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Enrichment of Pathogenic Alleles in the Brittle Cornea Gene, ZNF469, in Keratoconus

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This is a repository copy of Enrichment of pathogenic alleles in the brittle cornea gene, ZNF469, in keratoconus. White Rose Research Online URL for this paper: http://eprints.whiterose.ac.uk/87454/ Version: Accepted Version Article: Lechner, J, Porter, LF, Rice, A et al. (10 more authors) (2014) Enrichment of pathogenic alleles in the brittle cornea gene, ZNF469, in keratoconus. Human Molecular Genetics, 23 (20). 5527 - 5535. ISSN 0964-6906 https://doi.org/10.1093/hmg/ddu253 Reuse Unless indicated otherwise, fulltext items are protected by copyright with all rights reserved. The copyright exception in section 29 of the Copyright, Designs and Patents Act 1988 allows the making of a single copy solely for the purpose of non-commercial research or private study within the limits of fair dealing. The publisher or other rights-holder may allow further reproduction and re-use of this version - refer to the White Rose Research Online record for this item. Where records identify the publisher as the copyright holder, users can verify any specific terms of use on the publisher’s website. Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ Human Molecular Genetics Enrichment of pathogenic alleles in the brittle cornea gene, ZNF469, in keratoconus Journal: Human Molecular Genetics Manuscript ID: HMG-2014-D-00145.R1 Manuscript ForType: 2 General Peer Article - KReview Office Date Submitted by the Author: n/a Complete List of Authors: ,illoughby. Colin/ ni0ersity of Li0erpool. 1aculty of Health 2 Life Sciences Lechner. Judith/ 3ueen4s ni0ersity 5elfast. Centre for E7perimental Medicine 8orter. Louise/ Institute of Human De0elopment. ni0ersity of Manchester Rice. Aine/ ni0ersity of Leeds. Leeds Institute of Molecular Medicine 9itart. 9eroni:ue/ ni0ersity of Edinburgh. MRC Human Genetics nit. IGMM Armstrong. Da0id/ Royal 9ictoria Hospital. Dept of Ophthalmology Schorderet. Daniel/ Institute for Research in Ophthalmology. Department of Ophthalmology. ni0ersity of Lausanne Munier. 1rancis/ Jules-Gonin Eye Hospital. Ophthalmology ,right. Alan/ ni0ersity of Edinburgh. MRC Human Genetics nit. IGMM Inglehearn. Chris/ ni0ersity of Leeds. Molecular Medicine 5lack. Graeme/ ni0ersity of Manchester. Institute of Human De0elopment Simpson. Da0id/ 3ueen4s ni0ersity 5elfast. Centre for E7perimental Medicine Manson. 1orbes/ The ni0ersity of Manchester. Institute of Human De0elopment keratoconus. ZN1469. corneal thickness. Corneal Dystrophies. Hereditary. Key ,ords: mutation Page 1 of 32 Human Molecular Genetics 1 2 3 TITLE PAGE 4 5 6 Enrichment of pathogenic alleles in the brittle cornea gene, ZNF469, in keratoconus 7 8 9 Judith Lechner1,3, Louise F. Porter2,3 , Aine Rice4 , Veronique Vitart5 , David J. Armstrong6, 10 11 7,8,9 7,10 5 4 12 Daniel F. Schoderet , Francis L. Munier , Alan F. Wright , Chris Inglehearn , Graeme 13 2 1 2,12 11,12,* 14 Black , David A. Simpson , Forbes Manson , Colin E. Willoughby . 15 16 17 18 *Corresponding Author:For Peer Review 19 20 Prof Colin E. Willoughby 21 22 23 Department of Eye and Vision Science, 24 25 Institute of Ageing and Chronic Disease, 26 27 Faculty of Health & Life Sciences, 28 29 University of Liverpool, 30 31 32 3rd floor, UCD Building, 33 34 Daulby Street, 35 36 Liverpool, L69 3GA, 37 38 United Kingdom 39 40 Tel: +44 (0)151 706 4070 41 42 43 Email: [email protected] 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 1 Human Molecular Genetics Page 2 of 32 1 2 3 1Centre for Vision and Vascular Science, Queen’s University Belfast, Belfast, Northern 4 5 Ireland, BT12 6BA, United Kingdom 6 7 2Institute of Human Development, The University of Manchester, Manchester Academic 8 9 10 Health Science Centre, Central Manchester University Hospitals NHS Foundation Trust, 11 12 Manchester, M13 9WU, United Kingdom 13 14 3Joint First Authors 15 16 4Leeds Institute of Molecular Medicine, St. James's University Hospital, University of Leeds, 17 18 For Peer Review 19 Leeds LS9 7TF, United Kingdom 20 5 21 MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of 22 23 Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, Scotland, United Kingdom 24 25 6Department of Ophthalmology, Royal Victoria Hospital, Belfast, Northern Ireland, BT12 26 27 6BA, United Kingdom 28 29 7 30 IRO - Institute for Research in Ephthalmolo y, Sion, SwitGerland 31 8 32 Department of Ephthalmolo y, 8niversity of Lausanne, Lausanne, SwitGerland 33 34 9Faculty of Life Sciences, 1cole Polytechnique FHdHrale de Lausanne, Lausanne, SwitGerland 35 36 10 Jules-,onin 1ye 6ospital, Lausanne, SwitGerland 37 38 11 39 Department of 1ye and Vision Science, Institute of A ein and Chronic Disease, 8niversity 40 41 of Liverpool, Liverpool, L69 3,A, 8nited 