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Abosabie SAS, Abosabie SA, Alfaifi J, Alqahtani YA, Shati AA, Alotaibi NA, Alghamdi OA, Alotaibi GN, Baabdullah AA, Kabrah LK, Kamal NM, Oshi MAM, Abdallah EAA. Unraveling Alström syndrome: Homozygous mutation c.2729C>G in ALMS1 gene across an extended family. Mol Genet Genomic Med 2024; 12:e2314. [PMID: 37937857 PMCID: PMC10767606 DOI: 10.1002/mgg3.2314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 08/08/2023] [Accepted: 10/13/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND Alström syndrome (AS) represents an exceptionally rare genetic disorder characterized by a constellation of features including cardiomyopathy, progressive hearing and vision impairment, as well as obesity. This study seeks to elucidate the genetic underpinnings of this syndrome within the Saudi Arabian population. METHODS Employing an extended family cohort, we conducted an exhaustive molecular genetic assessment to delineate the presence of Alström syndrome. Additionally, we conducted an extensive review of existing literature from Saudi population to contextualize our findings within the broader understanding of the disorder in our country. RESULTS Within our studied extended family, we identified two individuals harboring the homozygous pathogenic mutation (c.2729C>G) in the ALMS1 gene [NM_015120.4:c.2729C>G (p.Ser910*)]. Notably, carrier status was observed in the parents, whereas some siblings exhibited typical alleles while others were carriers of the mutation. Intriguingly, a review of the literature unveiled six distinct reports documenting a total of 20 Alström syndrome patients within the Saudi Arabian population, each presenting with distinct novel mutations. CONCLUSIONS In cases featuring cardiomyopathy, obesity, and progressive hearing and vision loss, Alström syndrome merits inclusion within the differential diagnosis. To confirm the diagnosis, molecular genetic assessment of the ALMS1 gene is imperative, offering definitive clarity amidst the complex clinical presentation. This investigation reinforces the importance of genetic scrutiny for precise diagnosis and highlights the unique genetic landscape of Alström syndrome within the Saudi Arabian population.
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Affiliation(s)
| | - Sara A. Abosabie
- Faculty of MedicineCharité—Universitätsmedizin BerlinBerlinGermany
| | - Jaber Alfaifi
- Department of Child Health, College of MedicineUniversity of BishaBishaSaudi Arabia
| | - Youssef A. Alqahtani
- Department of Child Health, College of MedicineKing Khalid UniversityAbhaSaudi Arabia
| | - Ayed A. Shati
- Department of Child Health, College of MedicineKing Khalid UniversityAbhaSaudi Arabia
| | | | | | | | | | | | - Naglaa M. Kamal
- Department of Pediatrics and Pediatric Hepatology, Kasralainy Faculty of MedicineCairoEgypt
| | - Mohammed A. M. Oshi
- Departement of PediatricsGaafar Ibnauf Children's Emergency HospitalKhartoumSudan
| | - Enas A. A. Abdallah
- Department of Pediatrics and Pediatric Hepatology, Kasralainy Faculty of MedicineCairoEgypt
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Bea-Mascato B, Valverde D. Genotype-phenotype associations in Alström syndrome: a systematic review and meta-analysis. J Med Genet 2023; 61:18-26. [PMID: 37321834 PMCID: PMC10803979 DOI: 10.1136/jmg-2023-109175] [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: 01/20/2023] [Accepted: 05/29/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Alström syndrome (ALMS; #203800) is an ultrarare monogenic recessive disease. This syndrome is associated with variants in the ALMS1 gene, which encodes a centrosome-associated protein involved in the regulation of several ciliary and extraciliary processes, such as centrosome cohesion, apoptosis, cell cycle control and receptor trafficking. The type of variant associated with ALMS is mostly complete loss-of-function variants (97%) and they are mainly located in exons 8, 10 and 16 of the gene. Other studies in the literature have tried to establish a genotype-phenotype correlation in this syndrome with limited success. The difficulty in recruiting a large cohort in rare diseases is the main barrier to conducting this type of study. METHODS In this study we collected all cases of ALMS published to date. We created a database of patients who had a genetic diagnosis and an individualised clinical history. Lastly, we attempted to establish a genotype-phenotype correlation using the truncation site of the patient's longest allele as a grouping criteria. RESULTS We collected a total of 357 patients, of whom 227 had complete clinical information, complete genetic diagnosis and meta-information on sex and age. We have seen that there are five variants with high frequency, with p.(Arg2722Ter) being the most common variant, with 28 alleles. No gender differences in disease progression were detected. Finally, truncating variants in exon 10 seem to be correlated with a higher prevalence of liver disorders in patients with ALMS. CONCLUSION Pathogenic variants in exon 10 of the ALMS1 gene were associated with a higher prevalence of liver disease. However, the location of the variant in the ALMS1 gene does not have a major impact on the phenotype developed by the patient.
