1
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Zavarzadeh PG, Bonyadi M, Abedi Z. Whole-exome sequencing analysis in a case of primary congenital glaucoma due to the partial uniparental isodisomy. Genomics Inform 2022; 20:e28. [PMID: 36239105 PMCID: PMC9576475 DOI: 10.5808/gi.21044] [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: 08/06/2021] [Accepted: 08/29/2022] [Indexed: 11/20/2022] Open
Abstract
We described a clinical, laboratory, and genetic presentation of a pathogenic variant of the CYP1B1 gene through a report of a case of primary congenital glaucoma and a trio analysis of this candidate variant in the family with the sanger sequencing method and eventually completed our study with the secondary/incidental findings. This study reports a rare case of primary congenital glaucoma, an 8-year-old female child with a negative family history of glaucoma and uncontrolled intraocular pressure. This case’s whole-exome sequencing data analysis presents a homozygous pathogenic single nucleotide variant in the CYP1B1 gene (NM 000104:exon3:c.G1103A:p.R368H). At the same time, this pathogenic variant was obtained as a heterozygous state in her unaffected father but not her mother. The diagnosis was made based on molecular findings of whole-exome sequencing data analysis. Therefore, the clinical reports and bioinformatics findings supported the relation between the candidate pathogenic variant and the disease. However, it should not be forgotten that primary congenital glaucoma is not peculiar to the CYP1B1 gene. Since the chance of developing autosomal recessive disorders with low allele frequency and unrelated parents is extraordinary in offspring. However, further data analysis of whole-exome sequencing and sanger sequencing method were applied to obtain the type of mutation and how it was carried to the offspring.
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Affiliation(s)
| | - Morteza Bonyadi
- Department of Animal Sciences, University of Tabriz, Tabriz 5166-15731, Iran
| | - Zahra Abedi
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran 14155-6619, Iran
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2
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Zhang L, Hu Y, Lu J, Zhao P, Zhang X, Tan L, Li J, Xiao C, Zeng L, He X. Identification of the first congenital ichthyosis case caused by a homozygous deletion in the ALOX12B gene due to chromosome 17 mixed uniparental disomy. Front Genet 2022; 13:931833. [PMID: 36003334 PMCID: PMC9393266 DOI: 10.3389/fgene.2022.931833] [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: 04/29/2022] [Accepted: 06/27/2022] [Indexed: 11/18/2022] Open
Abstract
Uniparental disomy (UPD) is a rare genetic event caused by errors during gametogenesis and fertilization leading to two copies of a chromosome or chromosomal region inherited from one parent. MixUPD is one type of UPD that contains isodisomic and heterodisomic parts because of meiotic recombination. Using whole-exome sequencing (WES), we identified the first case of ichthyosis due to a maternal mixUPD on chromosome 17, which results in a homozygous deletion of partial intron 8 to exon 10 in ALOX12B, being predicted to lead to an internal protein deletion of 97 amino acids. We also performed a retrospective analysis of 198 patients with ALOX12B mutations. The results suggested that the exon 9 and 10 are located in the mutational hotspots of ALOX12B. In addition, our patient has microtia and congenital stenosis of the external auditory canals, which is very rare in patients with ALOX12B mutations. Our study reports the first case of autosomal recessive congenital ichthyosis (ARCI) due to a mixUPD of chromosome 17 and expands the spectrum of clinical manifestations of ARCI caused by mutations in the ALOX12B gene.
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Affiliation(s)
- Lei Zhang
- Precision Medical Center, Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Yanqiu Hu
- Precision Medical Center, Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Jingjing Lu
- Dermatology Department, Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Peiwei Zhao
- Precision Medical Center, Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Xiankai Zhang
- Precision Medical Center, Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Li Tan
- Precision Medical Center, Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Jun Li
- Otolaryngology Department, Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Cuiping Xiao
- Precision Medical Center, Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
- *Correspondence: Xuelian He, ; Cuiping Xiao, ; Linkong Zeng,
| | - Linkong Zeng
- Neonatology Department, Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
- *Correspondence: Xuelian He, ; Cuiping Xiao, ; Linkong Zeng,
| | - Xuelian He
- Precision Medical Center, Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
- *Correspondence: Xuelian He, ; Cuiping Xiao, ; Linkong Zeng,
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3
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Zhang Y, Zhang C, Shu JB, Zhang F. Atypical infantile-onset Pompe disease with good prognosis from mainland China: A case report. World J Clin Cases 2022; 10:3278-3283. [PMID: 35603335 PMCID: PMC9082720 DOI: 10.12998/wjcc.v10.i10.3278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 01/29/2022] [Accepted: 02/20/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Pompe disease has a broad disease spectrum, including infantile-onset Pompe disease (IOPD) and late-onset Pompe disease (LOPD) forms. It is a type of glycogen storage disorder belonging to autosomal recessive genetic disease, for an estimated incidence of 1/40000 among the neonatal population. In severe cases, the natural course is characterized by death due to cardiopulmonary failure in the first year after birth. However, the clinical outcomes have improved since the emergence of enzyme replacement therapy (ERT) was widely used. CASE SUMMARY The reported female case in China was an atypical IOPD, which demonstrates an unusual presentation of glycogen accumulation syndrome type II without obvious skeletal muscle involvement, and reviewed physical examination, biochemical examinations, chest radiograph, and acid α-glucosidase (GAA) mutation analysis. After 4-mo specific ERT, the case received 12-mo follow-up. Moreover, the patient has obtained a very good prognosis under ERT. CONCLUSION For the atypical IOPD patients, early diagnosis and treatment may contribute to good prognosis.
