A Novel Splice-Site Variation in COL5A1 Causes Keratoconus in an Indian Family

Objective. This study aims to clarify the association between keratoconus (KC) and potential pathogenic genetic variants in a three-generation South Indian family. Methods. In the present study, a three-generation KC family, which comprised 10 affected patients and nine unaffected individuals, was recruited. The family history and necessary ophthalmological exams, such as visual acuity and slit-lamp, were performed for all participants. Genomic DNA was extracted from peripheral blood leukocytes, and whole exome sequencing (WES) was performed using the genomic DNA of the proband (III:4) and two other family members (III:2, III:3). The acceptor-splice-site mutation was validated and verified using polymerase chain reaction (PCR) and Sanger sequencing. Gene functions and pathways associated with the identified mutations were subjected to in silico analysis. Results. A novel COL5A1 acceptor-splice-site mutation IVS50-4C > G was found in the 10 affected individuals in the three-generation KC family, but this was not found in any of the unaffected family members or unrelated healthy individuals. Gene functional analysis using the SpliceMan and ExonScan software predicted that the splice-site mutation was potentially associated with KC pathogenesis. This mutation might affect the assembly of the collagen triple helix. Conclusion. The present study confirmed the association between the COL5A1 gene and KC and identified a novel COL5A1 acceptor-splice-site mutation (IVS50-4C > G) in intron 50, which may affect the splicing of the adjacent exon 50.

Download Full-text

A splice site mutation of alpha-spectrin gene causing skipping of exon 18 in hereditary elliptocytosis

Blood ◽

10.1182/blood.v81.10.2791.2791 ◽

1993 ◽

Vol 81 (10) ◽

pp. 2791-2798 ◽

Cited By ~ 16

Author(s):

N Alloisio ◽

R Wilmotte ◽

J Marechal ◽

P Texier ◽

L Denoroy ◽

...

Keyword(s):

Splice Site ◽

Splice Site Mutation ◽

Low Grade ◽

Site Mutation ◽

Acceptor Splice Site ◽

Genetic Lesion ◽

Major Disadvantage ◽

Internal Position ◽

Alpha Spectrin ◽

Self Association

Abstract Spectrin Oran (alpha II/21) has been reported previously as a variant of the alpha II domain. Its expression level is low (10% of total spectrin) in heterozygotes denoting a major disadvantage of the mutated alpha-chain dimer or tetramer with respect to their normal counterparts. Spectrin Oran is associated with symptomatic elliptocytosis in the homozygous state. A 1-minute digestion time allowed to perceive a fast trypsin cleavage (not existing normally) after Arg 890 (helix 3 of repeating segment alpha 9). The responsible change was the lack of amino acids 822 to 862 (helix 2 of repeating segment alpha 8). Such a situation fits with the phasing of spectrin according to which mutated helix 2 and distorted helix 3 are adjacent to one another. The internal position of the structural change accounts for the slight self-association defect. The ultimate genetic lesion was a G to A substitution (intronic position-1) in the acceptor splice site of intron 17 resulting in skipping of exon 18. The substitution also created an acceptor splice site 1 base downstream, but the latter was used at a low grade.

Download Full-text

Progressive Myoclonic Epilepsy’-like presentation of Cerebrotendinous Xanthomatosis in an Indian Family with A Novel C.646+1G>A Splice Site Mutation

Epilepsy & Behavior Reports ◽

10.1016/j.ebr.2020.100401 ◽

2021 ◽

Vol 15 ◽

pp. 100401

Author(s):

Karan M. Desai ◽

Piyush Kumar ◽

Parthvi S. Ravat ◽

Sangeeta H. Ravat ◽

Neeraj Jain ◽

...

Keyword(s):

Splice Site ◽

Splice Site Mutation ◽

Myoclonic Epilepsy ◽

Cerebrotendinous Xanthomatosis ◽

Site Mutation ◽

Indian Family ◽

Progressive Myoclonic Epilepsy

Download Full-text

3′ acceptor splice site mutation in intron 50 leads to mild duchenne muscular dystrophy phenotype

Human Mutation ◽

10.1002/humu.1380110168 ◽

1998 ◽

Vol 11 (S1) ◽

pp. S209-S212 ◽

Cited By ~ 2

Author(s):

Kiriaki Kekou ◽

Lina Florentin ◽

Catherine Metaxotou

Keyword(s):

Duchenne Muscular Dystrophy ◽

Muscular Dystrophy ◽

Splice Site ◽

Splice Site Mutation ◽

Site Mutation ◽

Acceptor Splice Site

Download Full-text

An acceptor splice site mutation in intron 16 of the low density lipoprotein receptor gene leads to an elongated, internalization defective receptor

Atherosclerosis ◽

10.1016/0021-9150(93)90182-t ◽

1993 ◽

Vol 104 (1-2) ◽

pp. 117-128 ◽

Cited By ~ 12

Author(s):

P LOMBARDI ◽

M HOFFER ◽

B TOP ◽

E DEWIT ◽

J GEVERSLEUVEN ◽

...

