title: Secondary and tertiary structure modeling reveals effects of novel mutations in polycystic liver disease genes PRKCSH and SEC63.
abstract: Polycystic liver disease (PCLD) is characterized by intralobular bile duct cysts in the liver. It is caused by mutations in PRKCSH, encoding hepatocystin, and SEC63, encoding Sec63p. The main goals of this study were to screen for novel mutations and to analyze mutations for effects on protein structure and function. We screened 464 subjects including 76 probands by direct sequencing or conformation-sensitive capillary electrophoresis. We analyzed the effects of all known and novel mutations using a combination of splice site recognition, evolutionary conservation, secondary and tertiary structure predictions, PolyPhen, and pMut and sift. We identified a total of 26 novel mutations in PRKCSH (n = 14) and SEC63 (n = 12), including four splice site mutations, eight insertions/ deletions, six non-sense mutations, and eight missense mutations. Out of 48 PCLD mutations, 13 were predicted to affect splicing. Most mutations were located in highly conserved regions and homology modeling for two domains of Sec63p showed severe effects of the residue substitutions. In conclusion, we identified 26 novel mutations associated with PCLD and we provide in silico analysis in order to delineate the role of these mutations.
authors.affiliation: Department of Human Genetics, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands.
authors.forename: E
authors.initials: E
authors.lastname: Waanders
authors.forename: H
authors.initials: H
authors.lastname: Venselaar
authors.forename: R H M
authors.initials: RH
authors.lastname: te Morsche
authors.forename: D B
authors.initials: DB
authors.lastname: de Koning
authors.forename: P S
authors.initials: PS
authors.lastname: Kamath
authors.forename: V E
authors.initials: VE
authors.lastname: Torres
authors.forename: S
authors.initials: S
authors.lastname: Somlo
authors.forename: J P H
authors.initials: JP
authors.lastname: Drenth
mesh_terms: D002135:Calcium-Binding Proteins; D004252:DNA Mutational Analysis; D005959:Glucosidases / Q000737:chemistry / Q000235:genetics*; D006801:Humans; D047908:Intracellular Signaling Peptides and Proteins / Q000737:chemistry / Q000235:genetics*; D008565:Membrane Proteins / Q000737:chemistry / Q000235:genetics*; D008958:Models, Molecular; D018832:Molecular Chaperones; D009154:Mutation; D016891:Polycystic Kidney, Autosomal Dominant / Q000235:genetics*; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D016601:RNA-Binding Proteins
chemical_list: D002135:Calcium-Binding Proteins; D047908:Intracellular Signaling Peptides and Proteins; D008565:Membrane Proteins; D018832:Molecular Chaperones; D016601:RNA-Binding Proteins; C487464:SEC63 protein, human; D005959:Glucosidases; C070368:PRKCSH protein, human