1
|
Khabou B, Sahari UBM, Ben Issa A, Bouchaala W, Szenker-Ravi E, Yu Jin Ng A, Bonnard C, Mbarek H, Zeyaul I, Fakhfakh F, Kammoun F, Reversade B, Charfi Triki C. Characterization of a missense variant in COG5 in a Tunisian patient with COG5-CDG syndrome and insights into the effect of non-synonymous variants on COG5 protein. J Hum Genet 2024:10.1038/s10038-024-01273-2. [PMID: 38987656 DOI: 10.1038/s10038-024-01273-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 07/02/2024] [Accepted: 07/03/2024] [Indexed: 07/12/2024]
Abstract
The clinical diagnosis of patients with multisystem involvement including a pronounced neurologic damage is challenging. High-throughput sequencing methods remains crucial to provide an accurate diagnosis. In this study, we reported a Tunisian patient manifesting hypotonia and global developmental delay with visual and skin abnormalities. Exome sequencing was conducted followed by segregation analysis and, subsequently additional investigations. In silico analysis of non-synonymous variants (nsSNPs) described in COG5 in conserved positions was made. Results revealed a homozygous missense variant c.298 C > T (p.Leu100Phe) in the COG5 inherited from both parents. This variant altered both protein solubility and stability, in addition to a putative disruption of the COG5-COG7 interaction. This disruption has been confirmed using patient-derived cells in vitro in a COG5 co-immuno-precipitation, where interaction with binding partner COG7 was abrogated. Hence, we established the COG5-CDG diagnosis. Clinically, the patient shared common features with the already described cases with the report of the ichtyosis as a new manifestation. Conversely, the CADD scoring revealed 19 putatively pathogenic nsSNPs (Minor Allele Frequency MAF < 0.001, CADD > 30), 11 of which had a significant impact on the solubility and/or stability of COG5. These properties seem to be disrupted by six of the seven missense COG5-CDG variants. In conclusion, our study expands the genetic and phenotypic spectrum of COG5-CDG disease and highlight the utility of the next generation sequencing as a powerful tool in accurate diagnosis. Our results shed light on a likely molecular mechanism underlying the pathogenic effect of missense COG5 variants, which is the alteration of COG5 stability and solubility.
Collapse
Affiliation(s)
- Boudour Khabou
- Research laboratory of Neuropediatrics LR19ES15, Faculty of Medicine of Sfax, Sfax University, Sfax, Tunisia.
| | - Umar Bin Mohamad Sahari
- Laboratory of Regulatory Genomics, Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Abir Ben Issa
- Research laboratory of Neuropediatrics LR19ES15, Faculty of Medicine of Sfax, Sfax University, Sfax, Tunisia
| | - Wafa Bouchaala
- Research laboratory of Neuropediatrics LR19ES15, Faculty of Medicine of Sfax, Sfax University, Sfax, Tunisia
- Child Neurology department, Hedi Chaker University Hospital of Sfax, Sfax, Tunisia
- Faculty of Medicine of Sfax, Sfax University, Sfax, Tunisia
| | - Emmanuelle Szenker-Ravi
- Smart-Health Initiative, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | | | - Hamdi Mbarek
- Qatar Genome Program, Qatar Science and Technology Park, Qatar Foundation, Doha, Qatar
| | - Islam Zeyaul
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Education City, Qatar Foundation, Doha, Qatar
| | - Faiza Fakhfakh
- Laboratory of Molecular and Functional Genetics, Faculty of Sciences of Sfax, Sfax University, Sfax, Tunisia
| | - Fatma Kammoun
- Research laboratory of Neuropediatrics LR19ES15, Faculty of Medicine of Sfax, Sfax University, Sfax, Tunisia
- Child Neurology department, Hedi Chaker University Hospital of Sfax, Sfax, Tunisia
- Faculty of Medicine of Sfax, Sfax University, Sfax, Tunisia
| | - Bruno Reversade
- Smart-Health Initiative, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Medical Genetics Department, School of Medicine, Koç University, Istanbul, Turkey
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Chahnez Charfi Triki
- Research laboratory of Neuropediatrics LR19ES15, Faculty of Medicine of Sfax, Sfax University, Sfax, Tunisia
