Alternative titles; symbols
HGNC Approved Gene Symbol: IFT172
Cytogenetic location: 2p23.3 Genomic coordinates (GRCh38) : 2:27,444,377-27,489,743 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 2p23.3 | Bardet-Biedl syndrome 20 | 619471 | Autosomal recessive | 3 |
| Retinitis pigmentosa 71 | 616394 | Autosomal recessive | 3 | |
| Short-rib thoracic dysplasia 10 with or without polydactyly | 615630 | Autosomal recessive | 3 |
IFT172 is essential for primary cilia formation and plays a vital role in cilia-mediated signaling (Gorivodsky et al., 2009). `
By sequencing clones obtained from a size-fractionated brain cDNA library, Hirosawa et al. (1999) cloned SLB, which they designated KIAA1179. The deduced protein contains 1,090 amino acids and shares significant homology with the kinesin light chain repeat (see 600025) sequence. RT-PCR analysis revealed highest expression of SLB in testis and lowest expression in spleen. All other tissues and brain regions tested showed low-to-moderate expression.
Howard and Maurer (2000) cloned Slb from a rat pituitary cell cDNA library. The 1,749-amino acid protein contains 7 N-terminal WD40 repeats and a nuclear localization signal. Highest expression was found in rat testis and pituitary cells.
Using RT-PCR, Gorivodsky et al. (2009) detected early-onset and widespread expression of Ift172 mRNA in postimplantation mouse embryos.
By radiation hybrid analysis, Hirosawa et al. (1999) mapped the SLB gene to chromosome 2.
Gross (2014) mapped the IFT172 gene to chromosome 2p23.3 based on an alignment of the IFT172 sequence (GenBank BC137126) with the genomic sequence (GRCh37).
Howard and Maurer (2000) determined that rat Slb specifically binds to Lhx3 (600577) and Lhx4 (602146) with high affinity both in vitro and in vivo. Expression of the LIM-interacting domain of Slb reduced the expression of an Lhx3-responsive reporter gene.
Short-Rib Thoracic Dysplasia with or without Polydactyly 10
In 14 patients from 12 families with short-rib thoracic dysplasia with or without polydactyly (SRTD10; 615630), Halbritter et al. (2013) identified homozygous or compound heterozygous mutations in the IFT172 gene (see, e.g., 607386.0001-607386.0012). Fibroblasts from affected individuals showed disturbed ciliary composition, suggesting alteration of ciliary transport and signaling, and knockdown of ift172 in zebrafish recapitulated the human phenotype.
Retinitis Pigmentosa 71
In an unrelated woman and man with retinitis pigmentosa-71 (RP71; 616394), Bujakowska et al. (2015) identified homozygosity and compound heterozygosity, respectively, for mutations in the IFT172 gene (607386.0015-607386.0017) that segregated with disease in both families. The mutations were not present in public variant databases.
Bardet-Biedl Syndrome 20
In 2 sisters with Bardet-Biedl syndrome (BBS20; 619471), Bujakowska et al. (2015) identified compound heterozygosity for a missense mutation (H1567Q; 607386.0013) and a splicing mutation (607386.0014) in the IFT172 gene. Their unaffected parents were each heterozygous for one of the mutations.
In 2 brothers with BBS20, born of consanguineous parents of Melanesian origin, Schaefer et al. (2016) identified homozygosity for a splicing mutation in the IFT172 gene (607386.0018) that segregated with disease in the family.
In a Japanese girl with BBS20, Hirano et al. (2020) identified compound heterozygosity for 2 missense mutations in the IFT172 gene (L493R, 607386.0019 and H719Y, 607386.0020). Her unaffected parents were each heterozygous for one of the variants.
Associations Pending Confirmation
For discussion of a possible association between orofaciodigital syndrome and variation in the IFT172 gene, see 607386.0021.
In a screen for embryonic patterning mutations induced by ethylnitrosourea, Huangfu et al. (2003) identified 2 mouse mutants, wimple (wim) and flexo (fxo), that lack ventral neural cell types and show other phenotypes characteristic of defects in Sonic hedgehog (600725) signaling. Both mutations disrupt intraflagellar transport proteins: the wim mutation is an allele of the previously uncharacterized mouse homolog of Ift172, and fxo is a hypomorphic allele of polaris, the mouse homolog of Ift88 (600595). Genetic analysis showed that wim, polaris, and the intraflagellar transport motor protein Kif3a (604683) are required for hedgehog signaling at a step downstream of the hedgehog receptor Patched-1 (see 601309). Wimple embryos have an open anterior neural tube and lack a groove on the ventral midline of the anterior neural tube. In 5 of 8 wim embryos, nodal expression was observed bilaterally; the other 3 showed wildtype expression. Huangfu et al. (2003) concluded that intraflagellar transport machinery has an essential and vertebrate-specific role in hedgehog signal transduction.
