title: Splice-site mutations identified in PDE6A responsible for retinitis pigmentosa in consanguineous Pakistani families.
abstract: OBJECTIVE
  This study was conducted to localize and identify causal mutations associated with autosomal recessive retinitis pigmentosa (RP) in consanguineous familial cases of Pakistani origin.
  
  
  METHODS
  Ophthalmic examinations that included funduscopy and electroretinography (ERG) were performed to confirm the affectation status. Blood samples were collected from all participating individuals, and genomic DNA was extracted. A genome-wide scan was performed, and two-point logarithm of odds (LOD) scores were calculated. Sanger sequencing was performed to identify the causative variants. Subsequently, we performed whole exome sequencing to rule out the possibility of a second causal variant within the linkage interval. Sequence conservation was performed with alignment analyses of PDE6A orthologs, and in silico splicing analysis was completed with Human Splicing Finder version 2.4.1.
  
  
  RESULTS
  A large multigenerational consanguineous family diagnosed with early-onset RP was ascertained. An ophthalmic clinical examination consisting of fundus photography and electroretinography confirmed the diagnosis of RP. A genome-wide scan was performed, and suggestive two-point LOD scores were observed with markers on chromosome 5q. Haplotype analyses identified the region; however, the region did not segregate with the disease phenotype in the family. Subsequently, we performed a second genome-wide scan that excluded the entire genome except the chromosome 5q region harboring PDE6A. Next-generation whole exome sequencing identified a splice acceptor site mutation in intron 16: c.2028-1G>A, which was completely conserved in PDE6A orthologs and was absent in ethnically matched 350 control chromosomes, the 1000 Genomes database, and the NHLBI Exome Sequencing Project. Subsequently, we investigated our entire cohort of RP familial cases and identified a second family who harbored a splice acceptor site mutation in intron 10: c.1408-2A>G. In silico analysis suggested that these mutations will result in the elimination of wild-type splice acceptor sites that would result in either skipping of the respective exon or the creation of a new cryptic splice acceptor site; both possibilities would result in retinal photoreceptor cells that lack PDE6A wild-type protein.
  
  
  CONCLUSIONS
  we report two splice acceptor site variations in PDE6A in consanguineous Pakistani families who manifested cardinal symptoms of RP. Taken together with our previously published work, our data suggest that mutations in PDE6A account for about 2% of the total genetic load of RP in our cohort and possibly in the Pakistani population as well.
authors: The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore MD.
authors: Shahid Y
authors: SY
authors: Khan
authors: National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.
authors: Shahbaz
authors: S
authors: Ali
authors: National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.
authors: Muhammad Asif
authors: MA
authors: Naeem
authors: National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.
authors: Shaheen N
authors: SN
authors: Khan
authors: National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.
authors: Tayyab
authors: T
authors: Husnain
authors: Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan.
authors: Nadeem H
authors: NH
authors: Butt
authors: Layton Rahmatulla Benevolent Trust Hospital, Lahore Pakistan.
authors: Zaheeruddin A
authors: ZA
authors: Qazi
authors: Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan ; National Centre for Genetic Diseases, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad Pakistan.
authors: Javed
authors: J
authors: Akram
authors: National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan ; Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan ; National Centre for Genetic Diseases, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad Pakistan.
authors: Sheikh
authors: S
authors: Riazuddin
authors: Shiley Eye Institute, University of California San Diego, La Jolla CA.
authors: Radha
authors: R
authors: Ayyagari
authors: Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda MD.
authors: J Fielding
authors: JF
authors: Hejtmancik
authors: The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore MD.
authors: S Amer
authors: SA
authors: Riazuddin
mesh_terms: D000328:Adult; D002895:Chromosomes, Human, Pair 5 / Q000235:genetics; D003241:Consanguinity; D054707:Cyclic Nucleotide Phosphodiesterases, Type 6 / Q000235:genetics*; D004252:DNA Mutational Analysis; D005136:Eye Proteins / Q000235:genetics*; D005260:Female; D005808:Genes, Recessive; D005819:Genetic Markers; D006801:Humans; D008126:Lod Score; D008297:Male; D008875:Middle Aged; D009154:Mutation; D010154:Pakistan; D010375:Pedigree; D022821:RNA Splice Sites; D012174:Retinitis Pigmentosa / Q000235:genetics* / Q000473:pathology / Q000503:physiopathology; D055815:Young Adult
chemical_list: D005136:Eye Proteins; D005819:Genetic Markers; D022821:RNA Splice Sites; D054707:Cyclic Nucleotide Phosphodiesterases, Type 6; C410522:PDE6A protein, human