Keyword(s):

Splice Site ◽

Receptor Gene ◽

Low Density Lipoprotein ◽

Density Lipoprotein ◽

Splice Site Mutation ◽

Low Density ◽

Lipoprotein Receptor ◽

Site Mutation ◽

Acceptor Splice Site ◽

Density Lipoprotein Receptor

Download Full-text

An acceptor splice site mutation in the calcium-sensing receptor (CASR) gene in familial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism

Human Mutation ◽

10.1002/humu.1212 ◽

2001 ◽

Vol 18 (5) ◽

pp. 411-421 ◽

Cited By ~ 39

Author(s):

Lilia D?Souza-Li ◽

Lucie Canaff ◽

Natasa Janicic ◽

David E.C. Cole ◽

Geoffrey N. Hendy

Keyword(s):

Splice Site ◽

Splice Site Mutation ◽

Familial Hypocalciuric Hypercalcemia ◽

Calcium Sensing Receptor ◽

Site Mutation ◽

Acceptor Splice Site ◽

Casr Gene ◽

Calcium Sensing

Download Full-text

Splice site mutation in the human protein C gene associated with venous thrombosis: demonstration of exon skipping by ectopic transcript analysis

Blood ◽

10.1182/blood.v82.8.2423.bloodjournal8282423 ◽

1993 ◽

Vol 82 (8) ◽

pp. 2423-2432

Author(s):

B Lind ◽

WW van Solinge ◽

M Schwartz ◽

S Thorsen

Keyword(s):

Splice Site ◽

Protein C ◽

Family Members ◽

Exon Skipping ◽

Splice Site Mutation ◽

Peripheral Blood Lymphocytes ◽

Nucleotide Sequencing ◽

Liver Protein ◽

Site Mutation ◽

Protein C Deficiency

Heterozygosity for a G-->C mutation converting the highly conserved Gln184 (CAG) to His (CAC) was identified at the last nucleotide of exon 7 of the protein C gene in two family members with deep vein thrombosis. As the nucleotide is a part of the 5 splice site of intron G, it was examined how the mutation affected splicing of protein C pre- mRNA. Relevant protein C cDNA fragments were amplified with polymerase chain reaction after reverse transcription of ectopic mRNA from peripheral blood lymphocytes. Southern blot analysis and nucleotide sequencing of these fragments showed a fragment (A) corresponding to correctly spliced mRNA originating from the normal allele and a fragment (B) corresponding to a truncated mRNA lacking exon 7, originating from the mutant allele. A third fragment (C) lacking exons 7 and 8 was identified in both affected and unaffected family members, as well as in normal controls. Analysis of human liver protein C mRNA indicated that the ectopic lymphocyte mRNA was qualitatively representative for the tissue-specific mRNA. In conclusion, evidence is provided showing that the mutation abolishes formation of correctly spliced mRNA. This agrees with the observation that the mutation results in a type 1 protein C deficiency.

Download Full-text

Screening JAK2 Exon 12 in JAK2 V617F Negative Patients with Myeloproliferative Disorders Reveals a New Splice Site Mutation

Blood ◽

10.1182/blood.v112.11.5238.5238 ◽

2008 ◽

Vol 112 (11) ◽

pp. 5238-5238

Author(s):

C. Bento ◽

A. Estevinho ◽

I. Rapado ◽

S. Grande ◽

H. Matos ◽

...

Keyword(s):

Splice Site ◽

Genomic Dna ◽

Mutant Allele ◽

Splice Site Mutation ◽

Jak2 V617f ◽

Janus Kinase ◽

Site Mutation ◽

Mutational Status ◽

Low Levels ◽

V617f Mutation

Abstract Background. The identification of the somatic mutation V617F in exon 14 of the Janus kinase 2 gene (JAK2) has simplified the diagnosis of many patients affected with typical chronic myeloproliferative diseases (MPDs). In patients without the V617F the molecular basis of MPD are still unclear but, recently, mutations in exon 12 of the JAK2 gene have been identified in a minority of patients, associated with a selective increase in erythropoiesis resulting in polycythemia vera (PV) or idiopathic erythrocytosis (IE) (Scott et al, NEJM 2007). Aim. To determine the JAK2 exon 12 mutational status in a group of JAK2 V617F negative patients with PV or IE. Methods. Genomic DNA was extracted from peripheral blood leukocytes from 85 MPD patients (PV or IE) included in the present study. All the samples were tested for JAK2 V617F mutation by allele specific polymerase chain reaction (ASO-PCR) and those negative for V617F mutant allele were subjected to real time quantitative PCR (RQ-PCR) using hybridization probes. Subsequently, all JAK2 V617F negative samples by both ASO-PCR and RQ-PCR where subjected to direct sequencing to exclude JAK2 exon 12 mutations. Results. JAK2 V617F was positive in 78 (91.7%) of the 85 patients, however, in two of these patients the V617F mutation was only detected upon subjecting genomic DNA to RQ-PCR which revealed low levels of the mutant allele, 2.65 % and 3.98%. Analysis of the JAK2 exon 12 in the seven JAK2 V617F negative patients detected three previously described mutations: a duplication (V536-1546) and two deletions (H539-K540del+542K and R541-E543 delinsK)and a previously unreported splice site mutation detected in intron 12 (IVS12nt6 T-C). To our knowledge this was the first description of intronic mutations in the JAK2 gene. No mutations were detected in the remaining 3 (3.6%) patients. Conclusions. In this cohort study JAK2 mutations were observed in 82 (96,5%), of the 85 patients, of these 78 (95.12%) had the V617F allele. In two cases V617F was detected at low levels (2.65% and 3.98%) only by RQ-PCR, highlighting the need for sensitive techniques to detect somatic mutations. One of the patients, a young male with erythrocytosis and low serum Epo levels, revealed a previously unreported splicing mutation (IVS12 nt6: T-C). This study illustrates the heterogeneity at the DNA level in PV patients which may assist in better understanding the genotype and phenotype relationship in MPD patients and assist in further delineating the role of JAK2 in these disorders.

Download Full-text