Gorivodsky et al. (2009) found that a loss-of-function mutation in mouse Slb resulted in embryos with severe craniofacial malformations, failure to close the cranial neural tube, holoprosencephaly, heart edema, and extensive hemorrhages, leading to lethality between embryonic days 12.5 and 13.0. Transmission electron microscopic analysis showed that cilia outgrowth in cells of the neuroepithelium was initiated, but the axonemes were severely truncated and did not contain visible microtubules. Morphologic analysis revealed that Slb mutant embryos displayed a global brain-patterning defect along the dorsal-ventral and anterior-posterior axes. Functional analysis revealed that Slb played a crucial role in forebrain growth and patterning and in maintenance of the isthmic organizer, a signaling center essential for anterior-posterior patterning of the mid- and hindbrain regions. In addition, Ift172 was required for proper function of the embryonic node, an early embryonic organizer, and for formation of the head organizing center.
Halbritter et al. (2013) performed zebrafish knockdown of ift172 with 2 morpholino oligonucleotides and observed a similar phenotype with both: the morphants displayed ventral body-axis curvature, formation of kidney cysts, otolith defects, and hydrocephalus, as well as cartilage defects of the craniofacial skeleton. Knockdown of ift172 in a rhodopsin-GFP transgenic zebrafish line demonstrated that the level of rhodopsin-GFP was lower in ift172 morphants than controls, suggesting retinal degeneration. Scanning electron microscopy of the olfactory placode revealed ciliogenesis defects in morphants, including shortened and truncated cilia.
Bujakowska et al. (2015) generated ift172 knockdown zebrafish morphants and observed ventral curvature of the body and hydrocephaly. Staining of semi-thin coronal sections taken at 5 days postfertilization confirmed the altered cranial structure, revealing a thinner outer nuclear layer and disorganized photoreceptor outer segments in the retina.
In 5 patients from 4 families with short-rib thoracic dysplasia (SRTD10; 615630) with or without polydactyly, Halbritter et al. (2013) identified compound heterozygosity for a c.5179T-C transition (c.5179T-C, NM_015662.1) in exon 48 of the IFT172 gene, resulting in a cys1727-to-arg (C1727R) substitution at a highly conserved residue, and another mutation in IFT172. In 2 European American brothers (patients A3037-21 and A3037-22) with a clinical diagnosis of Mainzer-Saldino syndrome, 1 of whom developed end-stage renal disease (ESRD) at 20 years of age and also exhibited retinal degeneration, liver fibrosis, and obesity as well as brachydactyly and phalangeal cone-shaped epiphyses, the second mutation was a 4-bp deletion (c.4925_4928delGAGA; 607386.0002) in exon 46, resulting in a frameshift and premature termination (Arg1642LysfsTer32). In a Belgian girl (patient B1), originally described by Casteels et al. (2000), who presented at age 5 years with vision loss and night blindness and was also found to have surgically corrected polydactyly and other features consistent with a clinical diagnosis of Jeune syndrome, the second mutation was a 2-bp duplication (c.1671_1672dupAG; 607386.0008) in exon 16, resulting in a frameshift and premature termination (Val558GlufsTer12). In a French woman (patient NPH2161) with brachydactyly, retinal degeneration, cholestasis, and nephronophthisis, who developed ESRD at 34 years of age, the second mutation was an in-frame 6-bp deletion (c.1390_1395delGATATT) in exon 14, resulting in deletion of asp464 and ile465 (607386.0009). In a British male patient (patient SKDP-44.3), who had neonatal respiratory distress, retinal dystrophy, delayed speech, mild ventriculomegaly, narrow thorax, marked rhizomelic shortening, brachydactyly, mild renal structural abnormalities, and obesity, the second mutation was a 1-bp deletion (c.2158delC; 607386.0011) in exon 21, causing a frameshift predicted to result in premature termination (Arg720ValfsTer28). All of the parents in these families were unaffected and were each heterozygous for 1 of the mutations; none of the mutations were found in controls except C1727R, which was present in 1 of 6,503 controls from the NHLBI Exome Variant Server.