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Affiliation(s)
- Ying Zhang
- Department of Neonatal, Tianjin Children’s Hospital (Tianjin University Children's Hospital), Tianjin 300134, China
| | - Cheng Zhang
- Department of Neonatal, Tianjin Children’s Hospital (Tianjin University Children's Hospital), Tianjin 300134, China
| | - Jian-Bo Shu
- Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin Pediatric Research Institute, Tianjin Children’s Hospital (Tianjin University Children's Hospital), Tianjin 300134, China
| | - Fang Zhang
- Department of Neonatal, Tianjin Children’s Hospital (Tianjin University Children's Hospital), Tianjin 300134, China
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4
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de Faria DOS, 't Groen SLMI, Hoogeveen-Westerveld M, Nino MY, van der Ploeg AT, Bergsma AJ, Pijnappel WWMP. Update of the Pompe variant database for the prediction of clinical phenotypes: Novel disease-associated variants, common sequence variants, and results from newborn screening. Hum Mutat 2020; 42:119-134. [PMID: 33560568 PMCID: PMC7898817 DOI: 10.1002/humu.24148] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/06/2020] [Accepted: 11/30/2020] [Indexed: 12/16/2022]
Abstract
Pompe disease is an inherited disorder caused by disease-associated variants in the acid α-glucosidase gene (GAA). The Pompe disease GAA variant database (http://www.pompevariantdatabase.nl) is a curated, open-source, disease-specific database, and lists disease-associated GAA variants, in silico predictions, and clinical phenotypes reported until 2016. Here, we provide an update to include 226 disease-associated variants that were published until 2020. We also listed 148 common GAA sequence variants that do not cause Pompe disease. GAA variants with unknown severity that were identified only in newborn screening programs were listed as a new feature to indicate the reason why phenotypes were still unknown. Expression studies were performed for common missense variants to predict their severity. The updated Pompe disease GAA variant database now includes 648 disease-associated variants, 26 variants from newborn screening, and 237 variants with unknown severity. Regular updates of the Pompe disease GAA variant database will be required to improve genetic counseling and the study of genotype-phenotype relationships.
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Affiliation(s)
- Douglas O S de Faria
- Department of Pediatrics, Erasmus University Medical Center, Rotterdam, the Netherlands.,Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands.,Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Stijn L M In 't Groen
- Department of Pediatrics, Erasmus University Medical Center, Rotterdam, the Netherlands.,Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands.,Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, Rotterdam, the Netherlands
| | | | - Monica Y Nino
- Department of Pediatrics, Erasmus University Medical Center, Rotterdam, the Netherlands.,Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands.,Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Ans T van der Ploeg
- Department of Pediatrics, Erasmus University Medical Center, Rotterdam, the Netherlands.,Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Atze J Bergsma
- Department of Pediatrics, Erasmus University Medical Center, Rotterdam, the Netherlands.,Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands.,Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - W W M Pim Pijnappel
- Department of Pediatrics, Erasmus University Medical Center, Rotterdam, the Netherlands.,Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands.,Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, Rotterdam, the Netherlands
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5
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Katja K, Inga V, Ramona L, Almuth C, Maria MN. Mucopolysaccharidosis type I due to maternal uniparental disomy of chromosome 4 with partial isodisomy of 4p16.3p15.2. Mol Genet Metab Rep 2020; 25:100660. [PMID: 33117653 PMCID: PMC7582098 DOI: 10.1016/j.ymgmr.2020.100660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/06/2020] [Accepted: 10/06/2020] [Indexed: 12/27/2022] Open
Abstract
Mucopolysaccharidosis type I (MPS I) is a rare lysosomal storage disease caused by biallelic mutations in IDUA, the gene coding for the lysosomal enzyme alpha L-iduronidase. Clinically MPS I is a chronic progressive multisystem disease typically presenting with coarse facial features, skeletal deformities, joint contractures, and multi-organ involvement. Hurler syndrome (MPS IH) represents the severe end of the spectrum of mucopolysaccharidosis type I and is characterized by central nervous system involvement leading to childhood dementia. Here we report on a severe affected MPS IH patient who is homozygous for a splice site mutation (c.158 + 1G > A) in the IDUA gene. Further analyses revealed maternal uniparental disomy of chromosome 4 with partial isodisomy of the telomeric end of chromosome 4 (4.p16.3p15.2), representing an extraordinary mode of inheritance with a much lower re-occurrence risk for MPS I in the family.
