In a 3-year-old Indian girl with a short, narrow thorax and postaxial polydactyly (SRTD16; 617102), Girisha et al. (2016) identified homozygosity for a c.424C-T transition (c.424C-T, NM_016004.3) in exon 6 of the IFT52 gene, resulting in an arg142-to-ter (R142X) substitution. The proband's unaffected consanguineous parents were heterozygous for the mutation, which was not found in homozygosity in a local exome database or the 1000 Genomes Project, Exome Variant Server, ExAC, or CentoMD databases.

By RT-PCR in patient fibroblasts and in those of an age-matched control, Dupont et al. (2019) demonstrated that the c.424C-T mutation results in partial skipping of exon 6. Western blot confirmed the expression of a shorter protein corresponding to loss of 24 amino acids. The authors noted that the shorter protein was expressed to a much lower degree than wildtype, whereas the expected truncated protein resulting from R142X was not detected by Western blot. The authors concluded that the c.424C-T mutation results in a partially functioning protein rather than a total loss of IFT52 function. In Ift52 -/- IMCD3 cells, in which primary cilia were absent, expression of the IFT52 mutant lacking exon 6 restored primary cilia but to less-than-normal percentages, and there was a higher proportion of very short cilia compared to wildtype rescue. In addition, coimmunoprecipitation assays showed total abrogation of the interaction between the mutant protein and IFT52 direct partners IFT38 and IFT57 (606621).

In a fetus from a nonconsanguineous family (R98-277) with features of short-rib thoracic dysplasia without polydactyly (SRTD16; 617102), Zhang et al. (2016) identified compound heterozygosity for mutations in the IFT52 gene: a 1-bp deletion (c.878delT) in exon 10, causing a frameshift predicted to result in a premature stop codon (Leu293AlafsTer21); and a c.595G-A transition, resulting in an ala199-to-thr (A199T) substitution at a highly conserved residue. The unaffected parents were each heterozygous for 1 of the mutations, neither of which was found in public variant databases. RT-PCR of patient fibroblasts revealed significantly reduced levels of IFT52 compared to controls, and analysis of the products showed only sequences derived from the missense allele, suggesting degradation through nonsense-mediated decay of the transcript containing the frameshift variant. In addition, Western blot analysis demonstrated significant reduction of IFT52 protein in both fibroblasts and chondrocytes. Zhang et al. (2016) also observed significantly fewer ciliated patient fibroblasts compared to controls, and the average length of cilia was shorter than that in controls; patient cells also exhibited loss of length regulation, with an increased number of both highly shortened and elongated cilia relative to control cells.

For discussion of the c.595G-A transition in the IFT52 gene, resulting in an ala199-to-thr (A199T) substitution, that was found in compound heterozygous state in a fetus with short-rib thoracic dysplasia-16 (SRTD16; 617102) by Zhang et al. (2016), see 617094.0002.

In an 11-year-old girl with features of both retinal and skeletal ciliopathy, exhibiting early-onset retinal dystrophy as well as narrow chest, short ribs, and micromelic limbs (SRTD16; 617102), who was negative for mutation in known retinal degeneration-associated genes, Chen et al. (2018) identified homozygosity for a c.556A-G transition (c.556A-G, NM_016004) in exon 7 of the IFT52 gene, resulting in a thr186-to-ala (T186A) substitution at a highly conserved residue within the GIFT domain. Her unaffected first-cousin parents, maternal grandfather, and paternal grandmother were heterozygous for the mutation, which was not found in her 2 unaffected sibs, 100 unrelated controls, the YanHuang database, or other public variant databases, including ExAC and gnomAD. Immunofluorescence and immunoblot analysis of transfected hTERT-RPE1 cells showed reduced IFT52 expression in mutant cells compared to wildtype. In addition, average ciliary length was markedly reduced in cells overexpressing the T186A mutant compared to wildtype. Reduction in ciliary length was comparable between cells transfected with IFT52 siRNA and those transfected with the T186A mutant, consistent with a loss-of-function mechanism.

