Table of Contents  

Ben-Salem, Aljneibe, Khozaimy, Al-Kathiri, Alameri, Ali, and Al-Gazali: A novel splice site deletion in the OFD1 gene is responsible for oral–facial–digital syndrome type 1 in an Emirati child

Introduction

Oral–facial–digital syndrome type 1 [OFD1 (MIM 311200)] is a developmental condition belonging to the heterogeneous group of oral–facial–digital syndromes (OFDSs).1,2 It occurs in 1 out of 50 000 live births worldwide, with 75% of the cases being apparently sporadic.3 This condition is characterized by malformations of the face, oral cavity and digits. Facial anomalies include frontal bossing, hypertelorism, prominent root of the nose with a large funnel, pseudo-cleft in the upper lip and variable degrees of alopecia. Malformation of the oral cavity include short, thick frenulae, a cleft or high-arched palate, supernumerary or malpositioned teeth and a multilobulated tongue. Digital anomalies include brachydactyly, syndactyly, clinodactyly, camptodactyly, polydactyly and hypoplastic thumbs. There is usually a high degree of phenotypic variability in this syndrome.1,2 It has been shown that the central nervous system is affected in 50% of the cases.4,5 Most of the clinical features overlap with other OFDSs; however, the X-linked dominant pattern of inheritance and the polycystic kidney disease are typical of OFD1 and differentiate it from the other types of OFDS.1,2,6 Renal impairment can be present at birth or develop later on, often leading to renal failure that requires dialysis and/or renal transplantation in late childhood or adulthood.7,8 This syndrome is caused by a heterozygous mutation in the OFD1 gene, mapped to cryptogenic band Xp22.2–22.3 on the X chromosome.9,10 This gene encodes a 1011-amino acid protein that localizes to the centrosome and basal body of cilia required for primary cilia formation and left–right symmetry.1113 The OFD1 protein has five predicted coiled-coil domains, which are important for protein interaction, and a lissencephaly homology (LisH) domain possibly involved in microtubule regulation and cell migration.14,15 This protein showed widespread expression in different tissues, including those of the pancreas, kidney, skeletal muscle, liver, lung, placenta, brain and heart.14 This protein has a crucial role in human development and causes prenatal lethality in males.1 To date, the spectrum of mutations of the OFD1 gene extends to the phenotypic spectrum to include macrocephaly, intellectual disability, and ciliary dyskinaesia in patients with type 2 Simpson–Golabi–Behmel syndrome and Joubert syndrome.1618

Patient and methods

We ascertained an Emirati female patient with features of OFD1. Blood samples were collected in ethylenediaminetetraacetic acid tubes after obtaining informed written consent from the parents. Genomic DNA was extracted using the Flexigene DNA extraction kit (Qiagen Gmbh, Hilden, Germany) following the manufacturer’s instructions. Primers were designed using Primer3 software version 0.4.0 (Howard Hughes Medical Institute, Chevy Chase, MD, USA) (http://frodo.wi.mit.edu/) covering the coding and splice site regions of the OFD1 gene. All coding exons were amplified by polymerase chain reaction and subsequently sequenced using the BigDye Terminator kit v3.1 (Applied Biosystems, Carlsbad, CA, USA) on a 3130xl Genetic Analyzer system (Applied Biosystems). DNA chromatograms were inspected and analysed based on the complementary DNA sequence in accordance with the GenBank entries NM_003611.2 using the Sequencing Analysis® version 5.3 software (Applied Biosystems) and ClustalW2 (European Molecular Biology Laboratory–European Bioinformatics Institute, Hinxton, UK) (www.ebi.ac.uk/Tools/msa/clustalw2/). To evaluate the influence of the c.2757+1delG mutation on splicing signals, in silico prediction was carried out using the scan program (The University of Western Ontario, London, ON, Canada) (https://splice.uwo.ca/)19,20 along with the Human Splicing Finder software version 2.4.1 (Ensembl, Hinxton, UK) (www.umd.be/HSF/).21 The prediction was performed based on reference sequence ENST00000340096.

