Alternative titles; symbols
HGNC Approved Gene Symbol: IFT140
Cytogenetic location: 16p13.3 Genomic coordinates (GRCh38) : 16:1,510,427-1,612,072 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 16p13.3 | Retinitis pigmentosa 80 | 617781 | Autosomal recessive | 3 |
| Short-rib thoracic dysplasia 9 with or without polydactyly | 266920 | Autosomal recessive | 3 |
The IFT140 gene encodes a subunit of intraflagellar transport complex A (IFTA), which is involved in retrograde ciliary transport (summary by Perrault et al., 2012).
By sequencing clones obtained from a size-fractionated adult brain cDNA library, Nagase et al. (1998) cloned IFT140, which they called KIAA0590. The deduced protein contains 1,462 amino acids. It had an apparent molecular mass of more than 100 kD by SDS-PAGE. RT-PCR detected high expression in kidney, moderate expression in ovary, testis, prostate, and lung, and low expression in thymus, brain, heart, placenta, and skeletal muscle. Little to no expression was present in liver, pancreas, spleen, and small intestine.
Using an Ift140 lacZ-reporter mouse, Schmidts et al. (2013) observed more prominent expression of Ift140 in renal and retinal tissue of mouse embryos than in the skeleton, although immunofluorescence demonstrated clear localization of Ift140 to the ciliary axoneme in murine ATDC5 chondrocyte precursor cells.
Miller et al. (2013) reported that mouse Ift140 has 5 WD40 domains near the N terminus and 9 tetratricopeptide (TRP) repeats in the C-terminal half. Immunohistochemical analysis of embryonic mouse limb bud epithelium revealed localization of Ift140 to both the base and tip of primary cilium.
By transient expression of IFT140 in hTERT-RPE1 cells, Hull et al. (2016) observed localization of IFT140 to the basal body.
Using radiation hybrid analysis, Nagase et al. (1998) mapped the IFT140 gene to chromosome 16.
Gross (2012) mapped the IFT140 gene to chromosome 16p13.3 based on an alignment of the IFT140 sequence (GenBank BC035577) with the genomic sequence (GRCh37).
Miller et al. (2013) reported that the mouse Ift140 gene maps to chromosome 17 between markers rs3667809 and rs3684506.
Short-Rib Thoracic Dysplasia 9 with or without Polydactyly
In 10 patients from 6 unrelated families with short-rib thoracic dysplasia-9 (SRTD9; 266920) who had a clinical diagnosis of Mainzer-Saldino syndrome, Perrault et al. (2012) identified homozygous or compound heterozygous mutations in the IFT140 gene (see, e.g., 614620.0001-614620.0006). Mutations in the first patient were identified by ciliome sequencing and confirmed by Sanger sequencing. In addition, compound heterozygosity for mutations in IFT40 (614620.0002; 614620.0005) was identified in a patient with a clinical diagnosis of Jeune syndrome, or ATD. Heterozygous mutations in the IFT140 gene were found in 4 additional index patients with the disorder; a second pathogenic mutation was not detected in these patients. Clinical features of patients with biallelic mutations did not differ significantly from those with heterozygous mutations or from those with no mutation detected in the IFT40 gene. In vitro functional expression studies in retinal pigment epithelial cells demonstrated that the missense mutant IFT140 proteins had partial to complete loss of basal body localization and an increase of cytoplasmic staining. Fibroblasts from 2 unrelated patients showed absent cilia in a high proportion of cells compared to controls, indicating a defect in ciliogenesis and/or cilia maintenance. Although mutant IFT140 was localized along the cilia axoneme, there appeared to be a defect in retrograde ciliary transport with an abnormal distribution of other ciliary proteins. The findings indicated that IFT140 has a pivotal role in proper development and function of ciliated cells, and confirmed that Mainzer-Saldino syndrome is a skeletal ciliopathy.
