A novel splice-acceptor site mutation (IVS13-2A&gt;T) of polycystic kidney disease 1 (PKD1) gene resulting in an RNA processing defect with a 74-nucleotide deletion in exon 14 of the mRNA transcript

Thongnoppakhun, Anna; Rungroj, Nanyawan; Wilairat, Prapon; Vareesangthip, Kriengsak; Sirinavin, C; Yenchitsomanus, Pa‐thai

doi:10.1002/(sici)1098-1004(200001)15:1<115::aid-humu22>3.0.co;2-z

Cited by 6 publications

(9 citation statements)

References 19 publications

(15 reference statements)

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“…Blood samples were collected after informed consent for RNA and DNA preparations. Linkage analysis was performed by using 5 polymorphic DNA markers on chromosome 16p including D16S85 (3' HVR), SM7, 16AC2.5, SM6, and KG8 as previously described [19]. …”

Section: Methodsmentioning

confidence: 99%

“…The analysis of PKD1 transcript provides an opportunity for ex vivo study of splicing defects prior to identification of causative mutations. In addition, a long-range PCR (LR-PCR) for amplification of PKD1 -specific genomic sequence with the length of about 18 kb in the reiterated region covering exons 14–33 has also been established for further analysis of PKD1 [19]. Using these techniques, we have previously identified and reported two mutations causing splicing defects of PKD1 transcripts in Thai families with ADPKD [19,20].…”

Section: Introductionmentioning

confidence: 99%

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Novel and de novo PKD1 mutations identified by multiple restriction fragment-single strand conformation polymorphism (MRF-SSCP)

et al. 2004

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BackgroundWe have previously developed a long RT-PCR method for selective amplification of full-length PKD1 transcripts (13.6 kb) and a long-range PCR for amplification in the reiterated region (18 kb) covering exons 14 and 34 of the PKD1 gene. These have provided us with an opportunity to study PKD1 mutations especially in its reiterated region which is difficult to examine. In this report, we have further developed the method of multiple restriction fragment-single strand conformation polymorphism (MRF-SSCP) for analysis of PKD1 mutations in the patients with autosomal dominant polycystic kidney disease (ADPKD). Novel and de novo PKD1 mutations are identified and reported.MethodsFull-length PKD1 cDNA isolated from the patients with ADPKD was fractionated into nine overlapping segments by nested-PCR. Each segment was digested with sets of combined restriction endonucleases before the SSCP analysis. The fragments with aberrant migration were mapped, isolated, and sequenced. The presence of mutation was confirmed by the long-range genomic DNA amplification in the PKD1 region, sequencing, direct mutation detection, and segregation analysis in the affected family.ResultsFive PKD1 mutations identified are two frameshift mutations caused by two di-nucleotide (c. 5225_5226delAG and c.9451_9452delAT) deletions, a nonsense (Q1828X, c.5693C>T) mutation, a splicing defect attributable to 31 nucleotide deletion (g.33184_33214del31), and an in-frame deletion (L3287del, c.10070_10072delCTC). All mutations occurred within the reiterated region of the gene involving exons 15, 26, 15, 19 and 29, respectively. Three mutations (one frameshift, splicing defect, and in-frame deletion) are novel and two (one frameshift and nonsense) known. In addition, two mutations (nonsense and splicing defect) are possibly de novo.ConclusionThe MRF-SSCP method has been developed to analyze PCR products generated by the long RT-PCR and nested-PCR technique for screening PKD1 mutations in the full-length cDNA. Five mutations identified were all in the reiterated region of this gene, three of which were novel. The presence of de novo PKD1 mutations indicates that this gene is prone to mutations.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Novel and de novo PKD1 mutations identified by multiple restriction fragment-single strand conformation polymorphism (MRF-SSCP)

et al. 2004

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“…The second is a splice mutation (patient 1) that causes partial deletion (74 bp) of exon 14 and introduces a stop codon 400 bp downstream, which has already been described. 12 This splicing abnormality is caused by a mutation in the splice acceptor site of exon 14 and the use of a cryptic splice site in exon 14. The third is a splice site mutation that causes exon 44 to be skipped, thus deleting 45 amino acids coding for the tenth transmembrane Figure 3 Test of the expression of the two PKD1 alleles in patients 1-7.…”

Section: Resultsmentioning

confidence: 99%

“…[9][10][11] One involves a long range RT-PCR approach (PKD1 is expressed in lymphocytes) designed to amplify a 13 kb RT-PCR product. 12 This can probably not be used as a routine screening test in a hospital setting. The second approach involves PTT tests and sequencing of genomic DNA.…”

mentioning

confidence: 99%

Mutation screening of the PKD1 transcript by RT-PCR

Burtey¹,

Lossi²,

Bayle³

et al. 2002

Journal of Medical Genetics

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“…For example, one confirmed cause of polycystic kidney disease is a splice acceptor site mutation in human PKD1 that leads to aberrant splicing and loss of gene function (Thongnoppakhun et al, 2000). Therefore it is extremely important to understand the possible consequences that mutations affecting splice sites may have on gene function.…”

Section: Discussionmentioning

confidence: 99%

A splice acceptor mutation in C. elegans daf-19/Rfx disrupts functional specialization of male-specific ciliated neurons but does not affect ciliogenesis

Wells

Rowneki

Killian

2015

Gene

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A novel splice-acceptor site mutation (IVS13-2A>T) of polycystic kidney disease 1 (PKD1) gene resulting in an RNA processing defect with a 74-nucleotide deletion in exon 14 of the mRNA transcript

Cited by 6 publications

References 19 publications

Novel and de novo PKD1 mutations identified by multiple restriction fragment-single strand conformation polymorphism (MRF-SSCP)

Novel and de novo PKD1 mutations identified by multiple restriction fragment-single strand conformation polymorphism (MRF-SSCP)

Mutation screening of the PKD1 transcript by RT-PCR

A splice acceptor mutation in C. elegans daf-19/Rfx disrupts functional specialization of male-specific ciliated neurons but does not affect ciliogenesis

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