Results

Clinical data

The parents were not related but were from the same tribe of United Arab Emirates (UAE) origin. In the family history the mother had a sister with an intellectual disability. The parents had two children, the first of whom was a healthy female and the second of whom is the case presented here. The pregnancy of this second child was complicated by bleeding in the first 3 months of gestation. The delivery was normal and birth weight was 2.395 kg. She was assessed in the Genetic Clinic (Tawam Hospital, Al Ain) at 8 months of age. Examination revealed a weight of 7.620 kg (< 50th centile), a length 67.20 cm (< 10th centile) and a head circumference of 42.60 cm (10th centile). There were several dysmorphic features, including widely spaced eyes, a tented and thin upper lip, a bifid and lobulated tongue, a midline cleft palate, short, thick frenulae and a serrated gingival margin. Both hands were small but there were no digital anomalies. The child was hypotonic with some degree of head lag. Detailed ophthalmological examination was normal. Ultrasound of the kidneys was normal. Magnetic resonance imaging (MRI) of the brain showed agenesis of the corpus callosum and hypoplastic vermis.

Mutation analyses

Sanger DNA sequencing revealed a novel heterozygous single-nucleotide deletion, c.2757+1delG, affecting the splice donor site of exon 20, as illustrated in Figure 1. Prediction analyses using bioinformatics tools showed that this deletion affects the authentic splice site leading to the creation of a cryptic splice site at position c.2756 (Figure 2). The erroneous splicing will lead to frameshift and subsequently creation of a premature termination codon at amino acid position 922 of the protein (p.Lys920ArgfsX2).

FIGURE 1

Pedigree and molecular analysis of the OFD1 mutation. One sporadic case of an Emirati female with OFD1. DNA sequencing chromatograms revealed a de novo heterozygous mutation (c.2757+1delG) affecting the donor splice site of exon 20.

8-1-8-fig1.jpg
FIGURE 2

Prediction analyses of the c.2757+1delG mutation. Wild-type sequence shows the authentic splice site of exon 20 and the mutant sequence illustrates the deletion of the first nucleotide [G (guanine)] in intron 20. The table summarizes the potential splice sites in the mutant sequence.

8-1-8-fig2.jpg

Discussion

In this study, we reported a case of OFD1 in an Emirati family. DNA chromatograms showed that both parents harbour the wild-type sequence whereas the child is heterozygous for the c.2757+1delG mutation (Figure 1). This finding suggests that the deletion is a de novo mutation in this child, but it cannot exclude the possibility of mosaicism in the mother, which might occur in OFD1, especially with the history of intellectual disability in this family.22 Based on a splice prediction program, this mutation will abolish the authentic donor splice site of exon 20 resulting in a frameshift and premature termination codon (p.Lys920ArgfsX2). The truncated transcripts will lack the fifth coiled-coil domain and most probably will be subject to nonsense-mediated RNA decay (NMD), as the mutation is located more than 55 nucleotides before the last exon–exon boundary. Relative quantitative expression of OFD1 messenger RNA (mRNA) levels in two different families with Joubert syndrome (JBTS10) showed that only 30–58% of OFD1 expression remained, which suggests that truncated mRNAs are targeted by the NMD pathway.17 Most of the identified mutations in the OFD1 gene led to loss of function due to premature truncation of the protein.10,12,2326 Moreover, Tsurusaki and his colleagues27 speculated that mutations downstream of exon 17 leading to a longer, truncated transcript might result in a milder form of OFD1.