For discussion of the 4-bp deletion in the IFT172 gene (c.4925_4928delGAGA, NM_015662.1) that was found in compound heterozygous state in patients with short-rib thoracic dysplasia (SRTD10; 615630) without polydactyly by Halbritter et al. (2013), see 607386.0001.
In a Filipino sister and brother (patients A2052-21 and A2052-22) with short-rib thoracic dysplasia (SRTD10; 615630) without polydactyly, Halbritter et al. (2013) identified homozygosity for a c.4630C-T transition (c.4630C-T, NM_015662.1) in exon 42 of the IFT172 gene, resulting in an arg1544-to-cys (R1544C) substitution at a highly conserved residue. The sibs exhibited features overlapping those of asphyxiating thoracic dystrophy, Mainzer-Saldino syndrome, and Joubert syndrome (see 213300), including small bell-shaped thorax, trident acetabulum, brachydactyly, phalangeal cone-shaped epiphyses, nephronophthisis resulting in end-stage renal disease requiring transplantation at 4 years of age, retinal dystrophy, oculomotor apraxia, liver fibrosis, mental retardation, and cerebellar vermis hypoplasia. In a female fetus (patient SKDP-165.3) of Singaporean and Malaysian origin with thoracic dysplasia, trident acetabulum, postaxial hexadactyly of all 4 limbs, short long bones, early cystic dysplasia of the kidneys, liver fibrosis, ventricular septal defect, cleft lip/palate, hypoplasia of the nasal bridge and nose, and hydrocephalus, Halbritter et al. (2013) identified compound heterozygosity for the R1544C mutation and a c.3907C-T transition in exon 35 of the IFT172 gene, resulting in an arg1303-to-ter (R1303X; 607386.0012) nonsense mutation.
In a South American male patient (A3215-21) and a German female patient (F108-21) with short-rib thoracic dysplasia (SRTD10; 615630) without polydactyly, Halbritter et al. (2013) identified compound heterozygosity for a c.4607T-C transition (c.4607T-C, NM_015662.1) in exon 42 of the IFT172 gene, resulting in a leu1536-to-pro (L1536P) substitution at a highly conserved residue, and another mutation in IFT172. The South American male patient, who was clinically diagnosed with asphyxiating thoracic dystrophy and had mental retardation, short stature, thoracic dystrophy, and nephronophthisis resulting in end-stage renal disease (ESRD) requiring transplantation at age 13 years, carried a c.2716C-T transition in exon 25 on the second allele, resulting in a gln906-to-ter (Q906X; 607386.0005) substitution. The German female patient, who was clinically diagnosed with Mainzer-Saldino syndrome and exhibited brachydactyly, phalangeal cone-shaped epiphyses, nephronophthisis resulting in ESRD at 11 years of age, retinal degeneration, liver fibrosis, impaired glucose tolerance, and obesity, carried a 5-prime splice site mutation (c.3228+1G-A; 607386.0006) in intron 29 on the second allele.
For discussion of the gln906-to-ter (Q906X) mutation (c.2716C-T, NM_015662.1) in the IFT172 gene that was found in compound heterozygous state in a patient with short-rib thoracic dysplasia (SRTD10; 615630) without polydactyly by Halbritter et al. (2013), see 607386.0004.
For discussion of the splice site mutation in the IFT172 gene (c.3228+1G-A, NM_015662.1) that was found in compound heterozygous state in a patient with short-rib thoracic dysplasia (SRTD10; 615630) without polydactyly by Halbritter et al. (2013), see 607386.0004.
In a Pakistani girl (patient A3189-21) with short-rib thoracic dysplasia without polydactyly (SRTD10; 615630) who died at 12 years of age, Halbritter et al. (2013) identified homozygosity for a c.886C-T transition (c.886C-T, NM_015662.1) in exon 9 of the IFT172 gene, resulting in an arg296-to-trp (R296W) substitution at a highly conserved residue. The patient exhibited clinical features consistent with Mainzer-Saldino syndrome, including short stature, nephronophthisis resulting in end-stage renal disease by 9 years of age, retinal degeneration, and mental retardation.
For discussion of the 2-bp duplication in the IFT172 gene (c.1671_1672dupAG, NM_015662.1) that was found in compound heterozygous state in a patient with short-rib thoracic dysplasia (SRTD10; 615630) with polydactyly by Halbritter et al. (2013), see 607386.0001.