9in dom 42 43 12These authors contri0uted equally 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 2 Page 3 of 32 Human Molecular Genetics 1 2 3 ABSTRACT 4 5 6 9eratoconus, a common inherited ocular disorder resultin in pro ressive corneal thinnin , is 7 8 the leadin indication for corneal transplantation in the developed world. ,enome-wide 9 10 11 association studies have identified common SNPs 100.0 upstream of ZNF469 stron ly 12 13 associated with corneal thic.ness. 6omoGy ous mutations in ZNF469 and PRDM5 enes 14 15 result in 0rittle cornea syndrome type 1 and type 2 respectively. -rittle cornea syndrome is an 16 17 autosomal recessive eneraliGed connective tissue disorder associated with eItreme corneal 18 For Peer Review 19 20 thinnin and a hi h ris. of corneal rupture. Some individuals with heteroGy ous PRDM5 21 22 mutations in these 0rittle corneal syndrome enes demonstrate a carrier ocular phenotype, 23 24 which includes a mildly reduced corneal thic.ness, .eratoconus and 0lue sclera. )e 25 26 hypothesiGed that heteroGy ous variants in PRDM5 and ZNF469 predispose to the 27 28 development of isolated .eratoconus. )e found a si nificant enrichment of potentially 29 30 31 patholo ic heteroGy ous alleles in ZNF469 associated with the development of .eratoconus 32 33 (PJ0.00102) resultin in a relative ris. of 12.0. This enrichment of rare potentially 34 35 patho enic alleles in ZNF469 in 12.5% of .eratoconus patients represents a si nificant 36 37 mutational load, and hi hli hts ZNF469 as the most si nificant enetic factor responsi0le for 38 39 40 .eratoconus identified to date. 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 3 Human Molecular Genetics Page 4 of 32 1 2 3 I TRODUCTIO 4 5 6 9eratoconus (MIM 148300), a common 0ilateral, pro ressive corneal thinnin disorder (1), is 7 8 the leadin indication for corneal transplantation in the developed world, accountin for 25% 9 10 11 of the 2500 corneal transplants performed annually in the 89 and a similar proportion of the 12 13 32000 rafts performed annually in the 8SA (2). 9eratoconus usually arises in the teena e 14 15 years and presents a si nificant health 0urden in wor.-a e adults. The minimum incidence is 16 17 1 in 2000 0ut it is much more common in some ethnic roups (1, 3) . There is stron evidence 18 For Peer Review 19 20 for a herita0le component in the development of .eratoconus (4, 5). Most studies descri0e 21 22 autosomal dominant inheritance, with incomplete penetrance or varia0le eIpressivity (4). 23 24 6owever, in a enetic modellin study in a multi-ethnicity population a maLor recessive 25 26 enetic defect was the most parsimonious (6), althou h no recessive loci for .eratoconus 27 28 have 0een descri0ed to date. 29 30 31 32 The pro ressive corneal thinnin associated with .eratoconus (mean central corneal thic.ness 33 34 450-500 Mm) (7) results in myopia and irre ular corneal asti matism. In healthy humans 35 36 central corneal thic.ness (CCT) is a normally distri0uted quantitative trait with a mean of 536 37 38 Mm N 31 Mm (8) which has an estimated herita0ility up to 95% (9). ,enome-wide association 39 40 studies (,)AS) in the healthy 1uropean and Asian populations have identified CCT - 41 42 43 associated loci, with common SNPs upstream of zinc finger 469 (ZNF469 OMIM 612078P) the 44 45 most stron ly associated with CCT (10-14). Mutations in three enes (ZNF469, COL5A1 46 47 and COL8A2) close or within these identified loci are responsi0le for rare Mendelian 48 49 conditions that affect the corneal structure4 0rittle corneal syndrome, 1hlers-Danlos syndrome 50 51 52 and posterior polymorphous corneal dystrophy respectively (10-12). 53 54 55 -rittle cornea syndrome (-CS) is an autosomal recessive eneraliGed connective tissue 56 57 disorder associated with eItreme corneal thinnin (220-450 Mm) and a hi h ris. of corneal 58 59 60 4 Page 5 of 32 Human Molecular Genetics 1 2 3 rupture (15, 16). 6omoGy ous mutations in ZNF469 and PR d main-c ntaining pr tein 5 4 5 (PRDM5 OMIM 614161P) enes result in 0rittle cornea syndrome type 1 (-CS1 OMIM 6 7 229200P) (17) and 0rittle cornea syndrome type 2 (-CS2 OMIM 614170P) (15) respectively. 8 9 10 Some individuals with heteroGy ous PRDM5 mutations demonstrate a carrier ocular 11 12 phenotype which includes a mildly reduced CCT (480-505Mm), .eratoconus and 0lue sclera 13 14 (15). In one family with -CS2 there was a relationship 0etween the severity and a e of onset 15 16 of .eratoconus and PRDM5 mutational status. Family mem0ers with a homoGy ous PRDM5 17 18 For Peer Review 19 mutation (deletion of eIons 9–14) developed early and severe .eratoconus whereas one 20 21 heteroGy ous family mem0er developed .eratoconus which was clinically milder with a later 22 23 onset (15).
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  • RAB3GAP1 Gene RAB3 Gtpase Activating Protein Catalytic Subunit 1

