A novel CHD7 variant disrupting acceptor splice site in a patient with mild features of CHARGE syndrome: a case report.
Adolescent
Amino Acid Sequence
Base Sequence
CHARGE Syndrome
/ diagnostic imaging
DNA Helicases
/ genetics
DNA-Binding Proteins
/ genetics
Female
Frameshift Mutation
Genetic Association Studies
Genetic Predisposition to Disease
/ genetics
Heterozygote
Humans
Introns
Mutation
RNA Splice Sites
RNA Splicing
RNA, Messenger
Sequence Alignment
Temporal Bone
/ diagnostic imaging
Exome Sequencing
C.5535-1G > A splice site variant
CHARGE syndrome
CHD7
Congenital anomalies
cDNA analysis
Journal
BMC medical genetics
ISSN: 1471-2350
Titre abrégé: BMC Med Genet
Pays: England
ID NLM: 100968552
Informations de publication
Date de publication:
17 07 2019
17 07 2019
Historique:
received:
18
04
2019
accepted:
11
07
2019
entrez:
19
7
2019
pubmed:
19
7
2019
medline:
4
12
2019
Statut:
epublish
Résumé
CHARGE syndrome (MIM# 214800)-which is characterised by a number of congenital anomalies including coloboma, ear anomalies, deafness, facial anomalies, heart defects, atresia choanae, genital hypoplasia, growth retardation, and developmental delay-is caused by a heterozygous variant in the CHD7 (MIM# 608892) gene located on chromosome 8q12. We report the identification of a novel c.5535-1G > A variant in CHD7 and provide the evaluation of its effect on pre-mRNA splicing. In this study, we report on a female presenting features of CHARGE syndrome. A novel heterozygous CHD7 variant c.5535-1G > A located in the acceptor splice site of intron 26 was identified in the proband's DNA sample after analysis of whole exome sequencing data. In silico predictions indicating that the variant is probably pathogenic by affecting pre-mRNA splicing were verified by genetic analysis based on reverse transcription of the patient's RNA followed by PCR amplifications performed on synthesised cDNA and Sanger sequencing. Sanger sequencing of cDNA revealed that the c.5535-1G > A variant disrupts the original acceptor splice site and activates a cryptic splice site only one nucleotide downstream of the pathogenic variant site. This change causes the omission of the first nucleotide of exon 27, leading to a frameshift in the mRNA of the CHD7 gene. Our results suggest that the alteration induces the premature truncation of the CHD7 protein (UniProtKB: Q9P2D1), thus resulting in CHARGE syndrome. Genetic analysis of novel splice site variant underlines its importance for studying the pathogenic splicing mechanism as well as for confirming a diagnosis.
Sections du résumé
BACKGROUND
CHARGE syndrome (MIM# 214800)-which is characterised by a number of congenital anomalies including coloboma, ear anomalies, deafness, facial anomalies, heart defects, atresia choanae, genital hypoplasia, growth retardation, and developmental delay-is caused by a heterozygous variant in the CHD7 (MIM# 608892) gene located on chromosome 8q12. We report the identification of a novel c.5535-1G > A variant in CHD7 and provide the evaluation of its effect on pre-mRNA splicing.
CASE PRESENTATION
In this study, we report on a female presenting features of CHARGE syndrome. A novel heterozygous CHD7 variant c.5535-1G > A located in the acceptor splice site of intron 26 was identified in the proband's DNA sample after analysis of whole exome sequencing data. In silico predictions indicating that the variant is probably pathogenic by affecting pre-mRNA splicing were verified by genetic analysis based on reverse transcription of the patient's RNA followed by PCR amplifications performed on synthesised cDNA and Sanger sequencing. Sanger sequencing of cDNA revealed that the c.5535-1G > A variant disrupts the original acceptor splice site and activates a cryptic splice site only one nucleotide downstream of the pathogenic variant site. This change causes the omission of the first nucleotide of exon 27, leading to a frameshift in the mRNA of the CHD7 gene. Our results suggest that the alteration induces the premature truncation of the CHD7 protein (UniProtKB: Q9P2D1), thus resulting in CHARGE syndrome.
CONCLUSION
Genetic analysis of novel splice site variant underlines its importance for studying the pathogenic splicing mechanism as well as for confirming a diagnosis.
Identifiants
pubmed: 31315586
doi: 10.1186/s12881-019-0859-y
pii: 10.1186/s12881-019-0859-y
pmc: PMC6637606
doi:
Substances chimiques
DNA-Binding Proteins
0
RNA Splice Sites
0
RNA, Messenger
0
DNA Helicases
EC 3.6.4.-
CHD7 protein, human
EC 3.6.4.12
Types de publication
Case Reports
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
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