In silico Analysis of Non-Synonymous Single Nucleotide Polymorphisms (nsSNPs) in the SLC40A1 Gene Associated with Hemochromatosis Type 4
DOI:
https://doi.org/10.32350/bsr.83.03Keywords:
ferroportin (FPN), hemochromatosis type 4, In-silico analysis, non-synonymous single nucleotide polymorphisms (nsSNPs), protein modelling, SLC40A1Abstract
Background. Variants in SLC40A1, which encodes ferroportin (FPN), the only known mammalian cellular iron exporter, cause hemochromatosis type 4 (HH4), or ferroportin disease, a rare autosomal dominant disorder of iron metabolism. Non-synonymous single nucleotide polymorphisms (nsSNPs) in SLC40A1 may impair FPN folding, membrane localization, iron efflux or hepcidin responsiveness. Yet, researchers have not functionally annotated most catalogued variants. This in silico study systematically screened all coding-region nsSNPs of SLC40A1 using an integrated bioinformatics pipeline to priorities high-confidence deleterious candidates for experimental validation.
Methodology. The study retrieved 300 coding-region nsSNPs (RefSeq NM_014585.6; UniProt Q9NP59; dbSNP build 156) from NCBI dbSNP and Ensembl. Furthermore, the study assessed functional impact with PolyPhen-2, PROVEAN, SIFT and PhD-SNP; thermodynamic stability with I-Mutant 3.0 and MUpro; residue-level effects with Project HOPE; and secondary/tertiary structure with PSIPRED, I-TASSER and GalaxyRefine. We retained variants that all four functional predictors called deleterious and that at least one stability tool called destabilising.
Results. PolyPhen-2 classified 32.6% of nsSNPs as probably damaging, PROVEAN 33.6% as deleterious, SIFT 31.3% as not tolerated, and PhD-SNP 22.0% as disease-associated. I-Mutant 3.0 and MUpro predicted destabilisation for 32.3% and 33.7% of variants, respectively. Consensus filtering yielded 55 high-confidence deleterious nsSNPs; HOPE indicated that 38 substantially perturb FPN structure/function and 17 produced moderate effects. A total of 29 candidates corresponded to previously-reported variants; 26 were novel predictions.
Conclusion. The study concluded that 55 prioritized nsSNPs were computationally predicted candidates for experimental validation, not confirmed pathogenic mutations. Biochemical follow-up may accelerate genotype–phenotype understanding in this.
Highlights
- A total of 300 coding-region non-synonymous single nucleotide polymorphisms (nsSNPs) in SLC40A1 (ferroportin) were systematically screened in silico using four functional, two stability, and four structural prediction tools.
- Consensus-based filtering identified 55 high-confidence deleterious nsSNPs, comprising 29 previously reported variants and 26 novel predictions.
- Analysis using Project HOPE and I-TASSER indicated that 38 of the 55 prioritized variants may disrupt conserved transmembrane or functional domains of ferroportin.
- The prioritized variants were proposed as potential candidates for experimental validation through cellular iron-efflux and hepcidin-binding assays.
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