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Affiliation(s)
- Brais Bea-Mascato
- CINBIO, Universidad de Vigo, 36310 Vigo, Spain
- Grupo de Investigación en Enfermedades Raras y Medicina Pediátrica, Instituto de Investigación Sanitaria Galicia Sur (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Diana Valverde
- CINBIO, Universidad de Vigo, 36310 Vigo, Spain
- Grupo de Investigación en Enfermedades Raras y Medicina Pediátrica, Instituto de Investigación Sanitaria Galicia Sur (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
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3
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Chu G, Li P, Zhao Q, He R, Zhao Y. Mutation spectrum of Kallmann syndrome: identification of five novel mutations across ANOS1 and FGFR1. Reprod Biol Endocrinol 2023; 21:23. [PMID: 36859276 PMCID: PMC9976430 DOI: 10.1186/s12958-023-01074-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 02/14/2023] [Indexed: 03/03/2023] Open
Abstract
BACKGROUND Kallmann syndrome (KS) is a common type of idiopathic hypogonadotropic hypogonadism. To date, more than 30 genes including ANOS1 and FGFR1 have been identified in different genetic models of KS without affirmatory genotype-phenotype correlation, and novel mutations have been found. METHODS A total of 35 unrelated patients with clinical features of disorder of sex development were recruited. Custom-panel sequencing or whole-exome sequencing was performed to detect the pathogenic mutations. Sanger sequencing was performed to verify single-nucleotide variants. Copy number variation-sequencing (CNV-seq) was performed to determine CNVs. The pathogenicity of the identified variant was predicted in silico. mRNA transcript analysis and minigene reporter assay were performed to test the effect of the mutation on splicing. RESULTS ANOS1 gene c.709 T > A and c.711 G > T were evaluated as pathogenic by several commonly used software, and c.1063-2 A > T was verified by transcriptional splicing assay. The c.1063-2 A > T mutation activated a cryptic splice acceptor site downstream of the original splice acceptor site and resulted in an aberrant splicing of the 24-basepair at the 5' end of exon 8, yielding a new transcript with c.1063-1086 deletion. FRFR1 gene c.1835delA was assessed as pathogenic according to the ACMG guideline. The CNV of del(8)(p12p11.22)chr8:g.36140000_38460000del was judged as pathogenic according to the ACMG & ClinGen technical standards. CONCLUSIONS Herein, we identified three novel ANOS1 mutations and two novel FGFR1 variations in Chinese KS families. In silico prediction and functional experiment evaluated the pathogenesis of ANOS1 mutations. FRFR1 c.1835delA mutation and del(8)(p12p11.22)chr8:g.36140000_38460000del were assessed as pathogenic variations. Therefore, our study expands the spectrum of mutations associated with KS and provides diagnostic evidence for patients who carry the same mutation in the future.
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Affiliation(s)
- Guoming Chu
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, China
| | - Pingping Li
- Center of Reproductive Medicine, Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, China
| | - Qian Zhao
- Department of Pediatric Urology, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, China
| | - Rong He
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, China
| | - Yanyan Zhao
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, China.
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4
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Biji IK, Yadav S, Kulshrestha S, Saxena R, Kohli S, Verma IC, Kumar B, Puri RD. Computational biology insights into genotype-clinical phenotype-protein phenotype relationships between novel SLC26A2 variants identified in inherited skeletal dysplasias. Eur J Med Genet 2022; 65:104595. [PMID: 36007841 DOI: 10.1016/j.ejmg.2022.104595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 07/13/2022] [Accepted: 08/17/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND Pathogenic variants in the transmembrane sulfate transporter protein SLC26A2 are associated with different phenotypes of inherited chondrodysplasias. As limited data is published from India, in this study we sought to elucidate the molecular basis of inherited chondrodysplasias in an Indian cohort. METHODS Molecular screening of 32 fetuses with antenatally diagnosed lethal skeletal dysplasia was performed by next generation sequencing and Sanger sequencing. The genotype-protein phenotype characterization was done using computational biology techniques like homology modelling, stability and pathogenicity predictions. RESULTS We identified five rare autosomal recessive SLC26A2 [NM_000112.4] variants, including three homozygous c.796dupA(p.Thr266Asnfs*12), c.1724delA(p.Lys575Serfs*10), and c.1375_1377dup(p.Val459dup) and two heterozygous variants (c.532C > T(p.Arg178*)) and (c.1382C > T(p.Ala461Val)) in compound heterozygous form in a total of four foetuses. Genotype-protein phenotype annotations highlighted that the clinically severe achondrogenesis 1B causative c.796dupA(p.Thr266Asnfs*12) and c.1724delA(p.Lys575Serfs*10)variants impact SLC26A2 protein structure by deletion of the protein core and transmembrane STAS domains, respectively. In clinically moderate atelosteogenesis type 2 phenotype, the c.1382C > T(p.Ala461Val) variant is predicted to distort alpha helix conformation and alter the bonding properties and free energy dynamics of transmembrane domains and the c.532C > T(p.Arg178*) variant results in loss of both core transmembrane and STAS domains of the SLC26A2 protein. The c.1375_1377dup(p.Val459dup) variant identified in clinically milder atelosteogenesis type II-diastrophic dysplasia spectrum lethal phenotype is predicted to decrease the Qualitative Model Energy Analysis (QMean), which affects major geometrical aspects of the SLC26A2 protein structure. CONCLUSION We expand the spectrum of SLC26A2 related lethal chondrodysplasia and report three novel variants correlating clinical severity and protein phenotype within the lethal spectrum of this rare dysplasia. We demonstrate the relevance of structural characterization to aid novel variant reclassification to provide better prenatal management and reproductive options to families with lethal antenatal skeletal disorder.
