Identical IFT140 Variants Cause Variable Skeletal Ciliopathy Phenotypes-Challenges for the Accurate Diagnosis

Abstract

Ciliopathies are rare congenital disorders, caused by defects in the cilium, that cover a broad clinical spectrum. A subgroup of ciliopathies showing significant phenotypic overlap are known as skeletal ciliopathies and include Jeune asphyxiating thoracic dysplasia (JATD), Mainzer-Saldino syndrome (MZSDS), cranioectodermal dysplasia (CED), and short-rib polydactyly (SRP). Ciliopathies are heterogeneous disorders with >187 associated genes, of which some genes are described to cause more than one ciliopathy phenotype. Both the clinical and molecular overlap make accurate diagnosing of these disorders challenging. We describe two unrelated Polish patients presenting with a skeletal ciliopathy who share the same compound heterozygous variants in IFT140 (NM_014,714.4) r.2765_2768del; p.(Tyr923Leufs*28) and exon 27-30 duplication; p.(Tyr1152_Thr1394dup). Apart from overlapping clinical symptoms the patients also show phenotypic differences; patient 1 showed more resemblance to a Mainzer-Saldino syndrome (MZSDS) phenotype, while patient 2 was more similar to the phenotype of cranioectodermal dysplasia (CED). In addition, functional testing in patient-derived fibroblasts revealed a distinct cilium phenotyps for each patient, and strikingly, the cilium phenotype of CED-like patient 2 resembled that of known CED patients. Besides two variants in IFT140, in depth exome analysis of ciliopathy associated genes revealed a likely-pathogenic heterozygous variant in INTU for patient 2 that possibly affects the same IFT-A complex to which IFT140 belongs and thereby could add to the phenotype of patient 2. Taken together, by combining genetic data, functional test results, and clinical findings we were able to accurately diagnose patient 1 with "IFT140-related ciliopathy with MZSDS-like features" and patient 2 with "IFT140-related ciliopathy with CED-like features". This study emphasizes that identical variants in one ciliopathy associated gene can lead to a variable ciliopathy phenotype and that an in depth and integrated analysis of clinical, molecular and functional data is necessary to accurately diagnose ciliopathy patients.

Keywords: CED-like features; IFT140; MZSDS-like features; cilium phenotype; skeletal ciliopathy.

FIGURE 1

Phenotype and genotype of patients 1 and 2. Proximal limb shortening, narrow thorax, frontal bossing, high forehead, low set and simple ears is present in both patients (A,F,G,H). (A–E) Clinical features of patient 1: dolichocephalic head shape, full cheeks, micrognathia (A) obesity and hyperlordosis (B,C), brachydactyly and sandal gap (D,E). (F–J) Clinical features of patient 2: pectus excavatum (F), epicanthal folds and telecanthus, broad nasal bridge, everted lower lip (G), brachydactyly and sandal gap (I,J). (K) Sanger sequence of heterozygous variant r.2765_2768del in IFT140 (NM_014714.3: c.2767_2768+2del, p.(Tyr923Leufs*28)), representative for patient 1 and 2. (L) Schematic representation of the splicing effect caused by IFT140 r.2765_2768del. The coloured lines indicate the splicing between exons, in green the wildtype splicing between exon 21 and 22 and in red the aberrant splicing seen in patients 1 and 2. (M) Schematic overview of the heterozygous exon 27–30 duplication (p. (Tyr1152_Thr1394dup)) detected in patients 1 and 2. Orange bars indicate an increase in coverage and blue bars indicate a decrease in coverage.

FIGURE 2

Ciliopathy cilium phenotype clusters. The cilium phenotype clusters are based on two cilium parameters; cilium length (Y-axis) and IFT88 measurement (X-axis) published in Doornbos et al. (Doornbos et al., 2021). The confidence intervals (CI) of 0.5 and 0.9 are indicated per identifiable group, i.e. the control, ATD, and CED cohorts. The cilium phenotype of patient 1 showed a normal cilium length (3.71 ± 0.07 µm) and an increased IFT88 measurement (0.99 ± 0.08µm²), therefore it does not fit in any cluster. Patient 2 showed a decreased cilium length (3.04 ± 0.15 µm) and an increased IFT88 measurement (0.79 ± 0.08µm²), therefore it is positioned on the border of the CED cluster.