- Child Neurology department, Hedi Chaker University Hospital of Sfax, Sfax, Tunisia
- Faculty of Medicine of Sfax, Sfax University, Sfax, Tunisia
| |
Collapse
|
2
|
Sreedevi N, Swapna N, Maruthy S, Meghavathi H, Sylvester C. PMM2 -CDG T237M Mutation in a Patient with Cerebral Palsy-Like Phenotypes Reported from South India. Glob Med Genet 2023; 10:105-108. [PMID: 37274081 PMCID: PMC10234699 DOI: 10.1055/s-0043-1769494] [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] [Indexed: 06/06/2023] Open
Abstract
Congenital disorder of glycosylation (CDG) is an autosomal recessively inherited disorder. Hypotonia, stroke-like episodes, and peripheral neuropathy are also associated with the condition that typically develops during infancy. The patient, a 12-year-old girl born to healthy consanguineous parents, was diagnosed with cerebral palsy as a child. The affected patient has hypotonia, inadequate speech, strabismus, and developmental delay with mild mental retardation, which are key symptoms of CDG. Whole-exome sequencing (WES) identified the known missense pathogenic variant PMM2 c.710 C > T, p.T237M in the patient coding for the phosphomannomutase 2 (PMM2) confirming molecular testing of CDG. The patient's parents carried heterozygous PMM2 c.710 C > T variants. This study highlights the importance of WES in patients with a developmental disability or other neurological conditions, which is also useful in screening risk factors in couples with infertility or miscarriage issues.
Collapse
Affiliation(s)
- N. Sreedevi
- Department of Speech-Language Sciences, All India Institute of Speech and Hearing, Mysore, Karnataka, India
| | - N. Swapna
- Department of Speech-Language Pathology, All India Institute of Speech and Hearing, Mysore, Karnataka, India
| | - Santosh Maruthy
- Department of Speech-Language Sciences, All India Institute of Speech and Hearing, Mysore, Karnataka, India
| | - H.S. Meghavathi
- Unit for Human Genetics, All India Institute of Speech and Hearing, Mysore, Karnataka, India
| | - Charles Sylvester
- Unit for Human Genetics, All India Institute of Speech and Hearing, Mysore, Karnataka, India
| |
Collapse
|
3
|
González-Domínguez CA, Fiesco-Roa MO, Gómez-Carmona S, Kleinert-Altamirano API, He M, Daniel EJP, Raymond KM, Abreu-González M, Manrique-Hernández S, González-Jaimes A, Salinas-Marín R, Molina-Garay C, Carrillo-Sánchez K, Flores-Lagunes LL, Jiménez-Olivares M, Muñoz-Rivas A, Cruz-Muñoz ME, Ruíz-García M, Freeze HH, Mora-Montes HM, Alaez-Verson C, Martínez-Duncker I. ALG1-CDG Caused by Non-functional Alternative Splicing Involving a Novel Pathogenic Complex Allele. Front Genet 2021; 12:744884. [PMID: 34567092 PMCID: PMC8458739 DOI: 10.3389/fgene.2021.744884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 08/05/2021] [Indexed: 11/13/2022] Open
Abstract
This study reports on a Mexican mestizo patient with a multi-systemic syndrome including neurological involvement and a type I serum transferrin profile. Clinical exome sequencing revealed complex alleles in ALG1, the encoding gene for the chitobiosyldiphosphodolichol beta-mannosyltransferase that participates in the formation of the dolichol-pyrophosphate-GlcNAc2Man5, a lipid-linked glycan intermediate during N-glycan synthesis. The identified complex alleles were NM_019109.5(ALG1): c.[208 + 16_208 + 19dup; 208 + 25G > T] and NM_019109.5(ALG1): c.[208 + 16_208 + 19dup; 1312C > T]. Although both alleles carried the benign variant c.208 + 16_208 + 19dup, one allele carried a known ALG1 pathogenic variant (c.1312C > T), while the other carried a new uncharacterized variant (c.208 + 25G > T) causing non-functional alternative splicing that, in conjunction with the benign variant, defines the pathogenic protein effect (p.N70S_S71ins9). The presence in the patient’s serum of the pathognomonic N-linked mannose-deprived tetrasaccharide marker for ALG1-CDG (Neu5Acα2,6Galβ1,4-GlcNAcβ1,4GlcNAc) further supported this diagnosis. This is the first report of an ALG1-CDG patient from Latin America.