Using whole-exome sequencing, sequencing of a ciliopathy gene panel, and Sanger sequencing in a study of 64 probands clinically diagnosed with ATD and 2 with Mainzer, Schmidts et al. (2013) identified biallelic causative mutations in the IFT140 gene in 6 patients, including both MZSDS patients (see, e.g., 614620.0002 and 614620.0008-614620.0010). The patients presented with renal disease in early childhood and showed notable retinal involvement, but had a nonlethal thorax-related clinical course.
In a 6.5-year-old British boy with short stature, short ribs and narrow thorax, retinal dystrophy, and end-stage renal failure, who also exhibited brachydactyly and ectodermal features and received a clinical diagnosis of Sensenbrenner syndrome, Bayat et al. (2017) identified compound heterozygosity for a missense (G212R; 614620.0005) and a nonsense (R760X; 614620.0016) mutation in the IFT140 gene.
In a 10-year-old boy who exhibited features consistent with MZSDS, Helm et al. (2017) identified homozygosity for the G212R substitution in the IFT140 gene, which was inherited from his mother through chromosome 16 maternal heteroisodisomy.
Retinitis Pigmentosa 80
In 7 unrelated patients with nonsyndromic retinitis pigmentosa (RP80; 617781), Xu et al. (2015) identified compound heterozygous mutations in the ITF40 gene (see, e.g., 614620.0011-614620.0014). None of the patients exhibited any nonocular manifestations.
In 11 affected individuals from 5 unrelated families with nonsyndromic retinitis pigmentosa, Hull et al. (2016) identified homozygosity or compound heterozygosity for mutations in the IFT140 gene (see, e.g., 614620.0002, 614620.0013, and 614620.0015). The authors noted that the retinal dystrophy in these patients was milder than that associated with the syndromic disease (SRTD9).
In 10 Saudi probands with congenital severe retinopathy, Bifari et al. (2016) identified homozygosity for a missense mutation in the IFT140 gene (E664K; 614620.0001). Seven of the patients also exhibited developmental delay, and 5 had cone-shaped epiphyses on hand x-rays.
Using N-ethyl-N-nitrosourea to induce embryonic lethal mutations in mice, Miller et al. (2013) created the 'cauli' phenotype. Cauli homozygotes died at midgestation with global and catastrophic developmental defects, including exencephaly, spina bifida, massive craniofacial dysmorphism, digit anomalies, cardiovascular anomalies, and somite patterning defects. Linkage analysis followed by direct sequencing identified a T-to-A transversion in exon 19 of the Ift140 gene that was predicted to alter binding sites for splicing factors Srsf5 (600914) and Srsf6 (601944) in the Ift140 pre-mRNA, and to cause an ile855-to-lys (I855K) substitution in the protein. The I855 residue resides within a coiled-coil domain of Ift140 immediately upstream of the first TRP. Real-time PCR and Western blot analysis of Ift140 cauli/cauli embryos showed an approximately 30% decrease in Ift140 mRNA and a 70% decrease in Ift140 protein. Scanning electron microscopic examination of limb buds of Ift140 cauli/cauli embryos at embryonic day 10.5 revealed epithelial cells with indistinct borders and reduced number of cilia. Cilia also showed severely disrupted morphology, including bulbous appearance, consistent with accumulation of cargo at the tip due to a defect in retrograde transport. Molecular analysis of Ift140 cauli/cauli limb buds revealed altered spatial patterning and regulation of multiple growth factors, predominantly those in the cilia-dependent hedgehog (see 600725) signaling pathways. Miller et al. (2013) found that Ift140 -/- mice showed an identical phenotype to Ift140 cauli/cauli mice. The authors concluded that the cauli phenotype results from loss of Ift140 rather than altered function following amino acid substitution, and that cauli represents a ciliopathy.
