title: Exome sequencing provides additional evidence for the involvement of ARHGAP29 in Mendelian orofacial clefting and extends the phenotypic spectrum to isolated cleft palate.
abstract: Recent advances in genomics methodologies, in particular the availability of next-generation sequencing approaches have made it possible to identify risk loci throughout the genome, in particular the exome. In the current study, we present findings from an exome study conducted in five affected individuals of a multiplex family with cleft palate only.
  
  
  
  The GEnome MINIng (GEMINI) pipeline was used to functionally annotate the single nucleotide polymorphisms, insertions and deletions. Filtering methods were applied to identify variants that are clinically relevant and present in affected individuals at minor allele frequencies (≤1%) in the 1000 Genomes Project single nucleotide polymorphism database, Exome Aggregation Consortium, and Exome Variant Server databases. The bioinformatics tool Systems Tool for Craniofacial Expression-Based Gene Discovery was used to prioritize cleft candidates in our list of variants, and Sanger sequencing was used to validate the presence of identified variants in affected and unaffected relatives.
  
  
  
  Our analyses approach narrowed the candidates down to the novel missense variant in ARHGAP29 (GenBank: NM_004815.3, NP_004806.3;c.1654T>C [p.Ser552Pro]. A functional assay in zebrafish embryos showed that the encoded protein lacks the activity possessed by its wild-type counterpart, and migration assays revealed that keratinocytes transfected with wild-type ARHGAP29 migrated faster than counterparts transfected with the p.Ser552Pro ARHGAP29 variant or empty vector (control).
  
  
  
  These findings reveal ARHGAP29 to be a regulatory protein essential for proper development of the face, identifies an amino acid that is key for this, and provides a potential new diagnostic tool.Birth Defects Research 109:27-37, 2017. © 2016 Wiley Periodicals, Inc.
authors.affiliation: Department of Anatomy and Cell Biology, Iowa City, U.S.A.
authors.forename: Huan
authors.initials: H
authors.lastname: Liu
authors.affiliation: Department of Pediatrics, University of Iowa, Iowa City, U.S.A.
authors.forename: Tamara
authors.initials: T
authors.lastname: Busch
authors.affiliation: Department of Anatomy and Cell Biology, Iowa City, U.S.A.
authors.forename: Steven
authors.initials: S
authors.lastname: Eliason
authors.affiliation: Department of Biological Sciences, University of Delaware, Newark, DE, USA.
authors.forename: Deepti
authors.initials: D
authors.lastname: Anand
authors.affiliation: Department of Internal Medicine, University of Iowa, Iowa City, U.S.A.
authors.forename: Steven
authors.initials: S
authors.lastname: Bullard
authors.affiliation: Department of Oral Pathology, Radiology and Medicine, University of Iowa, Iowa City, U.S.A.
authors.forename: Lord J J
authors.initials: LJJ
authors.lastname: Gowans
authors.affiliation: Department of Pediatrics, University of Iowa, Iowa City, U.S.A.
authors.forename: Nichole
authors.initials: N
authors.lastname: Nidey
authors.affiliation: Department of Pediatrics, University of Iowa, Iowa City, U.S.A.
authors.forename: Aline
authors.initials: A
authors.lastname: Petrin
authors.affiliation: Department of Oral Pathology, Radiology and Medicine, University of Iowa, Iowa City, U.S.A.
authors.forename: Eno-Abasi
authors.initials: EA
authors.lastname: Augustine-Akpan
authors.affiliation: Department of Anatomy and Cell Biology, University of Kansas Medical Center Kansas City, KS, USA.
authors.forename: Irfan
authors.initials: I
authors.lastname: Saadi
authors.affiliation: Department of Anatomy and Cell Biology, Iowa City, U.S.A.
authors.forename: Martine
authors.initials: M
authors.lastname: Dunnwald
authors.affiliation: Department of Internal Medicine, University of Iowa, Iowa City, U.S.A.|Department of Biological Sciences, University of Delaware, Newark, DE, USA.|Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA.
authors.forename: Salil A
authors.initials: SA
authors.lastname: Lachke
authors.affiliation: Newcastle GOLD Service, Hunter Genetics, Waratah, NSW, Australia.
authors.forename: Ying
authors.initials: Y
authors.lastname: Zhu
authors.affiliation: Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, U.S.A.
authors.forename: Adebowale
authors.initials: A
authors.lastname: Adeyemo
authors.affiliation: Department of Anatomy and Cell Biology, Iowa City, U.S.A.|Dows Research Institute, University of Iowa, Iowa City, U.S.A.
authors.forename: Brad
authors.initials: B
authors.lastname: Amendt
authors.affiliation: Department of Medical Genetics, Sydney Children's Hospital, Sydney, Australia.|The Kinghorn Centre for Clinical Genomics, Sydney, Australia.
authors.forename: Tony
authors.initials: T
authors.lastname: Roscioli
authors.affiliation: Department of Anatomy and Cell Biology, Iowa City, U.S.A.
authors.forename: Robert
authors.initials: R
authors.lastname: Cornell
authors.affiliation: Department of Pediatrics, University of Iowa, Iowa City, U.S.A.
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Murray
authors.affiliation: Department of Oral Pathology, Radiology and Medicine, University of Iowa, Iowa City, U.S.A.|Dows Research Institute, University of Iowa, Iowa City, U.S.A.
authors.forename: Azeez
authors.initials: A
authors.lastname: Butali
mesh_terms: D000483:Alleles; D000818:Animals; D002971:Cleft Lip / Q000235:genetics; D002972:Cleft Palate / Q000235:genetics*; D019295:Computational Biology; D004195:Disease Models, Animal; D059472:Exome; D005260:Female; D020690:GTPase-Activating Proteins / Q000235:genetics* / Q000378:metabolism; D005787:Gene Frequency / Q000235:genetics; D055106:Genome-Wide Association Study; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012307:Risk Factors; D017422:Sequence Analysis, DNA / Q000379:methods; D000073359:Exome Sequencing; D015027:Zebrafish / Q000196:embryology / Q000235:genetics
chemical_list: C500429:ARHGAP29 protein, human; D020690:GTPase-Activating Proteins
keywords: cleft palate; exome; missense mutation