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Maryami F, Davoudi-Dehaghani E, Khalesi N, Rismani E, Rahimi H, Talebi S, Zeinali S. Identification and characterization of the largest deletion in the PCCA gene causing severe acute early-onset form of propionic acidemia. Mol Genet Genomics 2023; 298:905-917. [PMID: 37131081 DOI: 10.1007/s00438-023-02023-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 04/16/2023] [Indexed: 05/04/2023]
Abstract
Whole-exome sequencing (WES) is an excellent method for the diagnosis of diseases of uncertain or heterogeneous genetic origin. However, it has limitations for detecting structural variations such as InDels, which the bioinformatics analyzers must be aware of. This study aimed at using WES to evaluate the genetic cause of the metabolic crisis in a 3-day-old neonate admitted to the neonatal intensive care unit (NICU) and deceased after a few days. Tandem mass spectrometry (MS/MS) showed a significant increase in propionyl carnitine (C3), proposing methylmalonic acidemia (MMA) or propionic acidemia (PA). WES demonstrated a homozygous missense variant in exon 4 of the BTD gene (NM_000060.4(BTD):c.1330G > C), responsible for partial biotinidase deficiency. Segregation analysis of the BTD variant revealed the homozygous status of the asymptomatic mother. Furthermore, observation of the bam file, around genes responsible for PA or MMA, by Integrative Genomics Viewer (IGV) software displayed a homozygous large deletion in the PCCA gene. Comprehensive confirmatory studies identified and segregated a novel outframe deletion of 217,877 bp length, "NG_008768.1:g.185211_403087delinsTA", extended from intron 11 to 21 of the PCCA, inducing a premature termination codon and activation of nonsense-mediated mRNA decay (NMD). Homology modeling of the mutant PCCA demonstrated eliminating the protein's active site and critical functional domains. Thereupon, this novel variant is suggested as the largest deletion in the PCCA gene, causing an acute early-onset PA. These results could expand the PCCA variants spectrum, and improve the existing knowledge on the molecular basis of PA, as well as provide new evidence of pathogenicity of the variant (NM_000060.4(BTD):c.1330G > C.
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Affiliation(s)
- Fereshteh Maryami
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran
| | - Elham Davoudi-Dehaghani
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran
| | - Nasrin Khalesi
- Department of Pediatrics and Neonatal Intensive Care Unit, Ali-Asghar Children's Hospital, Iran University of Medical Sciences, Shahid Vahid Dastgerdi Street, Modarres Highway, Tehran, Iran.
| | - Elham Rismani
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran
| | - Hamzeh Rahimi
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran
- Texas Biomedical Research Center, San Antonio, USA
| | - Saeed Talebi
- Department of Medical Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran
- Department of Medical Genetics, Ali-Asghar Children's Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Sirous Zeinali
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran.
- Medical Genetics Lab, Kawsar Human Genetics Research Center, No. 41 Majlesi St., ValiAsr St., 1595645513, Tehran, Iran.
- Iranian Molecular Medicine Network, Pasteur Institute of Iran, Pasteur St, Tehran, Iran.
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Al Anazi AH, Ammar AS, Al-Hajj M, Cyrus C, Aljaafari D, Khoda I, Abdelfatah AK, Alsulaiman AA, Alanazi F, Alanazi R, Gandla D, Lad H, Barayan S, Keating BJ, Al-Ali AK. Whole-exome sequencing of a Saudi epilepsy cohort reveals association signals in known and potentially novel loci. Hum Genomics 2022; 16:71. [PMID: 36539902 PMCID: PMC9764464 DOI: 10.1186/s40246-022-00444-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Epilepsy, a serious chronic neurological condition effecting up to 100 million people globally, has clear genetic underpinnings including common and rare variants. In Saudi Arabia, the prevalence of epilepsy is high and caused mainly by perinatal and genetic factors. No whole-exome sequencing (WES) studies have been performed to date in Saudi Arabian epilepsy cohorts. This offers a unique opportunity for the discovery of rare genetic variants impacting this disease as there is a high rate of consanguinity among large tribal pedigrees. RESULTS We performed WES on 144 individuals diagnosed with epilepsy, to interrogate known epilepsy-related genes for known and functional novel variants. We also used an American College of Medical Genetics (ACMG) guideline-based variant prioritization approach in an attempt to discover putative causative variants. We identified 32 potentially causative pathogenic variants across 30 different genes in 44/144 (30%) of these Saudi epilepsy individuals. We also identified 232 variants of unknown significance (VUS) across 101 different genes in 133/144 (92%) subjects. Strong enrichment of variants of likely pathogenicity was observed in previously described epilepsy-associated loci, and a number of putative pathogenic variants in novel loci are also observed. CONCLUSION Several putative pathogenic variants in known epilepsy-related loci were identified for the first time in our population, in addition to several potential new loci which may be prioritized for further investigation.