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Affiliation(s)
- Ishpreet K Biji
- Institute of Medical Genetics & Genomics, Sir Ganga Ram Hospital, Delhi, 110060, India; Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, 201313, India
| | - Siddharth Yadav
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, 201313, India
| | - Samarth Kulshrestha
- Institute of Medical Genetics & Genomics, Sir Ganga Ram Hospital, Delhi, 110060, India
| | - Renu Saxena
- Institute of Medical Genetics & Genomics, Sir Ganga Ram Hospital, Delhi, 110060, India
| | - Sudha Kohli
- Institute of Medical Genetics & Genomics, Sir Ganga Ram Hospital, Delhi, 110060, India
| | - I C Verma
- Institute of Medical Genetics & Genomics, Sir Ganga Ram Hospital, Delhi, 110060, India
| | - Benu Kumar
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, 201313, India
| | - Ratna Dua Puri
- Institute of Medical Genetics & Genomics, Sir Ganga Ram Hospital, Delhi, 110060, India.
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5
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Alaifan MA, Abusharifah O, Bokhary RY, Banaganapalli B, Shaik NA, Kamal NM, Saadah OI. Granulomatous hepatitis in a Saudi child with IL2RA defect: a case report and literature review. Ther Adv Chronic Dis 2022; 13:20406223221116798. [PMID: 35968218 PMCID: PMC9373126 DOI: 10.1177/20406223221116798] [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: 12/18/2021] [Accepted: 06/30/2022] [Indexed: 11/17/2022] Open
Abstract
Interleukin-2 receptor alpha (IL2RA) defect (OMIM- # 606367) is an immune disease where affected patients are vulnerable to developing recurrent microbial infections in addition to lymphadenopathy and dermatological manifestations. This condition is known to be caused by pathogenic variants in the IL2RA gene, which are inherited in an autosomal recessive fashion. In this case report, we present a patient with IL2RA defect from Saudi Arabia who presented with chronic diarrhea, poor weight gain, mild villous atrophy, malnutrition, hepatomegaly, nonspecific inflammation, and an eczematous skin rash. His genetic analysis revealed a novel, homozygous, and likely pathogenic variant, that is, c.504 C>A (Cys168Ter), located in the exon 4of the IL2RA gene, which was inherited from his parents in an autosomal recessive mode of inheritance. This variant produces a 272-amino-acid shorter IL2RA protein chain, which most likely becomes degraded in the cytosol. Thus, we assume that the c.504 C>A is a null allele that abolishes the synthesis of IL2RA, malforms the IL-2 receptor complex, and eventually causes immunodeficiency manifestations. To our knowledge, this is the first time a person with IL2RA defect has shown signs of granulomatous hepatitis on a liver biopsy.