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Affiliation(s)
- Kloth Katja
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Vater Inga
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Lindschau Ramona
- International Center for Lysosomal Disorders (ICLD), Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Caliebe Almuth
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Muschol Nicole Maria
- International Center for Lysosomal Disorders (ICLD), Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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6
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Zhang P, Wu B, Lu Y, Ni Q, Liu R, Zhou W, Wang H. First maternal uniparental disomy for chromosome 2 with PREPL novel frameshift mutation of congenital myasthenic syndrome 22 in an infant. Mol Genet Genomic Med 2020; 8:e1144. [PMID: 31985178 PMCID: PMC7057094 DOI: 10.1002/mgg3.1144] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/07/2020] [Indexed: 11/11/2022] Open
Abstract
Background Congenital myasthenic syndrome 22 (CMS22) is a rare autosomal recessive disorder due to isolated PREPL deficiency and characterized by neonatal hypotonia, muscular weakness, and feeding difficulties. Eight such cases have already been reported, while maternal uniparental disomy with a PREPL pathogenic mutation has never been involved. Methods Trio whole‐exome sequencing (WES), comparative genomic hybridization microarray (arry‐CGH), and Sanger sequencing were performed on a 6‐month‐old girl with severe neonatal hypotonia and feeding difficulties. Also, the phenotype and genotype of reported CMS22 patients were reviewed. Results In this female infant, we identified a novel homozygous frameshift mutation in PREPL (c.1282_1285delTTTG, p.Phe428Argfs*18) by trio‐WES. Sanger sequencing confirmed that her mother was heterozygous and her father was normal. Trio‐WES data showed that 96.70% (1668/1725) variants on chromosome 2 were homozygous and maternally inherited, suggesting maternal uniparental disomy of chromosome 2 [UPD(2)mat]. Array‐CGH did not show copy number variants (CNVs) but revealed complete UPD(2). Conclusion To date, nine patients with CMS22 have been reported including our patient, and we report the youngest and the first UPD(2)mat with PREPL novel homozygous pathogenic mutation case, which expand the mutation spectrum of PREPL gene.
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Affiliation(s)
- Ping Zhang
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai, China.,Key Laboratory of Birth Defects, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Bingbing Wu
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai, China.,Key Laboratory of Birth Defects, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Yulan Lu
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai, China.,Key Laboratory of Birth Defects, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Qi Ni
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai, China.,Key Laboratory of Birth Defects, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Renchao Liu
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai, China.,Key Laboratory of Birth Defects, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Wenhao Zhou
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai, China.,Key Laboratory of Birth Defects, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China.,Department of Neonates, Key Laboratory of Neonatal Diseases, Ministry of Health, Children's Hospital of Fudan University, Shanghai, China
| | - Huijun Wang
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai, China.,Key Laboratory of Birth Defects, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
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7
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In 't Groen SLM, de Faria DOS, Iuliano A, van den Hout JMP, Douben H, Dijkhuizen T, Cassiman D, Witters P, Barba Romero MÁ, de Klein A, Somers-Bolman GM, Saris JJ, Hoefsloot LH, van der Ploeg AT, Bergsma AJ, Pijnappel WWMP. Novel GAA Variants and Mosaicism in Pompe Disease Identified by Extended Analyses of Patients with an Incomplete DNA Diagnosis. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 17:337-348. [PMID: 32071926 PMCID: PMC7013133 DOI: 10.1016/j.omtm.2019.12.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 12/31/2019] [Indexed: 12/20/2022]
Abstract
Pompe disease is a metabolic disorder caused by a deficiency of the glycogen-hydrolyzing lysosomal enzyme acid α-glucosidase (GAA), which leads to progressive muscle wasting. This autosomal-recessive disorder is the result of disease-associated variants located in the GAA gene. In the present study, we performed extended molecular diagnostic analysis to identify novel disease-associated variants in six suspected Pompe patients from four different families for which conventional diagnostic assays were insufficient. Additional assays, such as a generic-splicing assay, minigene analysis, SNP array analysis, and targeted Sanger sequencing, allowed the identification of an exonic deletion, a promoter deletion, and a novel splicing variant located in the 5′ UTR. Furthermore, we describe the diagnostic process for an infantile patient with an atypical phenotype, consisting of left ventricular hypertrophy but no signs of muscle weakness or motor problems. This led to the identification of a genetic mosaicism for a very severe GAA variant caused by a segmental uniparental isodisomy (UPD). With this study, we aim to emphasize the need for additional analyses to detect new disease-associated GAA variants and non-Mendelian genotypes in Pompe disease where conventional DNA diagnostic assays are insufficient.