Genotype–phenotype correlation studies showed a significant association between high-arched/cleft palate and missense and splice site mutations in the studied cases.2,10,2426 In addition, cystic kidneys are reported to be prevalent in patients with mutations in exons 9 and 12, particularly splice site mutations. Intellectual disability was more predominantly associated with mutations in exons 3, 8, 9, 13 and 16, while tooth abnormalities are more frequently associated with mutations in the coiled-coil domains.2,2426 The female child in this study showed dysmorphic features and brain abnormalities with no digital anomalies or renal impairments at this age. MRI of her brain showed agenesis of the corpus callosum and hypoplastic vermis, which have been shown to be the most common anomalies of the brain in patients with OFD1.26

Oral–facial–digital syndrome type 1 is known as ciliopathy because the protein is expressed at the base of cilia and is essential for their normal formation.6,1113 The cilia are involved in cell movement and different chemical pathways required for normal development and function of different part of the body.12,13 Diseases caused by defects in primary cilia displayed a broad spectrum of clinical features, including polydactyly, craniofacial abnormalities, structural brain malformations, situs inversus, obesity, diabetes and polycystic kidney disease, as shown in cases of Bardet–Biedl syndrome and Joubert syndrome.28 Primary cilia play a crucial role in the regulation of various signalling pathways such as sonic hedgehog, Wnt [wingless-type MMTV (mouse mammary tumour virus)] and platelet-derived growth factor, which are involved in vital functions in development and homeostasis.29 Therefore, disruptions of these pathways will affect the normal process of cell proliferation, fate determination and migration and central nervous system patterning.3034

In conclusion, we report a causative heterozygous splice site mutation affecting exon 20 in the OFD1 gene underlying the clinical features of OFD1 in a female child from the UAE. The child had the typical facial and oral manifestations of the syndrome but lacked the digital anomalies. This finding extends the spectrum of OFD1 mutations and highlights the major role of this gene during human development. The discovery of disease-causing mutations is important for adopting effective prevention and therapeutic approaches that might minimize the burden of genetic conditions in the UAE population.35

Acknowledgement

We are indebted to the patients and their family members for their participation in this research study. We would like to thank Ms Sania Al Hamad for collecting blood samples. We would like to express our gratitude to the Sheikh Hamdan Bin Rashid Al Maktoum Award for Medical Sciences for their financial support.

References

1. 

Toriello HV. Oral–facial–digital syndromes, 1992. Clin Dysmorphol 1993; 2:95–105. http://dx.doi.org/10.1097/00019605-199304000-00001

2. 

Gurrieri F, Franco B, Toriello H, Neri G. Oral–facial–digital syndromes: review and diagnostic guidelines. Am J Med Genet A 2007; 143A:3314–23. http://dx.doi.org/10.1002/ajmg.a.32032

3. 

Wahrman J, Berant M, Jacobs J, Aviad I, Ben-Hur N. The oral–facial–digital syndrome: a male-lethal condition in a boy with 47/xxy chromosomes. Pediatrics 1966; 37:812–21.

4. 

Connacher AA, Forsyth CC, Stewart WK. Orofaciodigital syndrome type I associated with polycystic kidneys and agenesis of the corpus callosum. J Med Genet 1987; 24:116–18. http://dx.doi.org/10.1136/jmg.24.2.116

5. 

Gorlin RJ, Psaume J. Orodigitofacial dysostosis – a new syndrome. A study of 22 cases. J Pediatr 1962; 61:520–30. http://dx.doi.org/10.1016/S0022-3476(62)80143-7

6. 

Toriello HV, Parisi MA. Cilia and the ciliopathies: an introduction. Am J Med Genet C Semin Med Genet 2009; 151C:261–2. http://dx.doi.org/10.1002/ajmg.c.30230

7. 

Odent S, Le Marec B, Toutain A, et al. Central nervous system malformations and early end-stage renal disease in oro-facio-digital syndrome type I: a review. Am J Med Genet 1998; 75:389–94. http://dx.doi.org/10.1002/(SICI)1096-8628(19980203)75:4<389::AID-AJMG8>3.0.CO;2-L

8. 

Stapleton FB, Bernstein J, Koh G, Roy S, Wilroy RS. Cystic kidneys in a patient with oral–facial–digital syndrome type I. Am J Kidney Dis 1982; 1:288–93. http://dx.doi.org/10.1016/S0272-6386(82)80027-9

9. 

