title: Sequencing the GRHL3 Coding Region Reveals Rare Truncating Mutations and a Common Susceptibility Variant for Nonsyndromic Cleft Palate.
abstract: Nonsyndromic cleft lip with/without cleft palate (nsCL/P) and nonsyndromic cleft palate only (nsCPO) are the most frequent subphenotypes of orofacial clefts. A common syndromic form of orofacial clefting is Van der Woude syndrome (VWS) where individuals have CL/P or CPO, often but not always associated with lower lip pits. Recently, ∼5% of VWS-affected individuals were identified with mutations in the grainy head-like 3 gene (GRHL3). To investigate GRHL3 in nonsyndromic clefting, we sequenced its coding region in 576 Europeans with nsCL/P and 96 with nsCPO. Most strikingly, nsCPO-affected individuals had a higher minor allele frequency for rs41268753 (0.099) than control subjects (0.049; p = 1.24 × 10(-2)). This association was replicated in nsCPO/control cohorts from Latvia, Yemen, and the UK (pcombined = 2.63 × 10(-5); ORallelic = 2.46 [95% CI 1.6-3.7]) and reached genome-wide significance in combination with imputed data from a GWAS in nsCPO triads (p = 2.73 × 10(-9)). Notably, rs41268753 is not associated with nsCL/P (p = 0.45). rs41268753 encodes the highly conserved p.Thr454Met (c.1361C>T) (GERP = 5.3), which prediction programs denote as deleterious, has a CADD score of 29.6, and increases protein binding capacity in silico. Sequencing also revealed four novel truncating GRHL3 mutations including two that were de novo in four families, where all nine individuals harboring mutations had nsCPO. This is important for genetic counseling: given that VWS is rare compared to nsCPO, our data suggest that dominant GRHL3 mutations are more likely to cause nonsyndromic than syndromic CPO. Thus, with rare dominant mutations and a common risk variant in the coding region, we have identified an important contribution for GRHL3 in nsCPO.
authors.affiliation: Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany. Electronic address: e.mangold@uni-bonn.de.
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Mangold
authors.affiliation: Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Department of Genomics, Life & Brain Center, University of Bonn, 53127 Bonn, Germany.
authors.forename: Anne C
authors.initials: AC
authors.lastname: Böhmer
authors.affiliation: Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Department of Genomics, Life & Brain Center, University of Bonn, 53127 Bonn, Germany.
authors.forename: Nina
authors.initials: N
authors.lastname: Ishorst
authors.affiliation: Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Department of Genomics, Life & Brain Center, University of Bonn, 53127 Bonn, Germany.
authors.forename: Ann-Kathrin
authors.initials: AK
authors.lastname: Hoebel
authors.affiliation: Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Department of Genomics, Life & Brain Center, University of Bonn, 53127 Bonn, Germany.
authors.forename: Pinar
authors.initials: P
authors.lastname: Gültepe
authors.affiliation: Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Department of Genomics, Life & Brain Center, University of Bonn, 53127 Bonn, Germany.
authors.forename: Hannah
authors.initials: H
authors.lastname: Schuenke
authors.affiliation: Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Department of Genomics, Life & Brain Center, University of Bonn, 53127 Bonn, Germany.
authors.forename: Johanna
authors.initials: J
authors.lastname: Klamt
authors.affiliation: Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Department of Genomics, Life & Brain Center, University of Bonn, 53127 Bonn, Germany.
authors.forename: Andrea
authors.initials: A
authors.lastname: Hofmann
authors.affiliation: Department of Orthodontics, University of Bonn, 53127 Bonn, Germany.
authors.forename: Lina
authors.initials: L
authors.lastname: Gölz
authors.affiliation: Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany.
authors.forename: Ruth
authors.initials: R
authors.lastname: Raff
authors.affiliation: Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Department of Genomics, Life & Brain Center, University of Bonn, 53127 Bonn, Germany.
authors.forename: Peter
authors.initials: P
authors.lastname: Tessmann
authors.affiliation: Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany.
authors.forename: Stefanie
authors.initials: S
authors.lastname: Nowak
authors.affiliation: Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Department of Genomics, Life & Brain Center, University of Bonn, 53127 Bonn, Germany; Department of Neonatology and Pediatric Intensive Care, Children's Hospital, University of Bonn, 53113 Bonn, Germany.