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Affiliation(s)
- Meshari A Alaifan
- Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ohood Abusharifah
- Department of Pediatrics, Maternity and Children Hospital Abha, Abha, Saudi Arabia
| | - Rana Yagoub Bokhary
- Department of Pathology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Babajan Banaganapalli
- Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Noor Ahmad Shaik
- Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Naglaa M Kamal
- Department of Pediatrics, Kasr Alainy Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Omar I Saadah
- Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, P.O. Box 80205, Jeddah 21589, Saudi Arabia
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6
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Borgio JF. Heterogeneity in biomarkers, mitogenome and genetic disorders of the Arab population with special emphasis on large-scale whole-exome sequencing. Arch Med Sci 2021; 19:765-783. [PMID: 37313193 PMCID: PMC10259412 DOI: 10.5114/aoms/145370] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/27/2021] [Indexed: 09/20/2024] Open
Abstract
More than 25 million DNA variations have been discovered as novel including major alleles from the Arab population. Exome studies on the Saudi genome discovered > 3000 novel nucleotide variants associated with > 1200 rare genetic disorders. Reclassification of many pathogenic variants in the Human Gene Mutation Database and ClinVar Database as benign through the Arab database facilitates building a detailed and comprehensive map of the human morbid genome. Intellectual disability comes first with the combined and observed carrier frequency of 0.06779 among Saudi Arabians; retinal dystrophy is the next highest. Genome studies have discovered interesting novel candidate disease marker variations in many genes from consanguineous families. More than 7 pathogenic variants in the C12orf57 gene are prominently associated with the etiology of developmental delay/intellectual impairment in Arab ancestries. Advances in large-scale genome studies open a new outlook on Mendelian genes and disorders. In the past half-dozen years, candidate genes of intellectual disability, neurogenetic disorders, blood and bleeding disorders and rare genetic diseases have been well documented through genomic medicine studies in combination with advanced computational biology applications. The Arab mitogenome exposed hundreds of variations in the mtDNA genome and ancestral sharing with Africa, the Near East and East Asia and its association with obesity. These recent discoveries in disease markers and molecular genetics of the Arab population will have a positive impact towards supporting genetic counsellors on reaching consanguineous families to manage stress linked to genetics and precision medicine. This narrative review summarizes the advances in molecular medical genetics and recent discoveries on pathogenic variants. Despite the fact that these initiatives are targeting the genetics and genomics of disorders prevalent in Arab populations, a lack of complete cooperation across the projects needed to be revisited to uncover the Arab population's prominent disease markers. This shows that further study is needed in genomics to fully comprehend the molecular abnormalities and associated pathogenesis that cause inherited disorders in Arab ancestries.
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Affiliation(s)
- J Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
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7
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Alsafwani RS, Nasser KK, Shinawi T, Banaganapalli B, ElSokary HA, Zaher ZF, Shaik NA, Abdelmohsen G, Al-Aama JY, Shapiro AJ, O Al-Radi O, Elango R, Alahmadi T. Novel MYO1D Missense Variant Identified Through Whole Exome Sequencing and Computational Biology Analysis Expands the Spectrum of Causal Genes of Laterality Defects. Front Med (Lausanne) 2021; 8:724826. [PMID: 34589502 PMCID: PMC8473696 DOI: 10.3389/fmed.2021.724826] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/10/2021] [Indexed: 11/13/2022] Open
Abstract
Laterality defects (LDs) or asymmetrically positioned organs are a group of rare developmental disorders caused by environmental and/or genetic factors. However, the exact molecular pathophysiology of LD is not yet fully characterised. In this context, studying Arab population presents an ideal opportunity to discover the novel molecular basis of diseases owing to the high rate of consanguinity and genetic disorders. Therefore, in the present study, we studied the molecular basis of LD in Arab patients, using next-generation sequencing method. We discovered an extremely rare novel missense variant in MYO1D gene (Pro765Ser) presenting with visceral heterotaxy and left isomerism with polysplenia syndrome. The proband in this index family has inherited this homozygous variant from her heterozygous parents following the autosomal recessive pattern. This is the first report to show MYO1D genetic variant causing left-right axis defects in humans, besides previous known evidence from zebrafish, frog and Drosophila models. Moreover, our multilevel bioinformatics-based structural (protein variant structural modelling, divergence, and stability) analysis has suggested that Ser765 causes minor structural drifts and stability changes, potentially affecting the biophysical and functional properties of MYO1D protein like calmodulin binding and microfilament motor activities. Functional bioinformatics analysis has shown that MYO1D is ubiquitously expressed across several human tissues and is reported to induce severe phenotypes in knockout mouse models. In conclusion, our findings show the expanded genetic spectrum of LD, which could potentially pave way for the novel drug target identification and development of personalised medicine for high-risk families.
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Affiliation(s)
- Rabab Said Alsafwani
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Khalidah K Nasser
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.,Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Thoraia Shinawi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Babajan Banaganapalli
- Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hanan Abdelhalim ElSokary
- Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Zhaher F Zaher
- Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia.,Pediatric Cardiac Center of Excellence, King Abdulaziz University Hospital, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Noor Ahmad Shaik
- Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Genetics, Al Borg Medical Laboratories, Jeddah, Saudi Arabia
| | - Gaser Abdelmohsen
- Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia.,Pediatric Cardiology Division, Department of Pediatrics, Cairo University, Kasr Al Ainy Faculty of Medicine, Cairo, Egypt
| | - Jumana Yousuf Al-Aama
- Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Adam J Shapiro
- Division of Pediatric Respiratory Medicine, McGill University Health Centre Research Institute, Montreal Children's Hospital, Montreal, QC, Canada
| | - Osman O Al-Radi
- Department of Surgery Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ramu Elango
- Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Turki Alahmadi
- Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia.,Pediatric Department, Faculty of Medicine in Rabigh, King Abdulaziz University, Jeddah, Saudi Arabia
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