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Integrative in silico analysis identifies functionally and regulatively relevant nsSNPs in the TRIB3 gene
Mona M Almramhi1, Sereen Y Alsubhi2, Bdoor M Alzahrani2
1Faculty of Applied Medical Sciences, Department of Medical Laboratory Sciences, King Abdulaziz University, Jeddah, Saudi Arabia; Editome: Precision Gene Editing Unit, King Fahad Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London, London, UK.
Background:
To date, a single missense variant (Q84R) in TRIB3 (Tribbles pseudokinase 3) has been experimentally characterised. Hence, the functional relevance of the vast majority of reported TRIB3 nonsynonymous single-nucleotide polymorphisms (nsSNPs) remains largely unexplored.
Method:
We conducted a multi-layered in silico analysis to prioritise TRIB3 nsSNPs with the highest likelihood of disrupting protein structure, stability, and function. A total of 366 TRIB3 nsSNPs was retrieved from public databases and initially screened using SIFT, PolyPhen-2, SNAP, and PhD-SNP, followed by a stringent consensus-based filtering strategy. Subsequently, we evaluated the potential effects of the prioritised nsSNPs on TRIB3 protein structure and function using PANTHER, SNPs&GO, Jalview, HOPE, I-Mutant, MUpro, MEDUSA, and MutPred2. Finally, we examined tissue-specific expression, interaction networks, and regulatory annotations using GTEx, GeneMANIA, STRING, HaploReg, and the Metabolic Disease Knowledge Portal (CMDKP).
Results:
Twelve high-confidence deleterious nsSNPs were consistently predicted and evaluated by all the tools used, namely, rs1242438181 (G69R), rs1016761523 (G69V), rs534352037 (Y71C), rs376597508 (M144K), rs1164746151 (F163S), rs2014979681 (C173R), rs149447454 (R181C), rs1445306127 (R181H), rs1411860615 (K184R), rs139447354 (R303W), rs201359012 (R303Q), and rs766581672 (W314R).
Conclusion:
Our integrative in silico approach identifies 12 high-risk TRIB3 missense variants that may contribute to metabolic dysfunction and provide a focused set of candidates for future functional and experimental validation.
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