In 2 fetuses from a family (F1) exhibiting short-rib thoracic dysplasia (SRTD16; 617102) with polydactyly, Dupont et al. (2019) identified compound heterozygosity for a maternally inherited c.293A-G transition (c.293A-G, NM_016004.2) in exon 4 of the IF52 gene, resulting in an asn98-to-ser (N98S) substitution at a highly conserved residue within the GIFT domain, and a paternally inherited 5-bp deletion/2-bp insertion (c.695_699delinsCA) in exon 8, resulting in an in-frame mutation (Ile232Met233delinsThr). One of the fetuses also had tortuous ureters and left pelviectasis. Functional analysis demonstrated that the N98S mutant did not significantly rescue the ciliopathy phenotypes of body curvature and pronephric cysts in ift52 -/- zebrafish embryos, in contrast to wildtype IFT52; and in Ift52 -/- IMCD3 cells lacking primary cilia, expression of the N98S mutant restored primary cilia to near-normal percentages, but there was a higher proportion of short cilia compared to wildtype rescue. Mass spectrometry analysis showed that significant interactions with proteins of the IFT-B complex were reduced by approximately one-half with the N98S mutant compared to wildtype IFT52, and coimmunoprecipitation assays revealed reduced interaction between the mutant protein and IFT52 direct partners IFT38 and IFT57 (606621) compared to wildtype. In addition, N98S did not rescue the centriole splitting observed in Ift52 -/- cells.

For discussion of the 5-bp deletion/2-bp insertion (c.695_699delinsCA, NM_016004.2) in exon 8 of the IFT52 gene, resulting in an in-frame mutation (Ile232Met233delinsThr), that was found in compound heterozygous state in 2 fetuses from a family (F1) with short-rib thoracic dysplasia-16 (SRTD16; 617102) with polydactyly by Dupont et al. (2019), see 617094.0005.

This variant is classified as a variant of unknown significance because its contribution to congenital anomalies of the kidney and urinary tract (CAKUT; see 610805) has not been confirmed.

Dupont et al. (2019) performed whole-exome sequencing in 48 patients from 26 families with CAKUT and identified a fetus from a consanguineous North African family (F2) that was homozygous for a c.775G-C transversion (c.775G-C, NM_016004.2) in the IFT52 gene, resulting in an asp259-to-his (D259H) substitution at a conserved residue. The mutation was present at a minor allele frequency of 0.0004081 in the gnomAD database, including 1 individual who was homozygous for D259H. The affected fetus had bilateral isolated multicystic renal dysplasia, with kidneys that were enlarged to 3 to 4 times the expected size in age-matched controls, showing voluminous cysts distributed in a disorderly way and without differentiated nephron structure. No skeletal defect was reported in the fetus. Two neonatal deaths of unknown cause also occurred in this family. Functional analysis demonstrated that the D259H mutant did not significantly rescue the ciliopathy phenotypes of body curvature and pronephric cysts in ift52 -/- zebrafish embryos, in contrast to wildtype IFT52; and in Ift52 -/- IMCD3 cells lacking primary cilia, expression of the D359H mutant restored primary cilia to near-normal percentages, but there was a higher proportion of short cilia compared to wildtype rescue. Mass spectrometry analysis showed that interactions with subunits of the IFT-B complex appeared to be slightly affected by the D259H mutation, including loss of IFT46 binding, and coimmunoprecipitation assays revealed reduced interaction between the mutant protein and IFT52 direct partners IFT38 and IFT57 (606621) compared to wildtype. In addition, D259H did not rescue the centriole splitting observed in Ift52 -/- cells. Noting that the effects of this mutation appeared to be less severe than the SRTD-associated N98S mutation (617094.0005), the authors suggested that this variant may participate in the development of multicystic dysplastic kidneys by interaction with other variants in other genes.