Exome sequencing and <scp>RNA</scp> analysis identify two novel <scp><i>CPLANE1</i></scp> variants causing Joubert syndrome

Fei, Hongjun; Wu, YingXing; Wang, Yanlin; Zhang, Junyu

doi:10.1002/mgg3.1877

Cited by 7 publications

(2 citation statements)

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“…As analyzed by prediction software, the CPLANE 1 protein contains 2 coiled-coil domains and may be a transmembrane protein. However, most of the known CPLANE1 variants reported prior to 2015 are distributed outside the coiled-coil and transmembrane domains ( Fei et al, 2022 ). The Nordic JS cohort study ( Romani et al, 2015 ) showed that the proportion of CPLANE1 variants is 12% and that CPLANE1 variants are more likely to cause simplex JS, with the CPLANE1 gene having an 8.9% mutation rate in simplex JS ( Fleming et al, 2017 ).…”

Section: Discussionmentioning

confidence: 99%

Exome sequencing confirms the clinical diagnosis of both joubert syndrome and klinefelter syndrome with keratoconus in a han Chinese family

Fang,

Ma,

Rong

et al. 2024

Front. Genet.

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IntroductionJoubert syndrome a rare genetic disorder, is characterized by abnormalities in the development of the central nervous system with “molar signs” on magnetic resonance imaging of the brain and accompanied by cerebellar vermis hypoplasia, ataxia, hypotonia, and developmental delay. Keratoconus (KC) is a kind of genetically predisposed eye disease that causes blindness characterized by a dilated thinning of the central or paracentral cornea conically projected forward, highly irregular astigmatism, and severe visual impairment. Klinefelter syndrome is caused by an extra X chromosome in the cells of male patients, and the main phenotype is tall stature and dysplasia with secondary sex characteristics. This study was intended to identify the genetic etiology and determine the clinical diagnosis of one Han Chinese family with specific clinical manifestations of keratoconus and multiorgan involvement.MethodsA comprehensive ocular and related general examination was performed on one patient and his asymptomatic parents and brother. Pathogenic genes were tested by exome sequencing. CNV-seq was used to verify the copy number variation, and peripheral blood was cultured for karyotype analysis. The pathogenicity of the identified variant was determined subject to ACMG guidelines. The Gene Expression Omnibus (GEO) dataset of keratoconus-related genes in the NCBI database was obtained to analyze the differentially expressed genes in corneal tissues of the keratoconus group and the normal control group, and analysis of protein-protein interaction networks (PPI) was performed.ResultsProband, a 25-year-old male, had sudden loss of vision in the left eye for 1 week. Best corrected visual acuity (BCVA): 0.5 (−1.00DS/-5.00DC*29°) in the right eye, counting fingers/40 cm in the left eye. Slit-lamp microscopy of the right eye showed mild anterior protrusion of the cornea and thinning of the cone-topped cornea. The left eye showed marked thinning of the central region of the cornea, rounded edema in the form of a cone-like bulge, epithelial bullae, edema and turbidity of the stroma, and bulging of the Descemet’s membrane. Cranial magnetic resonance imaging (MRI) revealed changes in the midbrain and cerebellum, with a “molar sign” and a “bat-winged” ventriculus quartus cerebri. General check-up: 168 cm in height, decreased muscle tone in all four limbs, knee jerk elicited, negative Babinski sign, abdominal reflexes elicited, finger-to-nose test positive, intentional tremor evident in both hands, positive Romberg’s sign, instability of gait, level I intellectual disability, poor adaptive behavior, communication disorders, teeth all dentures, a peculiar face with blepharophimosis, wide inner canthus distance, mild ptosis, severe positive epicanthus, high palatal arches, exotropia, hypotrichosis of beard and face, inconspicuous prominentia laryngea, and short upper and lower limbs. Exome sequencing detected compound heterozygous frameshift variants M1:c.9279dup:p.His3094Thrfs*18 and M2:c.6515_6522del:p.Lys2172Thrfs*37 in the patient’s CPLANE1 gene and the presence of duplication-type CNV on the X chromosome. Sanger sequencing showed that the mother and father carried the M1 and M2 variants, respectively, and the younger brother carried the M2 variant, which was a novel variant. CNV-seq analysis showed the presence of a duplication-type CNV Xp22.33-Xq28 (2757837-156030895) of approximately 155 Mb on the X chromosome of the proband, which was a de novo variant and carried by neither of the parents. The two heterozygous frameshift variants and duplication-type CNV were pathogenic according to the ACMG guidelines. Differential expression analysis of keratoconus-related genes showed that CPLANE1 was upregulated in the corneal tissues of keratoconus patients compared with normal controls, and such a difference was statistically significant (p = 0.000515, <0.05). PPI analysis showed that the CPLANE1-NPHP3 complex protein acted as a bridge between cilia and extracellular matrix tissue. According to the genetic test results and clinical phenotype analysis, the family was finally diagnosed with Joubert syndrome combined with Keratoconus and Klinefelter syndrome.DiscussionIn this study, we report a proband in a Han Chinese family with both Joubert syndrome and X-linked Klinefelter syndrome as well as keratoconus, and the phenotype spectrum of CPLANE1-Joubert syndrome may be expanded accordingly. Meanwhile, the significance of exome sequencing was emphasized in aiding the clinical diagnosis of complex cases, which is difficult to make.

