Assessing the Functional Properties of the TMCO1 Sequence Variants by Using In Silico Analyses

Dilek Pirim; Erva Ulusoy; Zeynep Kurt; Niyazi Kaya; Elif Uz-yıldırım

doi:10.29130/dubited.571528

TR EN

TMCO1 Gen Sekans Varyanlatlarının Fonksiyonel Özelliklerinin In Silico Analizlerlerle Değerlendirilmesi

Abstract

Transmembran and Coiled-Coil Domains 1 (TMCO1) proteini, TMCO1 geni tarafından kodlanır ve 7 ekzondan oluşur. Önceki çalışmalar serebrofasiotorasik displazili (SFTD) hastalarda çok sayıda TMCO1 varyantı tanımlamış ve TMCO1 lokusunun primer açık açılı glokom hastalığı ile (PAAG) ilişkili olduğunu göstermiştir. Bununla birlikte TMCO1 gen sekansı varyantlarının ilişkilerini bildiren sınırlı sayıda araştırma vardır ve elde edilen bulguların çoğu anlamsız mutasyonlar ve çerçeve kayması mutasyonlarının TMCO1 varyantlarının patojenliğini ve klinik fenotiplerle ilişkilerini belirtmektedir. Bu nedenle, TMCO1'de aminoasit değişikliklerine neden olan tek nükleotid varyantlarının fonksiyonel özellikleri henüz tam olarak açıklanamamıştır. Bu çalışmada aminoasit değişikliklerinin protein yapısı üzerindeki etkilerini, post-translasyon modifikasyonlardaki (PTM) ve TMCO1 proteini için düzenleyici mekanizmadaki olası rollerini belirledik. Yaygın olarak kullanılan in silico araçları (SIFT, MutationTaster2, Polyphen2) ile yaptığımız analizin değerlendirmesine göre 41 adet yanlış anlamlı mutasyon barındıran varyantı patojenik olarak sınıflandırdık. Bu 41 varyanttan dördü (p.K211Q, p.K105E, p.S235F, p.K237R) PTM ve düzenleyici protein bağlama bölgelerinde yer almaktadır, bu nedenle bu varyantların fonksiyon üzerinde etkili olduğunu düşündük. Bununla birlikte, rs1387528611 (s.Lys128Gln) varyantının (RegulomeDB skoru= 2b) düzenleyici varyant olabileceğine dair güçlü biyolojik kanıtlar olduğunu saptadık. In silico analizlerimizin sonuçları, TMCO1 ile ilişkili hastalık fenotiplerine katkıda bulunabilecek yanlış anlamlı TMCO1 varyantların fonksiyonel önemini ve insan hastalıklarındaki rollerini ortaya çıkarmak için in vivo değerlendirmenin işlevsel önemini vurgulamaktadır.

Keywords

TMCO1,Serebrofasiyotorasik displazi,RegulomeDB,SNV,Post-translasyonel modifikasyonlar,in silico analiz

Assessing the Functional Properties of the TMCO1 Sequence Variants by Using In Silico Analyses

Abstract

Transmembrane and Coiled-Coil Domains 1 (TMCO1) protein is encoded by TMCO1 gene consists of 7 exons. Previous studies have identified multiple TMCO1 variants in patients with cerebro-facio-thoracic dysplasia (CFTD) and TMCO1 locus was also shown to be associated with primary open angle glaucoma (POAG). However, there are limited number of research exist reporting associations of the TMCO1 gene sequence variants and majority of the findings affirm the pathogenicity of the nonsense and frameshift TMCO1 variants and their associations with clinical phenotypes. Thus functional properties of the single nucleotide variants causing amino acid changes in the TMCO1 are yet to be comprehensively elucidated. In this study, we evaluated the effects of amino acid substitutions on protein structure, identified their putative roles in post-translational modifications (PTM) and in regulatory mechanism for TMCO1 protein. We classified 41 missense variants as pathogenic based on combined scores of common in silico tools (SIFT, MutationTaster2, Polyphen2). Of these 41 variants, four (p.K211Q, p.K105E, p.S235F, p.K237R) were identified to be located in PTMs and regulatory protein binding sites; thus they were proposed to be putative functional variants. Moreover, rs1387528611 (p.Lys128Gln) had also strong evidence (RegulomeDB score=2b) for its possible regulatory function. The results of our in silico analyses highlight the functional importance of the missense TMCO1 variants that may contribute to the TMCO1-associated disease phenotypes and further in vivo evaluation yet to be needed to uncover their role in human diseases.

