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A Novel Mutation in the OAR Domain of PITX3 Associated with Congenital

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A Novel Mutation in the OAR Domain of PITX3 Associated with Congenital Fan et al. BMC Medical Genetics (2019) 20:42 https://doi.org/10.1186/s12881-019-0782-2 RESEARCH ARTICLE Open Access A novel mutation in the OAR domain of PITX3 associated with congenital posterior subcapsular cataract Qi Fan1,2,3,4,5, Dan Li1,2,3,4,5, Lei Cai1,2,3,4,5, Xiaodi Qiu1,2,3,4,5, Zhennan Zhao1,2,3,4,5, Jihong Wu1,2,3,4,5, Jin Yang1,2,3,4,5*† and Yi Lu1,2,3,4,5*† Abstract Background: Congenital cataract is the most common cause of blindness among children worldwide. The aim of this study was to identify causative mutations in a Chinese family with isolated autosomal dominant posterior subcapsular cataract. Methods: The proband and her parents underwent full ophthalmological examinations. DNA was extracted from the participants’ peripheral venous blood. The mutation was identified via panel-based next-generation sequencing (NGS) and was validated via Sanger sequencing. Results: Posterior subcapsular lenticular opacity was observed in both of the proband’s eyes. The novel deletion mutation c.797_814del, p.Ser266_Ala271del in the PITX3 gene was identified in the proband and her father. This mutation is located within the otp/aristaless/rax (OAR) domain at the COOH-terminus of the protein, which functions in DNA binding and transactivation. This mutation would result in a deletion of 6 amino acid residues at the C terminal of the protein. Conclusions: The mutation c.797_814del, p.Ser266_Ala271del is a novel mutation in the conserved DNA-binding OAR domain of PITX3 that causes congenital cataract. Keywords: Congenital cataract, PITX3, The OAR domain Background 100 causative genes for congenital cataract, including Congenital cataract is defined as lens opacity that occurs at many with minor additional features (e.g., ABCA3 [7], birth or during the first decade of life. With an estimated CRYAA [8]). Among these genes, over 30 causative genes incidence of 1 to 7.2 cases per 10,000 live births [1–3], con- have been implicated in association with isolated inher- genital cataract is responsible for 10 to 38% of pediatric ited congenital cataract. These genes may be arbitrarily blindness worldwide [4]. In approximately 70% of cases [5], divided into four major groups [9]: crystallin genes, congenital cataract presents as an isolated eye abnormality. membrane protein genes, cytoskeletal protein genes, and Congenital cataract can also occur in association with other DNA- or RNA-binding protein genes. ocular and/or systemic abnormalities, such as anterior seg- In recent years, the diagnostic use of gene panel ment mesenchymal dysgenesis (ASMD), Peters anomaly, next-generation sequencing (NGS) techniques have be- Lowe syndrome, and Nance-Horan syndrome. come commonplace for individuals with hereditary dis- Between 8.3 and 25% of congenital cataracts are her- eases [10]. It has enabled the analysis of a greater editary [6]. To date, genetic studies have identified over number of genes, with the advantage of being fast and inexpensive. We customized a gene capture panel to * Correspondence: [email protected]; [email protected] † identify genetic defects in ophthalmic diseases. It was Jin Yang and Yi Lu contributed equally to this work. designed to encompass the exons and untranslated 1Department of Ophthalmology and the Eye Institute, Eye and Ear, Nose, and Throat Hospital, Fudan University, 83 Fenyang Rd, Shanghai, People’s (UTR) regions of 790 genes related to eye disease, which Republic of China included retinal disease genes (FZD4, NDP, LRP5, Full list of author information is available at the end of the article © The Author(s). 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Fan et al. BMC Medical Genetics (2019) 20:42 Page 2 of 6 TIMP3,TLR4, ABCA4, RP1, and RP2, among others), sequence data were aligned to the reference human gen- neuro-ophthalmic disease genes (e.g., CRX, CRB1, OPA1, ome UCSC hg38 using Burrows-Wheeler Aligner, ver- OPA3), corneal disease genes (e.g., CHST6, TCF4, ZEB1), sion 0.7.10. The variants were filtered to eliminate glaucoma genes (e.g., ASB10, OPTN, MYOC) and others. benign variants with MAF (minor allele frequency) > In particular, this gene panel contains all of the reported 0.1% in the 1000 Genomes dataset, and the dbSNP, causative genes for congenital cataract, including the EXAC, Tumor Heart Freq_Hom, ESP6500, and internal CRYAA, CRYAB and PITX3 gene. databases. All 790 genes were considered equally. Fi- In this paper, we present two members of a nally, variant prioritization was performed by combining four-generation family with isolated autosomal dominant the total depth, quality score, MAF, potential deleterious posterior subcapsular