Table 4.
Functional prediction for TMPRSS3 missense variants from previous publications that were not identified in this study
| Variant | SIFT | PolyPhen-2 | PhyloP a | ConSeq b | PROSITE |
|---|---|---|---|---|---|
| c.268G>A (p.Ala90Thr) c |
Tolerated | Probably damaging |
2.85 | 5 (e) | Within LDLRA domain |
| c.308A>G (p.Asp103Gly) |
Affect protein function |
Probably damaging |
3.89 | 9 (f) | Tyrosine kinase phosphorylation site |
| c.325C>T (p.Arg109Trp) |
Affect protein function |
Probably damaging |
2.15 | 8 (f) | SRCR domain signature |
| c.413C>A (p.Ala138Glu) |
Affect protein function |
Possibly damaging |
3.22 | 7 (b) | Within SRCR domain |
| c.581G>T (p.Cys194Phe) |
Affect protein function |
Probably damaging |
4.72 | 8 (b) | Disulfide bridge, N-myristoylation site |
| c.646C>T (p.Arg216Cys) |
Affect protein function |
Probably damaging |
6.15 | 9 (f) | Protein kinase C phosphorylation site |
| c.647G>T (p.Arg216Leu) |
Affect protein function |
Probably damaging |
5.13 | 9 (f) | Protein kinase C phosphorylation site |
| c.753G>C (p.Trp251Cys) |
Affect protein function |
Probably damaging |
3.60 | 8 (b) | Close to histidine active site |
| c.916G>A (p.Ala306Thr) |
Tolerated | Probably damaging |
4.85 | 9 (s) | N-myristoylation site |
| c.1211C>T (p. Pro404Leu) d |
Affect protein function |
Probably damaging |
6.19 | 9 (f) | Serine active site |
Vertebrate Basewise Conservation for 44 species by PhyloP (phyloP44wayAll) from the UCSC Genome Browser, Build 36. Positive scores are assigned for nucleotides that are predicted to be conserved and represent −log p-values under a null hypothesis of neutral evolution.
ConSeq conservation scale ranges from 9 for conserved to 1 for variable. e = exposed; b = buried; f = functional (highly conserved and exposed); s = structural (highly conserved and buried)
This variant is catalogued in dbSNP as rs45598239 and the A allele is present in 5% of the CEU panel
This variant is catalogued in dbSNP as rs28939084 but no population frequency data is available