Collapse
Affiliation(s)
- Carlos Alberto González-Domínguez
- Laboratorio de Glicobiología Humana y Diagnóstico Molecular, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico.,Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Moisés O Fiesco-Roa
- Programa de Maestría y Doctorado en Ciencias Médicas, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, Mexico City, Mexico.,Laboratorio de Citogenética, Instituto Nacional de Pediatría, Mexico City, Mexico
| | | | - Anke Paula Ingrid Kleinert-Altamirano
- Centro de Rehabilitación e Inclusión Infantil Teletón, Tuxtla Gutiérrez, Mexico.,Palmieri Metabolic Disease Laboratory, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Miao He
- Hospital Regional de Alta Especialidad Ciudad Salud, Tapachula, Mexico
| | | | - Kimiyo M Raymond
- Department of Laboratory Medicine and Pathology, Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, United States
| | | | - Sandra Manrique-Hernández
- Laboratorio de Glicobiología Humana y Diagnóstico Molecular, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico.,Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Ana González-Jaimes
- Laboratorio de Glicobiología Humana y Diagnóstico Molecular, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Roberta Salinas-Marín
- Laboratorio de Glicobiología Humana y Diagnóstico Molecular, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Carolina Molina-Garay
- Laboratorio de Diagnóstico Genómico, Instituto Nacional de Medicina Genómica, Secretaría de Salud, Mexico City, Mexico
| | - Karol Carrillo-Sánchez
- Laboratorio de Diagnóstico Genómico, Instituto Nacional de Medicina Genómica, Secretaría de Salud, Mexico City, Mexico
| | - Luis Leonardo Flores-Lagunes
- Laboratorio de Diagnóstico Genómico, Instituto Nacional de Medicina Genómica, Secretaría de Salud, Mexico City, Mexico
| | - Marco Jiménez-Olivares
- Laboratorio de Diagnóstico Genómico, Instituto Nacional de Medicina Genómica, Secretaría de Salud, Mexico City, Mexico
| | - Anallely Muñoz-Rivas
- Laboratorio de Diagnóstico Genómico, Instituto Nacional de Medicina Genómica, Secretaría de Salud, Mexico City, Mexico
| | - Mario E Cruz-Muñoz
- Laboratorio de Inmunología Molecular, Facultad de Medicina, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Matilde Ruíz-García
- Departamento de Neurología, Instituto Nacional de Pediatría, Mexico City, Mexico
| | - Hudson H Freeze
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Héctor M Mora-Montes
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Mexico
| | - Carmen Alaez-Verson
- Laboratorio de Diagnóstico Genómico, Instituto Nacional de Medicina Genómica, Secretaría de Salud, Mexico City, Mexico
| | - Iván Martínez-Duncker
- Laboratorio de Glicobiología Humana y Diagnóstico Molecular, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico.,Sociedad Latinoamericana de Glicobiología A.C., Cuernavaca, Mexico
| |
Collapse
|
4
|
González-Domínguez C, Villarroel C, Rodríguez-Morales M, Manrique-Hernández S, González-Jaimes A, Olvera-Rodriguez F, Beutelspacher K, Molina-Garay C, Carrillo-Sánchez K, Flores-Lagunes L, Jiménez-Olivares M, Muñoz-Rivas A, Cruz-Muñoz M, Mora-Montes H, Salinas-Marín R, Alaez-Verson C, Martínez-Duncker I. Non-functional alternative splicing caused by a Latino pathogenic variant in a case of PMM2-CDG. Mol Genet Metab Rep 2021; 28:100781. [PMID: 34277356 PMCID: PMC8264207 DOI: 10.1016/j.ymgmr.2021.100781] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/26/2021] [Accepted: 06/27/2021] [Indexed: 12/13/2022] Open