cataract. The aim of this study was effect and the existence of mutation reports in common to identify causative mutations in the proband and her databases, such as The Human Gene Mutation Database family that resulted in congenital cataract by using a (HGMD), The Retinal Information Network (RetNet), gene panel. ClinVar, and Online Mendelian Inheritance in Man (OMIM). Variants were classified as benign, likely be- Methods nign, pathogenic, likely pathogenic or novel variants of All procedures were performed in accordance with the uncertain clinical significance according to the American Declaration of Helsinki and were approved by the Ethics College of Medical Genetics and Genomics (ACMG) Committee of the Eye & ENT Hospital of Fudan Univer- guidelines [12]. sity. Written informed consent was obtained from all in- dividuals who participated in this study and from PITX3 gene mutation validation responsible adults on behalf of minors. Sanger sequencing was used to confirm the detected vari- ant. First, polymerase chain reaction (PCR) was performed Patients onthesampleusingtheprimersF:5′-GTGTCCTGC Three members of a four-generation Chinese family CCTTATGCCTC-3′ and R:5′-GGAGGCTGTGAATC were enrolled in this study, including the proband (IV:3) GTTGC-3′ for PITX3. The PCR program included activa- and her parents (the father III:5 and the mother III:6). tion at 94 °C for 3 min; followed by 30 cycles of 94 °C for Two of them were affected with autosomal dominant 20 s, 60 °C for 20 s, and 72 °C for 40 s; and a final extension congenital cataract (the proband IV:3 and her father at 72 °C for 3 min. The PCR products were subjected to dir- III:5). They received a comprehensive ophthalmological ect DNA sequencing by Generay Biotechnology Co., Ltd. examination at the Department of Ophthalmology of the Eye & ENT Hospital of Fudan University. This examin- Results ation included tests of uncorrected visual acuity (UCVA) Clinical features and best corrected visual acuity (BCVA), Goldmann The pedigree of the family enrolled in this study is applanation tonometry, and detailed slit-lamp and fun- shown in Fig. 1 (Only the proband and her parents were dus examinations. Others family members were not en- enrolled in the study). There are four generations that rolled, but their affected status was obtained from the include 11 affected individuals, five unaffected individ- medical records of the local hospital from previous oph- uals and 8 spouses. The proband (IV:3) was born with thalmological examinations. bilateral congenital cataract. Her BCVA was 0.4 (logMar unit) in her right eye and 1.0 (logMar unit) in her left Panel-based next-generation sequencing eye when she was first referred to our hospital at the age Five milliliters of peripheral venous blood from the three of 10. Posterior subcapsular lenticular opacity was participants was collected in tubes containing EDTA. observed in both eyes, with heavier opacity in the left DNA was isolated from the whole-blood samples using a eye than in the right eye (Fig. 2 a, b, c and d). Cataract Gentra Puregene Blood Kit (Qiagen, Valencia, CA) in ac- extraction with posterior capsulotomy, anterior vitrec- cordance with the manufacturer’s protocol and was tomy and intraocular lens (IOL) implantation was per- stored at − 20 °C until used for sequencing. No DNA formed. One year after surgery, both eyes reached a from the other family members was available for tar- BCVA of 0.1 (logMar unit), with a clear optical axis. The geted mutation testing. proband’s father (III:5) had also suffered from congenital All three DNA samples were subjected to analysis cataract since childhood. He underwent cataract extrac- using panel-based NGS that involved a targeted gene re- tion with IOL implantation at the age of 18, resulting in gion capture protocol to identify genetic defects. This a bilateral BCVA of 0.7 (logMar unit). He presented with protocol and the capture probes were custom designed pseudophakia in both eyes and mild IOL dislocation in and produced by Beijing Genomics Institute (BGI, Shen- the right eye (Fig. 2 E and F). The patients had no ocular zhen, China), as previously reported. [11] The output or systemic abnormalities other than cataract. Fan et al. BMC Medical Genetics (2019) 20:42 Page 3 of 6 Fig. 1 Pedigree of the family enrolled in this study. Squares and circles represent males and females, respectively. Open and solid symbols indicate unaffected and affected individuals, respectively. Astericks indicate enrolled individuals. The proband, IV:3, is indicated with an arrow PITX3 mutation analysis cataract. Finally, one deletion mutation (c.797_814del, After the data acquisition and analysis, a total of 14,076 p.Ser266_Ala271del) in PITX3 was identified as a poten- raw variants were found in the 790 genes, and 211 vari- tially pathogenic mutation.
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