Short-Rib Thoracic Dysplasia 9
In a 17-year-old boy with short-rib thoracic dysplasia-9 (SRTD9; 266920) with a clinical diagnosis of Mainzer-Saldino syndrome, who exhibited a small thoracic cavity with short and thick ribs and had early-onset retinal dystrophy and chronic renal failure, Perrault et al. (2012) identified compound heterozygosity for 2 mutations in the IFT140 gene: a 1990G-A transition, resulting in a glu664-to-lys (E664K) substitution at a highly conserved residue, and a G-to-T transversion in intron 19 (2399+1G-T; 614620.0002), predicted to result in the skipping of exon 18. The mutations were detected by ciliome sequencing of the patient's DNA and confirmed by Sanger sequencing; they were not found in 200 control chromosomes. Five affected individuals from 2 additional consanguineous Saudi Arabian families with a clinical diagnosis of Mainzer-Saldino syndrome were found to be homozygous for the E664K mutation. In vitro functional expression studies in retinal pigment epithelial cells demonstrated that the mutant protein had partial to complete loss of basal body localization and an increase of cytoplasmic staining, indicating severe disorganization. Patient fibroblasts showed absent cilia in a high proportion of cells compared to controls, consistent with a defect in ciliogenesis and/or cilia maintenance. Although mutant IFT140 was localized along the cilia axoneme, there appeared to be a defect in retrograde ciliary transport with an abnormal distribution of other ciliary proteins. All patients had onset of retinal dystrophy in infancy with visual loss and nystagmus, and all exhibited skeletal anomalies, including short stature in most, phalangeal cone-shaped epiphyses, and metaphyseal defects in the hips (in 3). In contrast to the compound heterozygous patient, none of the Saudi Arabian patients had overt renal disease and their thorax phenotype was reported to be unremarkable. Four of the 5 Saudi Arabian patients had mild intellectual disability or autistic features with seizures, which may have been due to other factors.
Retinitis Pigmentosa 80
In 10 Saudi probands with congenital severe retinopathy (RP80; 617781), including 2 boys previously reported by Khan et al. (2014), Bifari et al. (2016) identified homozygosity for the E664K substitution (c.1990G-A, NM_014714.3) in the IFT140 gene. Some patients exhibited additional features, including developmental delay in 7 of the patients, and cone-shaped phalangeal epiphyses in the 5 who underwent hand x-rays. Noting that all but 1 of the families they studied harbored the E664K mutation, the authors suggested that this represented a founder effect or a mutation hotspot.
Short-Rib Thoracic Dysplasia 9
In an 18-month-old boy with short-rib thoracic dysplasia-9 (SRTD9; 266920), who had a clinical diagnosis of Jeune syndrome, Perrault et al. (2012) identified compound heterozygosity for a c.2399+1G-T transversion in intron 19 of the IFT140 gene, and a missense mutation (G212R; 614620.0005). The patient was hypotonic with poor feeding at birth and exhibited developmental delay, short thorax with short ribs, trident-shaped spurs on long bones, cone-shaped epiphyses of the phalanges, and increased echogenicity of the kidneys with nonspecific tubulointerstitial nephritis.
For discussion of the c.2399+1G-T mutation that Perrault et al. (2012) identified in compound heterozygous state in a 17-year-old boy with SRTD9, who had a clinical diagnosis of Mainzer-Saldino syndrome, see 614620.0001.
In a 39-year-old Austrian woman with a clinical diagnosis of Mainzer-Saldino syndrome, who had a small thorax, brachymesophalangism, and cone-shaped epiphyses, with childhood onset of retinal pigmentary dystrophy and small cystic kidneys resulting in end-stage renal disease by 12 years of age, Schmidts et al. (2013) identified compound heterozygosity for the c.2399+1G-T splice site mutation in the IFT140 gene and a c.4078T-C transition resulting in a cys1360-to-arg (C1360R; 614620.0007) substitution at a highly conserved residue.
