CoagVDb: a comprehensive database for coagulation factors and their associated SAPs

Area of Science:

• Medical Genetics
• Bioinformatics
• Hematology

Background:

• Accurate classification of single amino acid substitutions (SAPs), also known as non-synonymous SNPs (nsSNPs), is crucial in medical genetics.
• Understanding the functional impact of SAPs is key to elucidating disease mechanisms and complex phenotypes.
• The coagulation cascade pathway is vital for maintaining human homeostasis, making its variations significant.

Purpose of the Study:

• To develop an integrated database, CoagVDb, for comprehensive analysis of variations in coagulation factors.
• To classify single amino acid substitutions as deleterious or tolerated using integrated computational predictions and biological data.
• To provide a valuable resource for hematologists to explore protein structure-function relationships and genotype-phenotype correlations.

Main Methods:

• Integrated data from public databases (NCBI, OMIM, UniProt, PDB) and SAP information.
• Incorporated computational prediction scores to classify SAPs.
• Included diverse properties: amino acid composition, secondary structure, solvent accessibility, disorder, conservation, and disulfide bonds.

Main Results:

• Developed CoagVDb, an integrated database for coagulation factor variations.
• Classified SAPs using combined computational predictions and biological attributes.
• Enriched the database with gene, protein, and disease information.

Conclusions:

• CoagVDb serves as a specialized reference resource for hematologists.
• The database facilitates the study of protein structure-function relationships in coagulation.
• It aids in understanding disease genotype-phenotype correlations related to coagulation factor variations.