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Section: Discussionmentioning

confidence: 99%

Exome sequencing confirms the clinical diagnosis of both joubert syndrome and klinefelter syndrome with keratoconus in a han Chinese family

Fang,

Ma,

Rong

et al. 2024

Front. Genet.

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“…The genomic DNA extraction and phenotype‐driven whole exome sequencing (WES) were performed as previously described (Fei et al., 2022). Genomic DNA was isolated from peripheral blood lymphocytes of the proband (II2).…”

Section: Methodsmentioning

confidence: 99%

Aberrant splicing caused by a novel KMT2A variant in Wiedemann–Steiner syndrome

Niu,

Teng,

Zhang

2024

Molec Gen & Gen Med

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IntroductionWiedemann–Steiner syndrome (WSS) is a rare autosomal‐dominant disorder caused by KMT2A variants. The aim of this study was to characterize a novel KMT2A variant in a child with WSS and demonstrate integrated diagnostic approaches.MethodsA 3‐year‐old female with developmental delay, distinctive facial features, and anal fistula underwent whole exome sequencing (WES). RNA analysis was performed to assess splicing effects caused by a novel variant.ResultsWES identified novel heterozygous KMT2A c.5664+6T>C variant initially classified as a variant of uncertain significance. RNA analysis provided evidence of aberrant splicing (exon 20 skipping), allowing reclassification to likely pathogenic. The patient exhibited typical WSS features along with a potential novel finding of anal fistula.ConclusionThis report describes a novel non‐canonical splice site variant in KMT2A associated with WSS. RNA analysis was critical for variant reclassification. Detailed phenotypic evaluation revealed common and expanded WSS manifestations. This case highlights the importance of combining clinical assessment, DNA testing, and RNA functional assays for the diagnosis of rare genetic disorders.

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Exome sequencing and RNA analysis identify two novel CPLANE1 variants causing Joubert syndrome

Fei

Wang

et al. 2022

Molec Gen & Gen Med

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Background: Joubert syndrome (JS) is a genetically heterogeneous disorder; its genetic etiology involves more than 35 genes, and a limited number of studies have investigated the pathogenic mechanism of variants in patients with JS. RNA splicing analysis is critical to determine the functional significance for noncanonical splicing variants.Methods: Whole exome sequencing was performed to screen the causative gene variants in a JS family. Sanger sequencing was used to verify the variants. cDNA PCR products were analyzed and functional experiments were performed to determine the pathogenicity of the variants. Results:The clinical phenotypes and CPLANE1 variants in the JS patient were analyzed and proved consistent. We identified two novel heterozygous variants of CPLANE1 in the proband first, including c.4459del (frameshift variant) and c.7534-14G > A (intronic variant). We analyzed the pathogenic consequences of the 2 variants and classified the c.4459del as likely pathogenic according to the ACMG/AMP guidelines; however, the pathogenic significance of c.7534-14G > A was uncertain. Furthermore, we performed RNA splicing analysis and revealed that the noncanonical splicing variant (c.7534-14G > A) caused aberrant exon 37 skipping. It produced an aberrant transcript that was predicted to encode a C-terminal truncated protein. Conclusions:The genetic variation spectrum of JS caused by CPLANE1 was updated. Two novel variants further deepened our insight into the disease's molecular mechanism and confirmed the significance of diagnostic whole-exome sequencing.

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Exome sequencing and RNA analysis identify two novel CPLANE1 variants causing Joubert syndrome

Cited by 7 publications

References 31 publications

Exome sequencing confirms the clinical diagnosis of both joubert syndrome and klinefelter syndrome with keratoconus in a han Chinese family

Exome sequencing confirms the clinical diagnosis of both joubert syndrome and klinefelter syndrome with keratoconus in a han Chinese family

Aberrant splicing caused by a novel KMT2A variant in Wiedemann–Steiner syndrome

Exome sequencing and RNA analysis identify two novel CPLANE1 variants causing Joubert syndrome

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