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Affiliation(s)
- Stijn L M In 't Groen
- Department of Pediatrics, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands.,Department of Clinical Genetics, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands.,Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands
| | - Douglas O S de Faria
- Department of Pediatrics, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands.,Department of Clinical Genetics, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands.,Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands
| | - Alessandro Iuliano
- Department of Pediatrics, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands.,Department of Clinical Genetics, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands.,Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands
| | - Johanna M P van den Hout
- Department of Pediatrics, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands.,Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands
| | - Hannie Douben
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands
| | - Trijnie Dijkhuizen
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, the Netherlands
| | - David Cassiman
- Center for Metabolic Diseases, UZ and KU Leuven, 3000 Leuven, Belgium
| | - Peter Witters
- Center for Metabolic Diseases, UZ and KU Leuven, 3000 Leuven, Belgium
| | | | - Annelies de Klein
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands
| | - Galhana M Somers-Bolman
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands
| | - Jasper J Saris
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands
| | - Lies H Hoefsloot
- Department of Clinical Genetics, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands
| | - Ans T van der Ploeg
- Department of Pediatrics, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands.,Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands
| | - Atze J Bergsma
- Department of Pediatrics, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands.,Department of Clinical Genetics, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands.,Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands
| | - W W M Pim Pijnappel
- Department of Pediatrics, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands.,Department of Clinical Genetics, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands.,Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands
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8
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Niño MY, In 't Groen SLM, Bergsma AJ, van der Beek NAME, Kroos M, Hoogeveen-Westerveld M, van der Ploeg AT, Pijnappel WWMP. Extension of the Pompe mutation database by linking disease-associated variants to clinical severity. Hum Mutat 2019; 40:1954-1967. [PMID: 31254424 PMCID: PMC6851659 DOI: 10.1002/humu.23854] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 06/17/2019] [Accepted: 06/22/2019] [Indexed: 12/20/2022]
Abstract
Pompe disease is an autosomal recessive lysosomal storage disorder caused by disease‐associated variants in the acid alpha‐glucosidase (GAA) gene. The current Pompe mutation database provides a severity rating of GAA variants based on in silico predictions and expression studies. Here, we extended the database with clinical information of reported phenotypes. We added additional in silico predictions for effects on splicing and protein function and for cross reactive immunologic material (CRIM) status, minor allele frequencies, and molecular analyses. We analyzed 867 patients and 562 GAA variants. Based on their combination with a GAA null allele (i.e., complete deficiency of GAA enzyme activity), 49% of the 422 disease‐associated variants could be linked to classic infantile, childhood, or adult phenotypes. Predictions and immunoblot analyses identified 131 CRIM negative and 216 CRIM positive variants. While disease‐associated missense variants were found throughout the GAA protein, they were enriched up to seven‐fold in the catalytic site. Fifteen percent of disease‐associated missense variants were predicted to affect splicing. This should be confirmed using splicing assays. Inclusion of clinical severity rating in the Pompe mutation database provides an invaluable tool for diagnosis, prognosis of disease progression, treatment regimens, and the future development of personalized medicine for Pompe disease.
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Affiliation(s)
- Monica Y Niño
- Department of Pediatrics, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands.,Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Stijn L M In 't Groen
- Department of Pediatrics, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands.,Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Atze J Bergsma
- Department of Pediatrics, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands.,Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Nadine A M E van der Beek
- Department of Pediatrics, Erasmus University Medical Center, Rotterdam, The Netherlands.,Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marian Kroos
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Ans T van der Ploeg
- Department of Pediatrics, Erasmus University Medical Center, Rotterdam, The Netherlands.,Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - W W M Pim Pijnappel
- Department of Pediatrics, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands.,Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
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