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Computational analysis for the determination of deleterious nsSNPs in human MTHFD1 gene |
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| Institution: | 1. Institute of Transfusion Medicine and Immunohaematology, DRK Blood Donor Service Baden-Württemberg – Hessen, University Hospital Frankfurt, Sandhofstr. 1, 60528 Frankfurt, Germany;2. Department of Internal Medicine, University Hospital Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany |
| Abstract: | Single nucleotide polymorphisms (SNPs) are the most common genetic polymorphisms and play a major role in many inherited diseases. Methylenetetrahydrofolate dehydrogenase 1 (MTHFD1) is one of the enzymes involved in folate metabolism. In the present study, the functional and structural consequences of nsSNPs of human MTHFD1 gene was analyzed using various computational tools like SIFT, PolyPhen2, PANTHER, PROVEAN, SNAP2, nsSNPAnalyzer, PhD-SNP, SNPs&GO, I-Mutant, MuPro, ConSurf, InterPro, NCBI Conserved Domain Search tool, ModPred, SPARKS-X, RAMPAGE, FT Site and PyMol. Out of 327 nsSNPs form human MTHFD1 gene, total 45 SNPs were predicted as functionally most significant SNPs, among which 17 were highly conserved and functional, 17 were highly conserved and structural residues. Among 45 most significant SNPs, 15 were predicted to be involved in post translational modifications. The p.Gly165Arg may interfere in homodimer interface formation. The p.Asn439Lys and p.Asp445Asn may interfere in binding interactions of MTHFD1 protein with cesium cation and potassium. The two SNPs (p.Asp562Gly and p.Gly637Cys) might interfere in interactions of MTHFD1 with ligand. |
| Keywords: | Single nucleotide polymorphisms Folate metabolism MTHFD15"} {"#name":"keyword" "$":{"id":"kw0030"} "$$":[{"#name":"text" "_":"10-methylenetetrahydrofolate dehydrogenase 1 SIFT"} {"#name":"keyword" "$":{"id":"kw0040"} "$$":[{"#name":"text" "_":"sorting intolerant from tolerant SNPs&GO"} {"#name":"keyword" "$":{"id":"kw0050"} "$$":[{"#name":"text" "_":"single nucleotide polymorphisms and gene ontology nsSNPs"} {"#name":"keyword" "$":{"id":"kw0060"} "$$":[{"#name":"text" "_":"non-synonymous single nucleotide polymorphism THF"} {"#name":"keyword" "$":{"id":"kw0070"} "$$":[{"#name":"text" "_":"tetrahydrofolate NCBI"} {"#name":"keyword" "$":{"id":"kw0080"} "$$":[{"#name":"text" "_":"National Center for Biological Information PROVEAN"} {"#name":"keyword" "$":{"id":"kw0090"} "$$":[{"#name":"text" "_":"protein variation effect analyzer OMIM"} {"#name":"keyword" "$":{"id":"kw0100"} "$$":[{"#name":"text" "_":"online mendelian inheritance in man PhD-SNP"} {"#name":"keyword" "$":{"id":"kw0110"} "$$":[{"#name":"text" "_":"predictor of human deleterious single nucleotide polymorphisms DDG"} {"#name":"keyword" "$":{"id":"kw0120"} "$$":[{"#name":"text" "_":"Gibbs free energy change RI"} {"#name":"keyword" "$":{"id":"kw0130"} "$$":[{"#name":"text" "_":"reliability index PANTHER"} {"#name":"keyword" "$":{"id":"kw0140"} "$$":[{"#name":"text" "_":"protein analysis through evolutionary relationships PSEP"} {"#name":"keyword" "$":{"id":"kw0150"} "$$":[{"#name":"text" "_":"position-specific evolutionary preservation PolyPhen"} {"#name":"keyword" "$":{"id":"kw0160"} "$$":[{"#name":"text" "_":"polymorphism phenotyping |
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