Retinitis Pigmentosa 80
In a 67-year-old Caucasian British man (patient 2) with retinitis pigmentosa (RP80; 617781), who also had hearing loss but was negative for mutation in 9 Usher syndrome (see 276900)-associated genes, Hull et al. (2016) identified compound heterozygosity for the c.2399+1G-T splice site mutation (c.2399+1G-T, NM_014714.3) and a c.2815T-C transition in the IFT140 gene, resulting in a ser939-to-pro (S939P; 614620.0015) substitution. The proband's younger sister, who had RP without hearing loss, was also compound heterozygous for the IFT140 variants, whereas his unaffected son carried only one of the mutations. Both patients exhibited normal development without skeletal manifestations or renal failure. Transient transfection in hTERT-RPE1 cells followed by immunostaining demonstrated significantly reduced basal body localization with the S939P mutant compared to wildtype.
In an 18-year-old boy with short-rib thoracid dysplasia-9 without polydactyly (SRTD9; 266920), who had a clinical diagnosis of Mainzer-Saldino syndrome, Perrault et al. (2012) identified compound heterozygosity for 2 mutations in the IFT140 gene: a c.932A-G transition resulting in a tyr311-to-cys (Y311C) substitution that was predicted to be deleterious, and a 4-bp deletion (857_860del; 614620.0004), resulting in a frameshift and premature termination (Ile286LysfsTer6). Neither mutation was found in 200 control chromosomes. In vitro functional expression studies in retinal pigment epithelial cells demonstrated that the Y311C mutant protein had partial to complete loss of basal body localization and an increase of cytoplasmic staining. Fibroblasts of 1 patient showed absent cilia in a high proportion of cells compared to controls, indicating a defect in ciliogenesis and/or cilia maintenance. Although mutant IFT140 was localized along the cilia axoneme, there appeared to be a defect in retrograde ciliary transport with an abnormal distribution of other ciliary proteins. The patient had onset at birth of retinal dystrophy with visual loss, and nystagmus, phalangeal cone-shaped epiphyses in the feet, chronic renal failure, and cholestasis. Psychomotor development was normal.
For discussion of the 4-bp deletion (c.856_860del) in the IFT140 gene that was found in compound heterozygous state by Perrault et al. (2012) in a patient with short-rib thoracic dysplasia-9 without polydactyly (SRTD9; 266920), who had a clinical diagnosis of Mainzer-Saldino syndrome, see 614620.0003.
In 2 affected members of a family with short-rib thoracic dysplasia-9 without polydactyly (SRTD9; 266920), who had a clinical diagnosis of Mainzer-Saldino syndrome, Perrault et al. (2012) identified compound heterozygosity for 2 mutations in the IFT140 gene: a c.634G-A transition resulting in a gly212-to-arg (G212R) substitution, and a 1-bp duplication (c.3916dup; 614620.0006), resulting in a frameshift and premature termination (Ala1306GlyfsTer56). Neither mutation was found in 200 control chromosomes and both were predicted to be deleterious. In vitro functional expression studies in retinal pigment epithelial cells demonstrated that the G212R mutant protein had partial to complete loss of basal body localization and an increase of cytoplasmic staining. The patients had early-onset retinitis pigmentosa with poor visual acuity, chronic renal failure leading to end-stage renal disease, and cholestasis. The kidneys were hyperechogenic with loss of corticomedullary differentiation. Both also had skeletal anomalies, including short stature, craniosynostosis, and phalangeal cone-shaped epiphyses. Psychomotor development was normal at ages 4 and 10 years, respectively. Perrault et al. (2012) also identified compound heterozygosity for the G212R mutation and a splice site mutation in the IFT140 gene (614620.0002) in an 18-month-old boy with a clinical diagnosis of Jeune syndrome, who exhibited short thorax with short ribs and trident-shaped spurs on long bones.
In a 6.5-year-old British boy with short stature, short ribs and narrow thorax, retinal dystrophy, and end-stage renal failure, who also exhibited brachydactyly and ectodermal features and received a clinical diagnosis of Sensenbrenner syndrome (see 218330), Bayat et al. (2017) identified compound heterozygosity for the G212R mutation and a c.2278C-T transition in the IFT140 gene, resulting in an arg760-to-ter (R760X; 614620.0016) substitution. His unaffected parents were each heterozygous for 1 of the mutations.