Feather SA, Woolf AS, Donnai D, Malcolm S, Winter RM. The oral–facial–digital syndrome type 1 (OFD1), a cause of polycystic kidney disease and associated malformations, maps to Xp22.2–Xp22.3. Hum Mol Genet 1997; 6:1163–7. http://dx.doi.org/10.1093/hmg/6.7.1163

10. 

Ferrante MI, Giorgio G, Feather SA, et al. Identification of the gene for oral–facial–digital type I syndrome. Am J Hum Genet 2001; 68:569–76. http://dx.doi.org/10.1086/318802

11. 

Ferrante MI, Zullo A, Barra A, et al. Oral–facial–digital type I protein is required for primary cilia formation and left–right axis specification. Nat Genet 2006; 38:112–17. http://dx.doi.org/10.1038/ng1684

12. 

Romio L, Wright V, Price K, et al. OFD1, the gene mutated in oral–facial–digital syndrome type 1, is expressed in the metanephros and in human embryonic renal mesenchymal cells. J Am Soc Nephrol 2003; 14:680–9. http://dx.doi.org/10.1097/01.ASN.0000054497.48394.D2

13. 

Romio L, Fry AM, Winyard PJ, Malcolm S, Woolf AS, Feather SA. OFD1 is a centrosomal/basal body protein expressed during mesenchymal-epithelial transition in human nephrogenesis. J Am Soc Nephrol 2004; 15:2556–68. http://dx.doi.org/10.1097/01.ASN.0000140220.46477.5C

14. 

de Conciliis L, Marchitiello A, Wapenaar MC, et al. Characterization of Cxorf5 (71-7A), a novel human cDNA mapping to Xp22 and encoding a protein containing coiled-coil alpha-helical domains. Genomics 1998; 51:243–50. http://dx.doi.org/10.1006/geno.1998.5348

15. 

Emes RD, Ponting CP. A new sequence motif linking lissencephaly, Treacher Collins and oral–facial–digital type 1 syndromes, microtubule dynamics and cell migration. Hum Mol Genet 2001; 10:2813–20. http://dx.doi.org/10.1093/hmg/10.24.2813

16. 

Budny B, Chen W, Omran H, et al. A novel X-linked recessive mental retardation syndrome comprising macrocephaly and ciliary dysfunction is allelic to oral–facial–digital type I syndrome. Hum Genet 2006; 120:171–8. http://dx.doi.org/10.1007/s00439-006-0210-5

17. 

Coene KL, Roepman R, Doherty D, et al. OFD1 is mutated in X-linked Joubert syndrome and interacts with LCA5-encoded lebercilin. Am J Hum Genet 2009; 85:465–81. http://dx.doi.org/10.1016/j.ajhg.2009.09.002

18. 

Field M, Scheffer IE, Gill D, et al. Expanding the molecular basis and phenotypic spectrum of X-linked Joubert syndrome associated with OFD1 mutations. Eur J Hum Genet 2012; 20:806–9. http://dx.doi.org/10.1038/ejhg.2012.9

19. 

Schneider TD. Sequence walkers: a graphical method to display how binding proteins interact with DNA or RNA sequences. Nucleic Acids Res 1997; 25:4408–15. http://dx.doi.org/10.1093/nar/25.21.4408

20. 

Schneider TD. Information content of individual genetic sequences. J Theor Biol 1997; 189:427–41. http://dx.doi.org/10.1006/jtbi.1997.0540

21. 

Desmet FO, Hamroun D, Lalande M, Collod-Béroud G, Claustres M, Béroud C. Human Splicing Finder: an online bioinformatics tool to predict splicing signals. Nucleic Acids Res 2009; 37(9):e67. http://dx.doi.org/10.1093/nar/gkp215

22. 

Nishimura G, Kuwashima S, Kohno T, Teramoto C, Watanabe H, Kubota T. Fetal polycystic kidney disease in oro-facio-digital syndrome type I. Pediatr Radiol 1999; 29:506–8. http://dx.doi.org/10.1007/s002470050631

23. 

