title: Non-manifesting AHI1 truncations indicate localized loss-of-function tolerance in a severe Mendelian disease gene.
abstract: Determination of variant pathogenicity represents a major challenge in the era of high-throughput sequencing. Erroneous categorization may result if variants affect genes that are in fact dispensable. We demonstrate that this also applies to rare, apparently unambiguous truncating mutations of an established disease gene. By whole-exome sequencing (WES) in a consanguineous family with congenital non-syndromic deafness, we unexpectedly identified a homozygous nonsense variant, p.Arg1066*, in AHI1, a gene associated with Joubert syndrome (JBTS), a severe recessive ciliopathy. None of four homozygotes expressed any signs of JBTS, and one of them had normal hearing, which also ruled out p.Arg1066* as the cause of deafness. Homozygosity mapping and WES in the only other reported JBTS family with a homozygous C-terminal truncation (p.Trp1088Leufs*16) confirmed AHI1 as disease gene, but based on a more N-terminal missense mutation impairing WD40-repeat formation. Morpholinos against N-terminal zebrafish Ahi1, orthologous to where human mutations cluster, produced a ciliopathy, but targeting near human p.Arg1066 and p.Trp1088 did not. Most AHI1 mutations in JBTS patients result in truncated protein lacking WD40-repeats and the SH3 domain; disease was hitherto attributed to loss of these protein interaction modules. Our findings indicate that normal development does not require the C-terminal SH3 domain. This has far-reaching implications, considering that variants like p.Glu984* identified by preconception screening ('Kingsmore panel') do not necessarily indicate JBTS carriership. Genomes of individuals with consanguineous background are enriched for homozygous variants that may unmask dispensable regions of disease genes and unrecognized false positives in diagnostic large-scale sequencing and preconception carrier screening.
authors.affiliation: Medical Genetics Center, Cairo 11566, Egypt, Children's Hospital, Ain Shams University, Cairo 11566, Egypt.
authors.forename: Solaf M
authors.initials: SM
authors.lastname: Elsayed
authors.affiliation: Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA.
authors.forename: Jennifer B
authors.initials: JB
authors.lastname: Phillips
authors.affiliation: Institute of Human Genetics, University Hospital of Cologne, 50931 Cologne, Germany.
authors.forename: Raoul
authors.initials: R
authors.lastname: Heller
authors.affiliation: Institute of Human Genetics, University Hospital of Cologne, 50931 Cologne, Germany.
authors.forename: Michaela
authors.initials: M
authors.lastname: Thoenes
authors.affiliation: Medical Genetics Center, Cairo 11566, Egypt, Children's Hospital, Ain Shams University, Cairo 11566, Egypt.
authors.forename: Ezzat
authors.initials: E
authors.lastname: Elsobky
authors.affiliation: Cologne Center for Genomics (CCG) and Centre for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany.
authors.forename: Gudrun
authors.initials: G
authors.lastname: Nürnberg
authors.affiliation: Cologne Center for Genomics (CCG) and Centre for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50674 Cologne, Germany.
authors.forename: Peter
authors.initials: P
authors.lastname: Nürnberg
authors.affiliation: Institute of Human Genetics, University Hospital of Cologne, 50931 Cologne, Germany.
authors.forename: Saskia
authors.initials: S
authors.lastname: Seland
authors.affiliation: Institute of Human Genetics, University Hospital of Cologne, 50931 Cologne, Germany.
authors.forename: Inga
authors.initials: I
authors.lastname: Ebermann
authors.affiliation: Institute of Human Genetics, University Hospital of Cologne, 50931 Cologne, Germany, Cologne Center for Genomics (CCG) and Centre for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany.
authors.forename: Janine
authors.initials: J
authors.lastname: Altmüller
authors.affiliation: Cologne Center for Genomics (CCG) and Centre for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany.
authors.forename: Holger
authors.initials: H
authors.lastname: Thiele
authors.affiliation: Cologne Center for Genomics (CCG) and Centre for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany.
authors.forename: Mohammad
authors.initials: M
authors.lastname: Toliat
authors.affiliation: Department of Radiology, University of Cologne, 50937 Cologne, Germany.
authors.forename: Friederike
authors.initials: F
authors.lastname: Körber
authors.affiliation: Laboratory of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, 518000 Shenzhen, P. R. China.
authors.forename: Xue-Jia
authors.initials: XJ
authors.lastname: Hu
authors.affiliation: Laboratory of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, 518000 Shenzhen, P. R. China, College of Chemistry, Peking University, 100871 Beijing, P. R. China.
authors.forename: Yun-Dong
authors.initials: YD
authors.lastname: Wu
authors.affiliation: Department of Clinical Genetics, National Research Centre, Cairo 11566, Egypt.
authors.forename: Maha S
authors.initials: MS
authors.lastname: Zaki
authors.affiliation: Department of Clinical Genetics, National Research Centre, Cairo 11566, Egypt.
authors.forename: Ghada
authors.initials: G
authors.lastname: Abdel-Salam
authors.affiliation: Laboratory of Neurogenetics, Howard Hughes Medical Institute, Department of Neurosciences, University of California, La Jolla, San Diego, CA 92093, USA.
authors.forename: Joseph
authors.initials: J
authors.lastname: Gleeson
authors.affiliation: Department of Paediatric Neurology, University Children's Hospital of Zurich, 8032 Zurich, Switzerland and.
authors.forename: Eugen
authors.initials: E
authors.lastname: Boltshauser
authors.affiliation: Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA.
authors.forename: Monte
authors.initials: M
authors.lastname: Westerfield
authors.affiliation: Institute of Human Genetics, University Hospital of Cologne, 50931 Cologne, Germany, Center for Human Genetics, Bioscientia, 55218 Ingelheim, Germany hanno.bolz@uk-koeln.de.
authors.forename: Hanno J
authors.initials: HJ
authors.lastname: Bolz
mesh_terms: D000015:Abnormalities, Multiple / Q000175:diagnosis / Q000235:genetics; D048868:Adaptor Proteins, Signal Transducing / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D033942:Adaptor Proteins, Vesicular Transport; D000818:Animals; D001921:Brain / Q000473:pathology; D002531:Cerebellum / Q000002:abnormalities; D002874:Chromosome Mapping; D003241:Consanguinity; D004252:DNA Mutational Analysis; D004195:Disease Models, Animal; D019143:Evolution, Molecular; D059472:Exome; D005124:Eye Abnormalities / Q000175:diagnosis / Q000235:genetics; D005260:Female; D023061:Gene Order; D005808:Genes, Recessive; D056726:Genetic Association Studies; D056426:Genetic Loci; D006579:Heterozygote; D059014:High-Throughput Nucleotide Sequencing; D006720:Homozygote; D006801:Humans; D052177:Kidney Diseases, Cystic / Q000175:diagnosis / Q000235:genetics; D008279:Magnetic Resonance Imaging; D008297:Male; D008958:Models, Molecular; D009154:Mutation; D010375:Pedigree; D011487:Protein Conformation; D012160:Retina / Q000002:abnormalities; D015027:Zebrafish / Q000235:genetics
chemical_list: C487178:AHI1 protein, human; D048868:Adaptor Proteins, Signal Transducing; D033942:Adaptor Proteins, Vesicular Transport