In a 10-year-old boy with features of Mainzer-Saldino syndrome, who exhibited retinal dystrophy, acute-onset renal failure, and skeletal anomalies including bilateral coxa vara, broad femoral necks with mild bowing of the femoral diaphyses, and brachydactyly with shortened metacarpals and cone-shaped phalangeal epiphyses, Helm et al. (2017) identified homozygosity for the c.634G-A transition (c.634G-A, NM_014714.3) at the exon 6 donor splice site of the IFT140 gene, resulting in the G212R substitution at a conserved residue within the WD40 domain. His unaffected mother was heterozygous for the variant, but his father did not carry the mutation. Analysis of exome data indicated that the proband had chromosome 16 maternal heteroisodisomy, with segmental isodisomy at 16p13, suggesting that an early error in meiosis occurred in the maternal gamete. Helm et al. (2017) identified 2 different-sized PCR products from patient cells, the smaller of which was missing exon 6, resulting in frameshift and premature termination at residue 171. Functional analysis in ift140-morphant zebrafish demonstrated some improvement of gastrulation defects with the G212R mutant, but rescue was not as significant as that with wildtype IFT140, suggesting that G212R represents a partial loss-of-function variant.
For discussion of the 1-bp duplication at nucleotide 3916 (c.3916dup) in the IFT140 gene that was found in compound heterozygous state in a patient with short-rib thoracic dysplasia-9 (SRTD9; 266920) by Perrault et al. (2012), see 614620.0005.
For discussion of the cys1360-to-arg (C1360R) mutation in the IFT140 gene that was found in compound heterozygous state in a patient with short-rib thoracic dysplasia-9 without polydactyly (SRTD9; 266920) by Schmidts et al. (2013), see 614620.0002.
In 3 unrelated Serbian patients with short-rib thoracic dysplasia-9 without polydactyly (SRTD9; 266920), who had a clinical diagnosis of Jeune asphyxiating thoracic dystrophy, Schmidts et al. (2013) identified compound heterozygosity for a c.874C-T transition in the IFT140 gene, resulting in a val292-to-met (V292M) substitution at a conserved residue, and another mutation in IFT140. In 2 patients, the second mutation was a c.1565G-A transition, resulting in a gly522-to-glu (G522E; 614620.0009) substitution at a highly conserved residue. In the third patient, the second mutation was a 1-bp deletion (c.1380delC; 614620.0010), causing a frameshift predicted to result in a premature termination codon (Asn460LysfsTer28). The mutations segregated with disease in each family and were not found in 110 Serbian control chromosomes. Functional analysis in transfected RPE1 cells revealed impaired localization of mutant IFT40 to the centrosome. All 3 patients had a small thorax, brachymesophalangism, cone-shaped epiphyses, retinal dystrophy, and increased renal echogenicity with onset of end-stage renal disease by 7 years of age.
For discussion of the gly522-to-glu (G522E) mutation in the IFT140 gene that was found in compound heterozygous state in a patient with short-rib thoracic dysplasia-9 without polydactyly (SRTD9; 266920) by Schmidts et al. (2013), see 614620.0008.
For discussion of the 1-bp deletion (c.1380delC) in the IFT140 gene that was found in compound heterozygous state in a patient with short-rib thoracic dysplasia-9 without polydactyly (SRTD9; 266920) by Schmidts et al. (2013), see 614620.0008.
In a 43-year-old Han Chinese man (patient SRF71) with retinitis pigmentosa (RP80; 617781), Xu et al. (2015) identified compound heterozygosity for mutations in the IFT140 gene: a c.4196T-C transition (c.4196T-C, NM_014714.3), resulting in a leu1399-to-pro (L1399P) substitution at a highly conserved residue within the TPR9 domain, and a 4-bp deletion (c.1898_1901delATAA; 614620.0012), causing a frameshift predicted to result in a premature termination codon (Asn633SerfsTer10). His unaffected parents were each heterozygous for 1 of the mutations, and his unaffected sister did not carry either mutation. The 4-bp deletion was not found in the ExAC database, whereas the L1399P variant was present once, in the East Asian population (allele frequency, 1 in 5,762).