For discussion of the 6-bp deletion in the IFT172 gene (c.1390_1395delGATATT, NM_015662.1) that was found in compound heterozygous state in a patient with short-rib thoracic dysplasia (SRTD10; 615630) without polydactyly by Halbritter et al. (2013), see 607386.0001.
In 2 unrelated male infants of Turkish origin (patients UCL-87 and UCL-107) with short-rib thoracic dysplasia (SRTD10; 615630), Halbritter et al. (2013) identified homozygosity for a c.1232T-A transversion (c.1232T-A, NM_015662.1) in exon 13 of the IFT172 gene, resulting in an ile411-to-asn (I411N) substitution at a highly conserved residue. Both patients exhibited a small bell-shaped thorax, trident acetabulum, and liver fibrosis, and 1 had polydactyly of the feet. Both died in infancy: one at 3 months of age due to respiratory failure and the other at 18 months of age due to liver failure. The unaffected parents of 1 of the patients were heterozygous for the mutation.
For discussion of the 1-bp deletion in the IFT172 gene (c.2158delC, NM_015662.1) that was found in compound heterozygous state in a patient with short-rib thoracic dysplasia (SRTD10; 615630) without polydactyly by Halbritter et al. (2013), see 607386.0001.
For discussion of the arg1303-to-ter (R1303X) mutation in the IFT172 gene that was found in compound heterozygous state in a fetus with short-rib thoracic dysplasia (SRTD10; 615630) with polydactyly by Halbritter et al. (2013), see 607386.0003.
In 2 sisters (family 1) with Bardet-Biedl syndrome-20 (BBS20; 619471), Bujakowska et al. (2015) identified compound heterozygosity for mutations in the IFT172 gene: a c.4701C-A transversion (c.4701C-A, NM_015662.1) in exon 43, resulting in a his1567-to-gln (H1567Q) substitution at a highly conserved residue located just outside an alpha-helix near the last tetratricopeptide (TPR) domain, and a c.1525-1G-A transition in intron 15 (607386.0014) involving the essential splice acceptor site of exon 16, predicted to abolish the splice site and result in exon skipping. The unaffected parents were each heterozygous for one of the mutations. The missense mutation was not found in the dbSNP or Exome Variant Server (EVS) databases, whereas the splice site mutation was present in 1 of 13,005 alleles in the EVS database. Functional analysis in mouse IMCD3 cells showed that the average length of cilia was significantly shorter in cells expressing the H1567Q mutant compared to wildtype. In addition, rescue of the ift172 morphant zebrafish phenotype occurred to a lesser extent with the H1567Q mutant (4.2% fewer morphants) than with wildtype (17.9% fewer morphants). Bujakowska et al. (2015) concluded that H1567Q represents a hypomorphic mutation.
For discussion of the splice site mutation in intron 15 of the IFT172 gene (c.1525-1G-A, NM_015662.1) that was found in compound heterozygous state in patients with Bardet-Biedl syndrome-20 (BBS20; 619471) by Bujakowska et al. (2015), see 607386.0013.
In a 33-year-old French woman (family 2) with retinitis pigmentosa-71 (RP71; 616394), Bujakowska et al. (2015) identified homozygosity for a c.4815T-G transversion (c.4815T-G, NM_015662.1) in exon 44 of the IFT172 gene, resulting in an asp1605-to-glu (D1605E) substitution at a highly conserved residue within an alpha-helix in the C-terminal domain. Her consanguineous parents were both heterozygous for the mutation, which was not found in the dbSNP or Exome Variant Server databases. Functional analysis in mouse IMCD3 cells showed that the average length of cilia was significantly shorter in cells expressing the D1605E mutant compared to wildtype. In addition, rescue of the ift172 morphant zebrafish phenotype occurred to a lesser extent with the D1605E mutant (6.7% fewer morphants) than with wildtype (17.9% fewer morphants). Bujakowska et al. (2015) concluded that D1605E represents a hypomorphic mutation.