Keywords

TMCO1,Cerebro-facio-thoracic dysplasia,RegulomeDB,SNV,post-translational modifications,in silico analyses

References

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Primary Language

English

Subjects

Engineering

Journal Section

Research Article

Authors

Dilek Pirim ^*
0000-0002-0522-9432
Türkiye

Erva Ulusoy This is me
0000-0002-2643-0362

Zeynep Kurt
0000-0003-2466-2335

Niyazi Kaya
0000-0002-5122-3824

Elif Uz-yıldırım ^* This is me
0000-0002-1459-5485
Türkiye

Publication Date

July 31, 2019

Submission Date

May 30, 2019

Acceptance Date

June 24, 2019

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Year 2019 Volume: 7 Number: 3

DOI

https://doi.org/10.29130/dubited.571528

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https://izlik.org/JA96NS93GC

APA

Pirim, D., Ulusoy, E., Kurt, Z., Kaya, N., & Uz-yıldırım, E. (2019). Assessing the Functional Properties of the TMCO1 Sequence Variants by Using In Silico Analyses. Duzce University Journal of Science and Technology, 7(3), 1931-1946. https://doi.org/10.29130/dubited.571528

AMA

1.Pirim D, Ulusoy E, Kurt Z, Kaya N, Uz-yıldırım E. Assessing the Functional Properties of the TMCO1 Sequence Variants by Using In Silico Analyses. DUBİTED. 2019;7(3):1931-1946. doi:10.29130/dubited.571528

Chicago

Pirim, Dilek, Erva Ulusoy, Zeynep Kurt, Niyazi Kaya, and Elif Uz-yıldırım. 2019. “Assessing the Functional Properties of the TMCO1 Sequence Variants by Using In Silico Analyses”. Duzce University Journal of Science and Technology 7 (3): 1931-46. https://doi.org/10.29130/dubited.571528.

EndNote

Pirim D, Ulusoy E, Kurt Z, Kaya N, Uz-yıldırım E (July 1, 2019) Assessing the Functional Properties of the TMCO1 Sequence Variants by Using In Silico Analyses. Duzce University Journal of Science and Technology 7 3 1931–1946.

IEEE

[1]D. Pirim, E. Ulusoy, Z. Kurt, N. Kaya, and E. Uz-yıldırım, “Assessing the Functional Properties of the TMCO1 Sequence Variants by Using In Silico Analyses”, DUBİTED, vol. 7, no. 3, pp. 1931–1946, July 2019, doi: 10.29130/dubited.571528.

ISNAD

Pirim, Dilek - Ulusoy, Erva - Kurt, Zeynep - Kaya, Niyazi - Uz-yıldırım, Elif. “Assessing the Functional Properties of the TMCO1 Sequence Variants by Using In Silico Analyses”. Duzce University Journal of Science and Technology 7/3 (July 1, 2019): 1931-1946. https://doi.org/10.29130/dubited.571528.

JAMA

1.Pirim D, Ulusoy E, Kurt Z, Kaya N, Uz-yıldırım E. Assessing the Functional Properties of the TMCO1 Sequence Variants by Using In Silico Analyses. DUBİTED. 2019;7:1931–1946.

MLA

Pirim, Dilek, et al. “Assessing the Functional Properties of the TMCO1 Sequence Variants by Using In Silico Analyses”. Duzce University Journal of Science and Technology, vol. 7, no. 3, July 2019, pp. 1931-46, doi:10.29130/dubited.571528.

Vancouver

1.Dilek Pirim, Erva Ulusoy, Zeynep Kurt, Niyazi Kaya, Elif Uz-yıldırım. Assessing the Functional Properties of the TMCO1 Sequence Variants by Using In Silico Analyses. DUBİTED. 2019 Jul. 1;7(3):1931-46. doi:10.29130/dubited.571528

TMCO1 Gen Sekans Varyanlatlarının Fonksiyonel Özelliklerinin In Silico Analizlerlerle Değerlendirilmesi

Abstract

Keywords

Assessing the Functional Properties of the TMCO1 Sequence Variants by Using In Silico Analyses

Abstract

Keywords

References

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Acceptance Date

Published in Issue

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