Rakkolainen A, Ala-Mello S, Kristo P, Orpana A, Järvelä I. Four novel mutations in the OFD1 (Cxorf5) gene in Finnish patients with oral–facial–digital syndrome 1. J Med Genet 2002; 39:292–6. http://dx.doi.org/10.1136/jmg.39.4.292

24. 

Thauvin-Robinet C, Cossée M, Cormier-Daire V, et al. Clinical, molecular, and genotype-phenotype correlation studies from 25 cases of oral–facial–digital syndrome type 1: a French and Belgian collaborative study. J Med Genet 2006; 43:54–61. http://dx.doi.org/10.1136/jmg.2004.027672

25. 

Prattichizzo C, Macca M, Novelli V, et al. Mutational spectrum of the oral–facial–digital type I syndrome: a study on a large collection of patients. Hum Mutat 2008; 29:1237–46. http://dx.doi.org/10.1002/humu.20792

26. 

Bisschoff IJ, Zeschnigk C, Horn D, et al. Novel mutations including deletions of the entire OFD1 gene in 30 families with type 1 orofaciodigital syndrome: a study of the extensive clinical variability. Hum Mutat 2013; 34:237–47. http://dx.doi.org/10.1002/humu.22224

27. 

Tsurusaki Y, Kosho T, Hatasaki K, et al. Exome sequencing in a family with an X-linked lethal malformation syndrome: clinical consequences of hemizygous truncating OFD1 mutations in male patients. Clin Genet 2013; 83:135–44. http://dx.doi.org/10.1111/j.1399-0004.2012.01885.x

28. 

Nigg EA, Raff JW. Centrioles, centrosomes, and cilia in health and disease. Cell 2009; 139:663–78. http://dx.doi.org/10.1016/j.cell.2009.10.036

29. 

Lee JH, Gleeson JG. The role of primary cilia in neuronal function. Neurobiol Dis 2010; 38:167–72. http://dx.doi.org/10.1016/j.nbd.2009.12.022

30. 

Wechsler-Reya RJ, Scott MP. Control of neuronal precursor proliferation in the cerebellum by Sonic Hedgehog. Neuron 1999; 22:103–14. http://dx.doi.org/10.1016/S0896-6273(00)80682-0

31. 

Huangfu D, Liu A, Rakeman AS, Murcia NS, Niswander L, Anderson KV. Hedgehog signalling in the mouse requires intraflagellar transport proteins. Nature 2003; 426(6962):83–7. http://dx.doi.org/10.1038/nature02061

32. 

Schneider L, Clement CA, Teilmann SC, et al. PDGFRalphaalpha signaling is regulated through the primary cilium in fibroblasts. Curr Biol 2005; 15:1861–6. http://dx.doi.org/10.1016/j.cub.2005.09.012

33. 

Simons M, Gloy J, Ganner A, et al. Inversin, the gene product mutated in nephronophthisis type II, functions as a molecular switch between Wnt signaling pathways. Nat Genet 2005; 37:537–43. http://dx.doi.org/10.1038/ng1552

34. 

Wallingford JB, Habas R. The developmental biology of Dishevelled: an enigmatic protein governing cell fate and cell polarity. Development 2005; 132:4421–36. http://dx.doi.org/10.1242/dev.02068

35. 

Al-Gazali L, Ali BR. Mutations of a country: a mutation review of single gene disorders in the United Arab Emirates (UAE). Hum Mutat 2010; 31:505–20. http://dx.doi.org/10.1002/humu.21232





Add comment 





Home  Editorial Board  Search  Current Issue  Archive Issues  Announcements  Aims & Scope  About the Journal  How to Submit  Contact Us
Find out how to become a part of the HMJ  |   CLICK HERE >>
© Copyright 2012 - 2013 HMJ - HAMDAN Medical Journal. All Rights Reserved         Website Developed By Cedar Solutions INDIA