Research Article
Computational Methods to Work as First-Pass Filter in Deleterious SNP Analysis of Alkaptonuria
Table 2
List of SNPs that were predicted to be functional significance by FASTSNP.
| | SNPs ID | Allele frequency and change | Region | Possible functional effect | Ranking and Level of risk |
| | rs7652072 | A/G (No frequency) | Intron | Splicing site | 3-4 (Medium to high) | | rs55661952 | C/T (No frequency) | 5′UTR (−201A>G) | Promoter/regulatory region | 1–3 (Low to medium) | | rs2733829 | C/T (No frequency) | 5′UTR (−339C>T) | Promoter/regulatory region | 1–3 (Low to medium) | | rs28942100 | C/T (No frequency) | nsSNP (P230S) | Missense (conservative) | 2-3 (Low to medium) | | rs28941783 | A(0.000)/G(1.000) | nsSNP (G161R) | Missense (conservative); Splicing regulation | 2-3 (Low to medium) | | rs35702995 | A(0.996)/C(0.004) | nsSNP (E87A) | Missense (conservative); Splicing regulation | 2-3 (Low to medium) | | rs2255543 | A(0.514)/T(0.700) | nsSNP (Q80H) | Missense (conservative); Splicing regulation | 2-3 (Low to medium) | | rs2293734 | G/T (No frequency) | csSNP (P158P) | Sense/synonymous; Splicing regulation | 2-3 (Low to medium) |
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SNP IDs which were highlighted in bold were found to be deleterious by SIFT, PANTHER, PolyPhen and I-Mutant 2.0.
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