In a 38-year-old Dutch man (family 3) with retinitis pigmentosa-71 (RP71; 616394), Bujakowska et al. (2015) identified compound heterozygosity for mutations in the IFT172 gene: a c.770T-C transition (c.770T-C, NM_015662.1) in exon 8, resulting in a leu257-to-pro (L257P) substitution at a residue conserved in mammals that was predicted to affect the sixth WD40 repeat, and a c.3112-5T-A transversion in intron 28 (607386.0017), predicted to result in insertion of 1 amino acid (Lys1037_Glu1038insGln), altering an alpha-helix in the eighth tetratricopeptide (TPR) domain. The patient's unaffected parents and brother were each heterozygous for 1 of the mutations, neither of which was found in genomic variant databases. In zebrafish ift172 knockdown experiments, coinjection of wildtype IFT172 reduced the total morphant count by 17.9%, whereas the L257P mutant was unable to rescue the morphant zebrafish phenotype. Functional analysis in mouse IMCD3 cells showed that, unlike wildtype IFT172, the L257P mutant failed to localize in cilia; immunofluorescence studies in rat retinas showed diffuse expression in the inner segment of photoreceptor cells with the L257P mutant, compared to the characteristic punctate staining in the photoreceptor cilia of wildtype IFT172. Bujakowska et al. (2015) concluded that L257P represents a null allele and that the N-terminal part of the IFT172 protein is involved in its localization to the cilia.
For discussion of the splice site mutation in intron 28 of the IFT172 gene (c.3112-5T-A, NM_015662.1) that was found in compound heterozygous state in a patient with retinitis pigmentosa-71 (RP71; 616394) by Bujakowska et al. (2015), see 607386.0016.
In 2 brothers with Bardet-Biedl syndrome-20 (BBS20; 619471), who were born of consanguineous parents of Melanesian origin, Schaefer et al. (2016) identified homozygosity for a splicing mutation (c.4428+3A-G, NM_015662.2) in intron 40 of the IFT172 gene. Sanger sequencing confirmed the mutation and its segregation with disease in the family; it was not found in an in-house database or in the dbSNP, 1000 Genomes Project, EVS, or ExAC databases. Analysis of patient mRNA showed that the mutation results in variable splicing, with an in-frame deletion of 39 amino acids (Tyr1439_Asn1477del), corresponding to exon 40, in the major alternative splicing isoform of IFT172.
In a Japanese girl (patient 2) with Bardet-Biedl syndrome-20 (BBS20; 619471), originally reported by Saida et al. (2014), Hirano et al. (2020) performed exome sequencing and identified compound heterozygosity for 2 missense mutations in the IFT172 gene, a c.1478T-G transversion (c.1478T-G, NM_015662), resulting in a leu493-to-arg (L493R) substitution, and a c.2155C-T transition, resulting in a his719-to-tyr (H719Y) substitution (607386.0020), both at highly conserved residues. The L493R mutation was not found in public variant databases, but the H719Y variant was present at a minor allele frequency of 0.000008 in the TOPMed database. Both mutations were confirmed by Sanger sequencing, and the patient's unaffected parents were each heterozygous for one of the mutations.
For discussion of the c.2155C-T transition (c.2155C-T, NM_015662) in the IFT172 gene, resulting in a his719-to-tyr (H719Y) substitution, that was found in compound heterozygous state in a Japanese girl with Bardet-Biedl syndrome (BBS20; 619471) by Hirano et al. (2020), see 607386.0019.
This variant is classified as a variant of unknown significance because its contribution to orofaciodigital syndrome (see 311200) has not been confirmed.
Yamada et al. (2019) reported a 3-year-old Japanese boy with postaxial polydactyly, brachymetaphalangy, short stature with delayed bone age, developmental delay, and congenital heart disease with laterality defects including single atrium, atrioventricular septal defect, and persistent left superior vena cava, who also had a bifid tongue, multiple hypertrophic oral frenula, and a missing left incisor. Trio whole-exome sequencing revealed compound heterozygous mutations in the IFT172 gene: a splice site mutation (c.39+5G-A, NM_015662.2) in intron 1, and a c.1478T-G transversion, resulting in a leu493-to-arg (L493R; 607386.0022) substitution at a highly conserved residue within the eighth WD40 repeat. His unaffected parents were each heterozygous for one of the mutations. The splicing mutation was observed in only 1 of 3,000 Japanese controls, and the missense mutation had never been detected in a Japanese cohort and was not found in the gnomAD database. RNA-seq of peripheral blood from the proband showed only the missense variant, indicating that the transcript derived from the splicing variant was subject to nonsense-mediated decay.
This variant is classified as a variant of unknown significance because its contribution to orofaciodigital syndrome (see 311200) has not been confirmed.
For discussion of the c.1478T-G transversion (c.1478T-G, NM_015662.2) in the IFT172 gene, resulting in a leu493-to-arg (L493R) substitution, that was found in compound heterozygous state in a 3-year-old Japanese boy with orofaciodigital syndrome by Yamada et al. (2019), see 607386.0001.
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