For discussion of the 4-bp deletion (c.1898_1901delATAA, NM_014714.3) in the IFT140 gene, causing a frameshift predicted to result in a premature termination codon (Asn633SerfsTer10), that was found in compound heterozygous state in a Han Chinese man with retinitis pigmentosa (RP80; 617781) by Xu et al. (2015), see 614620.0011.
In a 9-year-old Han Chinese boy (patient SRF117) who was noted to have retinal dystrophy in infancy (RP80; 617781), Xu et al. (2015) identified compound heterozygosity for mutations in the IFT140 gene: a c.1451C-T transition (c.1451C-T, NM_014714.3), resulting in a thr484-to-met (T484M) substitution, and a c.985T-C transition, resulting in a cys329-to-arg (C329R; 614620.0014) substitution at a highly conserved residue. (The c.1451C-T substitution was referred to as c.1452C-T in Figure 2.) His unaffected parents were each heterozygous for 1 of the mutations. The C329R mutation was not found in the ExAC database, whereas the T484M substitution was present at low frequency (allele frequency, 5 in 120,980 overall, and 2 in 8,640 in the East Asian population).
In 3 affected sibs and their affected first cousin once removed from a large consanguineous Pakistani family (family 1) with nonsyndromic RP, Hull et al. (2016) identified homozygosity for the T484M mutation (c.1451C-T, NM_014714.3) in the ITF140 gene, which segregated with disease in the family. Transient transfection in hTERT-RPE1 cells followed by immunostaining demonstrated significantly reduced basal body localization with the T484M mutant compared to wildtype.
For discussion of the c.985T-C transition (c.985T-C, NM_014714.3) in the IFT140 gene, resulting in a cys329-to-arg (C329R) substitution, that was found in compound heterozygous state in a Han Chinese boy with retinitis pigmentosa (RP80; 617781) by Xu et al. (2015), see 614620.0013.
For discussion of the c.2815T-C transition (c.2815T-C, NM_014714.3) in the IFT140 gene, resulting in a ser939-to-pro (S939P) substitution, that was found in compound heterozygous state in a Caucasian British brother and sister with retinitis pigmentosa (RP80; 617781) by Hull et al. (2016), see 614620.0002.
For discussion of the c.2278C-T transition in the IFT140 gene, resulting in an arg760-to-ter (R760X) substitution, that was found by Bayat et al. (2017) in compound heterozygous state in a 6.5-year-old British boy with short stature, short ribs and narrow thorax, retinal dystrophy, and end-stage renal failure, as well as brachydactyly and ectodermal features (SRTD9; 266920), see 614620.0005.
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Gross, M. B. Personal Communication. Baltimore, Md. 5/3/2012.
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Schmidts, M., Frank, V., Eisenberger, T., al Turki, S., Bizet, A. A., Antony, D., Rix, S., Decker, C., Bachmann, N., Bald, M., Vinke, T., Toenshoff, B., and 20 others. Combined NGS approaches identify mutations in the intraflagellar transport gene IFT140 in skeletal ciliopathies with early progressive kidney disease. Hum. Mutat. 34: 714-724, 2013. [PubMed: 23418020] [Full Text: https://doi.org/10.1002/humu.22294]
Xu, M., Yang, L., Wang, F., Li, H., Wang, X., Wang, W., Ge, Z., Wang, K., Zhao, L., Li, H., Li, Y., Sui, R., Chen, R. Mutations in human IFT140 cause non-syndromic retinal degeneration. Hum. Genet. 134: 1069-1078, 2015. [PubMed: 26216056] [Full Text: https://doi.org/10.1007/s00439-015-1586-x]