authors.forename: Heiko
authors.initials: H
authors.lastname: Reutter
authors.affiliation: Clinic for Maxillofacial Surgery, University Hospital Leipzig, 04103 Leipzig, Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Hemprich
authors.affiliation: Department of Oral and Maxillofacial Surgery, Head and Neck Centre, Asklepios Klinik Nord, Heidberg, 22417 Hamburg, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Kreusch
authors.affiliation: Department of Oral and Maxillofacial Surgery, University of Göttingen, 37075 Göttingen, Germany.
authors.forename: Franz-Josef
authors.initials: FJ
authors.lastname: Kramer
authors.affiliation: Department of Orthodontics, University of Cologne, 50931 Cologne, Germany.
authors.forename: Bert
authors.initials: B
authors.lastname: Braumann
authors.affiliation: Department of Oral and Maxillo-Facial-Plastic Surgery, University of Bonn, 53111 Bonn, Germany.
authors.forename: Rudolf
authors.initials: R
authors.lastname: Reich
authors.affiliation: Department of Cleft Lip and Cleft Palate Surgery, Humboldt University of Berlin, 13353 Berlin, Germany.
authors.forename: Gül
authors.initials: G
authors.lastname: Schmidt
authors.affiliation: Department of Orthodontics, University of Bonn, 53127 Bonn, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Jäger
authors.affiliation: Section of Phoniatrics and Pedaudiology, Department of Otolaryngology - Head and Neck Surgery, University of Ulm, 89070 Ulm, Germany.
authors.forename: Rudolf
authors.initials: R
authors.lastname: Reiter
authors.affiliation: Section of Phoniatrics and Pedaudiology, Department of Otolaryngology - Head and Neck Surgery, University of Ulm, 89070 Ulm, Germany.
authors.forename: Sibylle
authors.initials: S
authors.lastname: Brosch
authors.affiliation: Medical Genetics and Mitochondrial Research Group, Latvian Biomedical Research and Study Centre, Riga 1067, Latvia.
authors.forename: Janis
authors.initials: J
authors.lastname: Stavusis
authors.affiliation: Institute of Child Health, University College London, London WC1N 1EH, UK.
authors.forename: Miho
authors.initials: M
authors.lastname: Ishida
authors.affiliation: Institute of Child Health, University College London, London WC1N 1EH, UK.
authors.forename: Rimante
authors.initials: R
authors.lastname: Seselgyte
authors.affiliation: Institute of Child Health, University College London, London WC1N 1EH, UK.
authors.forename: Gudrun E
authors.initials: GE
authors.lastname: Moore
authors.affiliation: Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Department of Genomics, Life & Brain Center, University of Bonn, 53127 Bonn, Germany.
authors.forename: Markus M
authors.initials: MM
authors.lastname: Nöthen
authors.affiliation: Institute of Human Genetics, Ulm University, 89073 Ulm, Germany.
authors.forename: Guntram
authors.initials: G
authors.lastname: Borck
authors.affiliation: Orthodontic Department, College of Dentistry, Thamar University, Thamar, Yemen.
authors.forename: Khalid A
authors.initials: KA
authors.lastname: Aldhorae
authors.affiliation: Medical Genetics and Mitochondrial Research Group, Latvian Biomedical Research and Study Centre, Riga 1067, Latvia.
authors.forename: Baiba
authors.initials: B
authors.lastname: Lace
authors.affiliation: Institute of Child Health, University College London, London WC1N 1EH, UK.
authors.forename: Philip
authors.initials: P
authors.lastname: Stanier
authors.affiliation: Institute of Medical Biometry, Informatics and Epidemiology, University of Bonn, 53127 Bonn, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Knapp
authors.affiliation: Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Department of Genomics, Life & Brain Center, University of Bonn, 53127 Bonn, Germany.
authors.forename: Kerstin U
authors.initials: KU
authors.lastname: Ludwig
mesh_terms: D000015:Abnormalities, Multiple / Q000175:diagnosis / Q000235:genetics; D000483:Alleles; D016022:Case-Control Studies; D002971:Cleft Lip / Q000175:diagnosis / Q000235:genetics; D002972:Cleft Palate / Q000175:diagnosis / Q000235:genetics*; D003560:Cysts / Q000175:diagnosis / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics*; D020022:Genetic Predisposition to Disease; D006801:Humans; D008046:Lip / Q000002:abnormalities; D009154:Mutation; D016366:Open Reading Frames; D020641:Polymorphism, Single Nucleotide; D044469:Racial Groups / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D004268:DNA-Binding Proteins; C473143:GRHL3 protein, human; D014157:Transcription Factors