Abstract
We report on a Mexican mestizo with a multisystemic syndrome including neurological involvement and a type I serum transferrin isoelectric focusing (Tf IEF) pattern. Diagnosis of PMM2-CDG was obtained by clinical exome sequencing (CES) that revealed compound heterozygous variants in PMM2, the encoding gene for the phosphomannomutase 2 (PMM2). This enzyme catalyzes the conversion of mannose-6-P to mannose-1-P required for the synthesis of GDP-Man and Dol-P-Man, donor substrates for glycosylation reactions. The identified variants were c.422G>A (R141H) and c.178G>T, the former being the most frequent PMM2 pathogenic mutation and the latter a previously uncharacterized variant restricted to the Latino population with conflicting interpretations of pathogenicity and that we here report causes leaky non-functional alternative splicing (p.V60Cfs*3).
Collapse
Affiliation(s)
- C.A. González-Domínguez
- Laboratorio de Glicobiología Humana y Diagnóstico Molecular, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - C.E. Villarroel
- Departamento de Genética, Instituto Nacional de Pediatría, Ciudad de México 04530, Mexico
| | - M. Rodríguez-Morales
- Departamento de Genética, Instituto Nacional de Pediatría, Ciudad de México 04530, Mexico
| | - S. Manrique-Hernández
- Laboratorio de Glicobiología Humana y Diagnóstico Molecular, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - A. González-Jaimes
- Laboratorio de Glicobiología Humana y Diagnóstico Molecular, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico
| | - F. Olvera-Rodriguez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - K. Beutelspacher
- Laboratorio de Glicobiología Humana y Diagnóstico Molecular, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico
| | - C. Molina-Garay
- Laboratorio de Diagnóstico Genómico, Instituto Nacional de Medicina Genómica, Secretaría de Salud, Ciudad de México 14610, Mexico
| | - K. Carrillo-Sánchez
- Laboratorio de Diagnóstico Genómico, Instituto Nacional de Medicina Genómica, Secretaría de Salud, Ciudad de México 14610, Mexico
| | - L.L. Flores-Lagunes
- Laboratorio de Diagnóstico Genómico, Instituto Nacional de Medicina Genómica, Secretaría de Salud, Ciudad de México 14610, Mexico
| | - M. Jiménez-Olivares
- Laboratorio de Diagnóstico Genómico, Instituto Nacional de Medicina Genómica, Secretaría de Salud, Ciudad de México 14610, Mexico
| | - A. Muñoz-Rivas
- Laboratorio de Diagnóstico Genómico, Instituto Nacional de Medicina Genómica, Secretaría de Salud, Ciudad de México 14610, Mexico
| | - M.E. Cruz-Muñoz
- Laboratorio de Inmunología Molecular, Facultad de Medicina, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico
| | - H.M. Mora-Montes
- Departamento de Biología, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Guanajuato 36050, Mexico
| | - R. Salinas-Marín
- Laboratorio de Glicobiología Humana y Diagnóstico Molecular, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico
| | - C. Alaez-Verson
- Laboratorio de Diagnóstico Genómico, Instituto Nacional de Medicina Genómica, Secretaría de Salud, Ciudad de México 14610, Mexico
| | - I. Martínez-Duncker
- Laboratorio de Glicobiología Humana y Diagnóstico Molecular, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico
- Corresponding author.
| |
Collapse
|