform X10
XM_054314532.1 → XP_054170507.1 intraflagellar transport protein 140 homolog isoform X10
XM_054314533.1 → XP_054170508.1 intraflagellar transport protein 140 homolog isoform X10
XM_054314531.1 → XP_054170506.1 intraflagellar transport protein 140 homolog isoform X10
XM_054314521.1 → XP_054170496.1 intraflagellar transport protein 140 homolog isoform X5