Table 2.
Frequency of Variants and in Silico Predictions of Mutation Effects
| BEST1 Mutation | Amino Acid Change | Previously Reported | Gnomad Frequency | Sub Pop. Frequency (Origin) | SIFT (Score) | PolyPhen (Score, Sensitivity, Specificity) | CADD Score (PHREDD) |
|---|---|---|---|---|---|---|---|
| c.103G>A | p.Glu35Lys | Reported (Tian 2017, Stone 2017) | Not listed | Not listed | Damaging (0.01) | PD (1.000, 0.00, 1.00) | 2.24 (21.7) |
| c.125T>C | p.Leu41Pro | Reported (Kramer 2003, Zhao 2012, Burguess 2018) | 5/251264 | 0.0000615 (African) | Tolerated (0.13) | PD (0.966, 0.78, 0.95) | 1.16 (14.4) |
| c.353A>C | p.Asp118Ala | Novel | Not listed | Not listed | Damaging (0.02) | PD (1.000, 0.00, 1.00) | 4.16 (29.8) |
| c.418C>G | p.Leu140Val | Reported (Davidson 2009) | 5/150144 | 0.0002202 (South Asian) | Damaging (0.03) | PD (0.998, 0.27, 0.99) | 2.63 (22.8) |
| c.422G>A | p.Arg141His | Reported (White 2000, Schatz 2010, Kinnick 2011, Stone 2017, ...) | 96/181002 | 0.003275 (Finnish) | Damaging (0.00) | PD (1.000, 0.00, 1.00) | 4.42 (33) |
| c.604C>T | p.Arg202Trp | Davidson 2011 | 4/251348 | 0.0000578 (Latino) | Damaging (0.03) | PD (1.000, 0.00, 1.00) | 3.82 (26.4) |
| c.671T>A | p.Leu224Gln | Novel | Not listed | Not listed | Damaging (0.00) | PD (1.000, 0.00, 1.00) | 3.93 (27.3) |
| c.816_818delTGT | p.Val273del | Novel | Not listed | Not listed | Unable | Unable | Unable |
| c.830C>T | p.Thr277Met | Reported (Zaneveld 2015, Luo 2018, Zhong 2017, Tian 2017) | 3/251476 | 0.00003266 (South Asian) | Damaging (0.00) | PD (1.000, 0.00, 1.00) | 3.41 (24.8) |
Probably damaging (PD). PHREDD scaled C-score of 20 to 30 indicate the top 1% of all single nucleotide variants that are likely to cause disease and PHREDD scaled C-score of 30 to 40 indicate the top 0.1% of all single nucleotide variants (SNVs) that are likely to cause disease.