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Affiliation(s)
- Abdulrahman H. Al Anazi
- grid.411975.f0000 0004 0607 035XDepartment of Neurosurgery, King Fahd Hospital of the University, Alkhobar, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Ahmed S. Ammar
- grid.411975.f0000 0004 0607 035XDepartment of Neurosurgery, King Fahd Hospital of the University, Alkhobar, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Mahmoud Al-Hajj
- grid.415296.d0000 0004 0607 1539Department of Neurosurgery, King Fahd Hospital, Alhafof, Saudi Arabia
| | - Cyril Cyrus
- grid.411975.f0000 0004 0607 035XDepartment of Clinical Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, P. O. Box 1982, 31441 Dammam, Saudi Arabia
| | - Danah Aljaafari
- grid.411975.f0000 0004 0607 035XDepartment of Neurology, King Fahd Hospital of the University, Alkhobar, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Iname Khoda
- grid.411975.f0000 0004 0607 035XDepartment of Neurology, King Fahd Hospital of the University, Alkhobar, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Ahmed K. Abdelfatah
- grid.411975.f0000 0004 0607 035XDepartment of Neurosurgery, King Fahd Hospital of the University, Alkhobar, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Abdullah A. Alsulaiman
- grid.411975.f0000 0004 0607 035XDepartment of Neurology, King Fahd Hospital of the University, Alkhobar, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Firas Alanazi
- grid.411975.f0000 0004 0607 035XDepartment of Neurosurgery, King Fahd Hospital of the University, Alkhobar, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Rawan Alanazi
- grid.411975.f0000 0004 0607 035XDepartment of Neurosurgery, King Fahd Hospital of the University, Alkhobar, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Divya Gandla
- grid.25879.310000 0004 1936 8972Department of Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA USA
| | - Hetal Lad
- grid.25879.310000 0004 1936 8972Department of Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA USA
| | - Samar Barayan
- grid.411975.f0000 0004 0607 035XDepartment of Neurosurgery, King Fahd Hospital of the University, Alkhobar, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Brendan J. Keating
- grid.25879.310000 0004 1936 8972Department of Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA USA
| | - Amein K. Al-Ali
- grid.411975.f0000 0004 0607 035XDepartment of Clinical Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, P. O. Box 1982, 31441 Dammam, Saudi Arabia
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A novel delins (c.773_819+47delinsAA) mutation of the PCCA gene associated with neonatal-onset propionic acidemia: a case report. BMC MEDICAL GENETICS 2020; 21:166. [PMID: 32819290 PMCID: PMC7441651 DOI: 10.1186/s12881-020-01102-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 08/05/2020] [Indexed: 11/10/2022]
Abstract
Background Propionic acidemia (PA)(OMIM#606054) is an inborn error of branched-chain amino acid metabolism, caused by defects in the propionyl-CoA carboxylase (PCC) enzyme which encoded by the PCCA and PCCB genes. Case presentation Here we report a Chinese neonate diagnosed with suspected PA based on the clinical symptoms, gas chromatography-mass spectrometry (GC/MS), and brain imaging tests. Targeted next-generation sequencing (NGS) was performed on the proband. We detected only one heterozygous recurrent nonsense variant (c.937C > T, p.Arg313Ter) in the PCCA gene. When we manually checked the binary alignment map (BAM) diagram of PCCA gene, we found a heterozygous deletion chr13:100915039-100915132delinsAA (c.773_819 + 47delinsAA) (GRCh37.p13) inside the exon 10 in the PCCA gene. The results were validated by Sanger sequencing and qPCR method in the family: the variant (c.937C > T, p.Arg313Ter) was in the maternal allele, and the delins was in the paternal allele. When the mother was pregnant again, prenatal diagnosis was carried out through amniocentesis at 18 weeks gestation, the fetus carried neither of the two mutations. After birth, newborn screening was undertaken, the result was negative. Conclusions We identified a recurrent c.937C > T and a novel c.773_819 + 47delinsAA mutations in the PCCA gene, which may be the genetic cause of the phenotype of this patient. Our findings expanded the spectrum of causative genotype-phenotype of the PCCA gene. For the cases, the NGS results revealed only a heterozygous mutation in autosomal recessive disease when the gene is associated with phenotypes, it is necessary to manually check the BAM diagram to improve the detection rate. Targeted NGS is an effective technique to detect the various genetic lesions responsible for the PA in one step. Genetic testing is essential for genetic counselling and prenatal diagnosis in the family to avoid birth defects.
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