    RAB3GAP1 Gene RAB3 Gtpase Activating Protein Catalytic Subunit 1

    RAB3GAP1 gene RAB3 GTPase activating protein catalytic subunit 1 Normal Function The RAB3GAP1 gene provides instructions for making a protein that helps regulate the activity of specialized proteins called GTPases, which control a variety of functions in cells. To perform its function, the RAB3GAP1 protein interacts with another protein called RAB3GAP2 (produced from the RAB3GAP2 gene) to form the RAB3GAP complex. Often referred to as molecular switches, GTPases can be turned on and off. They are turned on (active) when they are attached (bound) to a molecule called GTP and are turned off (inactive) when they are bound to another molecule called GDP. The RAB3GAP complex turns on a GTPase known as RAB18 by exchanging GTP for the attached GDP. When active, RAB18 is involved in a process called vesicle trafficking, which moves proteins and other molecules within cells in sac-like structures called vesicles. RAB18 regulates the movement of substances between compartments in cells and the storage and release of fats (lipids) by structures called lipid droplets. The protein also appears to play a role in a process called autophagy, which helps clear unneeded materials from cells. RAB18 is important for the organization of a cell structure called the endoplasmic reticulum, which is involved in protein processing and transport. The RAB3GAP complex is also thought to inactivate another GTPase known as RAB3 by stimulating a reaction that turns the attached GTP into GDP. RAB3 plays a role in the release of hormones and brain chemicals (neurotransmitters) from cells. Health Conditions Related to Genetic Changes RAB18 deficiency More than 60 RAB3GAP1 gene mutations have been found to cause RAB18 deficiency, resulting in conditions that affect the eyes, brain, and reproductive system.
  • A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

    A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

    A User’s Guide to the Encyclopedia of DNA Elements (ENCODE) The ENCODE Project Consortium"* Abstract The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome. Citation: The ENCODE Project Consortium (2011) A User’s Guide to the Encyclopedia of DNA Elements (ENCODE). PLoS Biol 9(4): e1001046. doi:10.1371/ journal.pbio.1001046 Academic Editor: Peter B. Becker, Adolf Butenandt Institute, Germany Received September 23, 2010; Accepted March 10, 2011; Published April 19, 2011 Copyright: ß 2011 The ENCODE Project Consortium. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: Funded by the National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA. The role of the NIH Project Management Group in the preparation of this paper was limited to coordination and scientific management of the ENCODE Consortium.