Table 3 Assessment of potential functional relevance of identified variants
Sift[20] | PolyPhen[21] | Mutation taster[22] | SNP&GO[23] | FATHMM[24] | MutPred[25] | ||
|---|---|---|---|---|---|---|---|
BMP2 | |||||||
rs2273073 | Ser37Ala | - tolerated | - tolerated | - aas changed | - aas changed | - tolerated | - score 0.123 |
- heterozygous in TGP | - score 0.61 | - neutral | |||||
- known disease mutation at this position (HGMD CM034611) | - disease associated variation | ||||||
- protein features (might be) affected | (probability – 0.527) | ||||||
- splice site changes | |||||||
rs235768 | Arg190Ser | - functional relevance cannot be predicted explicit | - functional relevance cannot be predicted explicit | - aas changed | - aas changed | - tolerated | - score 0.293 |
- homozygous in TGP | - score -0.45 | - neutral | |||||
- protein features (might be) affected | - disease associated variation | ||||||
- splice site changes | (probability – 0.974) | ||||||
BMP4 | |||||||
rs17563 | Val152Ala | - tolerated | - tolerated | - aas changed | - aas changed | - tolerated | - score 0.145 |
- homozygous in TGP | - score -0.08 | - neutral | |||||
- protein features (might be) affected | - disease associated variation | ||||||
- splice site changes | (probability – 0.755) | ||||||
c.899G > C | Arg300Pro | - substantial evidence for functional consequences | - substantial evidence for functional consequences | - disease causing | - aas changed | - tolerated | - score 0.381 |
- aas changed | - score -0.78 | - neutral | |||||
- protein features (might be) affected | - disease associated variation | ||||||
- splice site changes | (probability – 0.906) | ||||||
BMP7 | |||||||
rs192121279 | Thr105Met | - deleterious | - unknown | - not found | n.a. | - No dbSNP mapping(s) | - score 0.466 |
- neutral | |||||||
c.611 + 3366C > T | intronic | n.a. | n.a. | n.a. | n.a. | -n.a. | n.a. |
rs61733438 | Asn321Ser | - tolerated | - tolerated | - disease causing | - aas changed | - tolerated | - score 0.278 |
- aas changed | - score -0.92 | - neutral | |||||
- heterozygous in TGP | - disease associated variation | ||||||
- protein features (might be) affected | |||||||
- splice site changes | (probability – 0.848) | ||||||
rs2148328 | Ala399Gly | - tolerated | - unknown | - aas changed | - aas changed | - No dbSNP mapping(s) | - score 0.540 |
- protein features (might be) affected | - “Actionable Hypotheses”$ |