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Liu Y, Sheng W, Hou S, Hou M, Zhang Y, Wang X, Zhang S, Zhou F, Cai C, Wang W. Functional Characterization of a Novel SLC4A4 Variant and Uniparental Isodisomy in Proximal Renal Tubular Acidosis Patient. Biochem Genet 2023:10.1007/s10528-023-10554-y. [PMID: 37952039 DOI: 10.1007/s10528-023-10554-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/20/2023] [Indexed: 11/14/2023]
Abstract
SLC4A4 variants are the etiologies of inherited proximal renal tubular acidosis (pRTA), which results in metabolic acidosis, hypokalemia, glaucoma, band keratopathy, and cataract. This study aims to characterize SLC4A4 variant and uniparental isodisomy of chromosome 4 in a patient, and analyse the functional characterization of SLC4A4 variants. This study analyzed renal tubular acidosis disease genes by whole exome sequencing (WES). H3M2 algorithm was used to analyze the run of homozygosity region in chromosomal regions in trio-WES data. The pathogenicity analysis of variants was performed using bioinformatics tools. Additionally, protein stability was analyzed by cycloheximide chase assay. Whole-cell patch clamping was used to examine the electrophysiological properties of NBCe1-A. A novel homozygous SLC4A4 variant was identified in the patient: a missense variant c.496C > T, p. Arg166Trp (NM_003759.4). But the father was heterozygous variant carrier, and the mother did not detect the variant. The H3M2 and UPDio algorithm revealed paternal uniparental isodisomy on chromosome 4 in the patient. SIFT, Poly Phen-2, FATHMM and Mutant Taster showed that the variant might be pathogenic. The tertiary structure analysis showed that the variant could cause structural damage to NBCe1 protein. Foldx results showed that the protein stability of the variant was slightly reduced. Cycloheximide chase assay demonstrated that the variant affects protein stability. The result of electrophysiological studies showed that the variant altered Na+/HCO3- cotransport activity of protein. In conclusion, the study is the first to report a pRTA patient with Arg166Trp variant with UPiD (4) pat and analyze the function of Arg166Trp variant.
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Affiliation(s)
- Yan Liu
- Clinical Pediatric College of Tianjin Medical University, Tianjin Medical University, Tianjin, 300134, China
- Department of Nephrology, Tianjin Children's Hospital (Tianjin University Children's Hospital), No.238 Longyan Road, Beichen District, Tianjin, 300134, China
| | - Wenchao Sheng
- Clinical Pediatric College of Tianjin Medical University, Tianjin Medical University, Tianjin, 300134, China
| | - Shaowei Hou
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin, 300070, China
| | - Mengzhu Hou
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Tianjin University Children's Hospital), No.238 Longyan Road, Beichen District, Tianjin, 300134, China
- Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, 300134, China
| | - Ying Zhang
- Clinical Pediatric College of Tianjin Medical University, Tianjin Medical University, Tianjin, 300134, China
| | - Xuetao Wang
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Tianjin University Children's Hospital), No.238 Longyan Road, Beichen District, Tianjin, 300134, China
- Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, 300134, China
| | - Shuyue Zhang
- Clinical Pediatric College of Tianjin Medical University, Tianjin Medical University, Tianjin, 300134, China
| | - Feiyu Zhou
- Clinical Pediatric College of Tianjin Medical University, Tianjin Medical University, Tianjin, 300134, China
| | - Chunquan Cai
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Tianjin University Children's Hospital), No.238 Longyan Road, Beichen District, Tianjin, 300134, China.
- Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, 300134, China.
| | - Wenhong Wang
- Department of Nephrology, Tianjin Children's Hospital (Tianjin University Children's Hospital), No.238 Longyan Road, Beichen District, Tianjin, 300134, China.
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Villafuerte-De la Cruz R, Chacon-Camacho OF, Rodriguez-Martinez AC, Xilotl-De Jesus N, Arce-Gonzalez R, Rodriguez-De la Torre C, Valdez-Garcia JE, Rojas-Martinez A, Zenteno JC. Case report: Disease phenotype associated with simultaneous biallelic mutations in ABCA4 and USH2A due to uniparental disomy of chromosome 1. Front Genet 2022; 13:949437. [PMID: 36051698 PMCID: PMC9424670 DOI: 10.3389/fgene.2022.949437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/18/2022] [Indexed: 11/29/2022] Open
Abstract
Inherited retinal diseases (IRDs) represent a spectrum of clinically and genetically heterogeneous disorders. Our study describes an IRD patient carrying ABCA4 and USH2A pathogenic biallelic mutations as a result of paternal uniparental disomy (UPD) in chromosome 1. The proband is a 9-year-old girl born from non-consanguineous parents. Both parents were asymptomatic and denied family history of ocular disease. Clinical history and ophthalmologic examination of the proband were consistent with Stargardt disease. Whispered voice testing disclosed moderate hearing loss. Next-generation sequencing and Sanger sequencing identified pathogenic variants in ABCA4 (c.4926C>G and c.5044_5058del) and USH2A (c.2276G>T). All variants were present homozygously in DNA from the proband and heterozygously in DNA from the father. No variants were found in maternal DNA. Further analysis of single nucleotide polymorphisms confirmed paternal UPD of chromosome 1. This is the first known patient with confirmed UPD for two recessively mutated IRD genes. Our study expands on the genetic heterogeneity of IRDs and highlights the importance of UPD as a mechanism of autosomal recessive disease in non-consanguineous parents. Moreover, a long-term follow-up is essential for the identification of retinal features that may develop as a result of USH2A-related conditions.
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Affiliation(s)
| | - O. F. Chacon-Camacho
- Carrera Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Genetics Department, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
| | - A. C. Rodriguez-Martinez
- Department of Ophthalmology, University Hospital and Faculty of Medicine, Autonomous University of Nuevo Leon (UANL), Monterrey, Mexico
| | - N. Xilotl-De Jesus
- Genetics Department, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
| | - R. Arce-Gonzalez
- Genetics Department, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
| | | | - J. E. Valdez-Garcia
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico
| | - A. Rojas-Martinez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico
- Institute for Obesity Research, Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico
- *Correspondence: A. Rojas-Martinez, ; J. C. Zenteno,
| | - J. C. Zenteno
- Genetics Department, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
- Biochemistry Department, Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
- *Correspondence: A. Rojas-Martinez, ; J. C. Zenteno,
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