Table 3.
Results of benchmarking analysis
| SERPINA1 mutation | Species | Sequence Identity (%) | SVM probability | ΔΔG (FoldX) | PolyPhen-2 Score |
|---|---|---|---|---|---|
| Pathogenic sequence variants (ClinVar) | |||||
| P369L | Homo sapiens | 100 | 0.8496 | 1.510 | 1.0000 |
| P369S | Homo sapiens | 100 | 0.8353 | 4.410 | 1.0000 |
| P369T | Homo sapiens | 100 | 0.8599 | 2.810 | 1.0000 |
| M358R | Homo sapiens | 100 | 0.7853 | 0.431 | 0.0190 |
| E342K | Homo sapiens | 100 | 0.8413 | 2.090 | 1.0000 |
| E264V | Homo sapiens | 100 | 0.8619 | 1.660 | 1.0000 |
| D256V | Homo sapiens | 100 | 0.8708 | 1.950 | 0.9850 |
| G225R | Homo sapiens | 100 | 0.8975 | 5.160 | 0.9820 |
| R223C | Homo sapiens | 100 | 0.8954 | −0.350 | 0.9950 |
| I92N | Homo sapiens | 100 | 0.8215 | 3.600 | 1.0000 |
| G67E | Homo sapiens | 100 | 0.8680 | 26.290 | 1.0000 |
| S53F | Homo sapiens | 100 | 0.8687 | 19.860 | 1.0000 |
| L41P | Homo sapiens | 100 | 0.7585 | 3.240 | 0.6010 |
| R39C | Homo sapiens | 100 | 0.8672 | 2.110 | 1.0000 |
| A336T | Homo sapiens | 100 | 0.8479 | 3.450 | 1.0000 |
| G115S | Homo sapiens | 100 | 0.7826 | 1.610 | 0.9990 |
| F52S | Homo sapiens | 100 | 0.7900 | 6.020 | 1.0000 |
| Benign sequence variants (ClinVar) | |||||
| E376D | Homo sapiens | N/A | 0.2991 | 1.850 | 0 |
| E363K | Homo sapiens | N/A | 0.4172 | −0.900 | 0.11 |
| A284S | Homo sapiens | N/A | 0.3445 | −0.240 | 0.139 |
| V213A | Homo sapiens | N/A | 0.1161 | −0.100 | 0 |
| R101H | Homo sapiens | N/A | 0.0576 | −0.533 | 0 |
| Benign sequence variants (Primate neutral variants) | |||||
| P21Q | Hylobates sp. ECACC | 95 | 0.363 | 0.72 | 0.014 |
| F23L | Papio anubis | 92 | 0.3762 | 0.38 | 0 |
| T27A | Gorilla gorilla | 98 | 0.4118 | 1.34 | 0 |
| N29K | Hylobates sp. ECACC | 95 | 0.4365 | −0.63 | 0.178 |
| N29S | Papio anubis | 92 | 0.0839 | 0.13 | 0 |
| T48S | Hylobates sp. ECACC | 95 | 0.4991 | 0.51 | 0 |
| I50V | Gorilla gorilla | 98 | 0.6687 | 0.96 | 0.767 |
| D74S | Chlorocebus sabaeus | 92 | 0.0588 | 0.38 | 0 |
| N81H | Pongo abelii | 96 | 0.462 | 0.27 | 0.007 |
| I92V | Pongo abelii; Hylobates sp. ECACC | 96; 95 | 0.7931 | 1.06 | 0.006 |
| Q105K | Papio anubis | 92 | 0.2178 | −0.5 | 0.001 |
| N116S | Gorilla gorilla | 98 | 0.751 | 1.9 | 0.311 |
| K136N | Papio anubis | 92 | 0.4292 | 0.07 | 0 |
| E141D | Pongo abelii | 96 | 0.4052 | 0.77 | 0.002 |
| G148E | Chlorocebus sabaeus | 92 | 0.219 | −0.46 | 0 |
| D159N | Papio anubis | 92 | 0.165 | −1.21 | 0 |
| Q212E | Pongo abelii | 96 | 0.2568 | 0.35 | 0 |
| V213A | Hylobates sp. ECACC | 95 | 0.1161 | −0.1 | 0 |
| Q230Y | Papio anubis | 92 | 0.0803 | 0.49 | 0 |
| Q230H | Hylobates sp. ECACC | 95 | 0.0545 | 0.41 | 0 |
| K233E | Papio anubis | 92 | 0.0787 | 0.58 | 0 |
| D270E | Hylobates sp. ECACC | 95 | 0.2543 | −0.03 | 0 |
| I271V | Gorilla gorilla | 98 | 0.1015 | 0.52 | 0 |
| D280N | Pongo abelii | 96 | 0.1407 | 0.82 | 0 |
| S285N | Chlorocebus sabaeus | 92 | 0.0554 | −1.6 | 0 |
| S292A | Chlorocebus sabaeus | 92 | 0.3206 | −0.14 | 0.003 |
| S301R | Pongo abelii | 96 | 0.1328 | −0.54 | 0.011 |
| S301T | Hylobates sp. ECACC | 95 | 0.0724 | 0 | 0 |
| S313G | Hylobates sp. ECACC | 95 | 0.606 | 0.63 | 0.05 |
| E324D | Chlorocebus sabaeus | 92 | 0.0978 | 0.62 | 0 |
| A332V | Homo sapiens | 99 | 0.1255 | 1.88 | 0.99 |
| I360V | Gorilla gorilla | 98 | 0.1547 | 0.73 | 0 |
| L383H | Hylobates sp. ECACC | 95 | 0.8834 | 3.08 | 1 |
| M385I | Papio anubis | 92 | 0.7686 | 3.15 | 0.001 |
| M385 V | Pan troglodytes; Pongo abelii | 99; 96 | 0.7566 | 2.44 | 0.001 |
All variants are reported without the 24 amino acid precursor unless otherwise stated
Scores in bold, pathogenic; scores in italics, possibly pathogenic; scores in normal text, benign. SVM Support vector machine