Determination of damaging SNP’s in SHANK3 gene with in silico methods
Abstract Background Asperger's syndrome, autism, and other neurodevelopmental diseases are all included under the general term autism spectrum disorder. The SHANK3 gene has a significant role in autism spectrum disorder; mutations in this gene are seen in roughly 1–2% of patients with both auti...
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| Format: | Article |
| Language: | English |
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SpringerOpen
2025-02-01
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| Series: | Egyptian Journal of Medical Human Genetics |
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| Online Access: | https://doi.org/10.1186/s43042-025-00642-6 |
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| author | İrem Gülfem Albayrak Şeyma Yektar Süeda Kaya |
| author_facet | İrem Gülfem Albayrak Şeyma Yektar Süeda Kaya |
| author_sort | İrem Gülfem Albayrak |
| collection | DOAJ |
| description | Abstract Background Asperger's syndrome, autism, and other neurodevelopmental diseases are all included under the general term autism spectrum disorder. The SHANK3 gene has a significant role in autism spectrum disorder; mutations in this gene are seen in roughly 1–2% of patients with both autism and intellectual disability. This genetic association provides insight concerning SHANK3's potential significance in the disorder's development. There is considerable evidence associating SHANK3 mutations to autism spectrum disorder; hence, it is worthwhile to investigate the underlying molecular genetic mechanisms of the disease. Results This research uses in silico approaches such as SIFT, PolyPhen-2, I-Mutant 2.0, and Project HOPE to find harmful SNPs, which are the single nucleotide polymorphisms the most prevalent types of genetic variation in humans, in the SHANK3 gene. After the analysis, from the NCBI dbSNP database, 1535 missense SNPs in the SHANK3 gene were identified, with 54 classified as deleterious. Among these, 30 SNPs were confirmed damaging by both SIFT and PolyPhen-2, and 28 led to increased protein stability while two decreased it. In the presented research, effects on protein structure of this SNPs are discussed. Conclusions This in silico study improves our understanding of the complicated molecular changes associated with the SHANK3 gene and contributes to a more comprehensive understanding of the genetic landscape. By deepening our knowledge of the genetic basis and molecular pathways linked to SHANK3 mutations, our findings may offer direction for focused experimental validations and treatment strategies for autism spectrum disorder. |
| format | Article |
| id | doaj-art-c7b58e175d324d5085619473d9cc89f2 |
| institution | Kabale University |
| issn | 2090-2441 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | SpringerOpen |
| record_format | Article |
| series | Egyptian Journal of Medical Human Genetics |
| spelling | doaj-art-c7b58e175d324d5085619473d9cc89f22025-02-09T12:40:08ZengSpringerOpenEgyptian Journal of Medical Human Genetics2090-24412025-02-012611910.1186/s43042-025-00642-6Determination of damaging SNP’s in SHANK3 gene with in silico methodsİrem Gülfem Albayrak0Şeyma Yektar1Süeda Kaya2Department of Molecular Biology and Genetics, Faculty of Engineering and Natural Sciences, Uskudar UniversityDepartment of Software Engineering, Faculty of Engineering and Natural Sciences, Uskudar UniversityDepartment of Software Engineering, Faculty of Engineering and Natural Sciences, Uskudar UniversityAbstract Background Asperger's syndrome, autism, and other neurodevelopmental diseases are all included under the general term autism spectrum disorder. The SHANK3 gene has a significant role in autism spectrum disorder; mutations in this gene are seen in roughly 1–2% of patients with both autism and intellectual disability. This genetic association provides insight concerning SHANK3's potential significance in the disorder's development. There is considerable evidence associating SHANK3 mutations to autism spectrum disorder; hence, it is worthwhile to investigate the underlying molecular genetic mechanisms of the disease. Results This research uses in silico approaches such as SIFT, PolyPhen-2, I-Mutant 2.0, and Project HOPE to find harmful SNPs, which are the single nucleotide polymorphisms the most prevalent types of genetic variation in humans, in the SHANK3 gene. After the analysis, from the NCBI dbSNP database, 1535 missense SNPs in the SHANK3 gene were identified, with 54 classified as deleterious. Among these, 30 SNPs were confirmed damaging by both SIFT and PolyPhen-2, and 28 led to increased protein stability while two decreased it. In the presented research, effects on protein structure of this SNPs are discussed. Conclusions This in silico study improves our understanding of the complicated molecular changes associated with the SHANK3 gene and contributes to a more comprehensive understanding of the genetic landscape. By deepening our knowledge of the genetic basis and molecular pathways linked to SHANK3 mutations, our findings may offer direction for focused experimental validations and treatment strategies for autism spectrum disorder.https://doi.org/10.1186/s43042-025-00642-6Autism Spectrum DisorderPolymorphismSHANK3 |
| spellingShingle | İrem Gülfem Albayrak Şeyma Yektar Süeda Kaya Determination of damaging SNP’s in SHANK3 gene with in silico methods Egyptian Journal of Medical Human Genetics Autism Spectrum Disorder Polymorphism SHANK3 |
| title | Determination of damaging SNP’s in SHANK3 gene with in silico methods |
| title_full | Determination of damaging SNP’s in SHANK3 gene with in silico methods |
| title_fullStr | Determination of damaging SNP’s in SHANK3 gene with in silico methods |
| title_full_unstemmed | Determination of damaging SNP’s in SHANK3 gene with in silico methods |
| title_short | Determination of damaging SNP’s in SHANK3 gene with in silico methods |
| title_sort | determination of damaging snp s in shank3 gene with in silico methods |
| topic | Autism Spectrum Disorder Polymorphism SHANK3 |
| url | https://doi.org/10.1186/s43042-025-00642-6 |
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