Table 2.
Rare and novel variant identified
| Gene | Region | Variant | rs | Frequency | Protein prediction | Splicing prediction | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Coding DNA | Putative protein | 1000 G | ExAC/ gnomAD | n. of homoz. | PP2 | SIFT | Grantham distance | Align GVGD | MaxEnt, NNSPLICE, GeneSplicer, HSF, SSPNN | |||
| ABCA3 | Coding | c.745 C > A | p.(Pro249Thr) | Novel | 0 | 0 | 0 | Benign (0.063) | Deleterious (0.03) | 38 | C0 | – |
| c.863 G > A | p.(Arg288Lys) [13, 25] | rs117603931 | 0.002 | 0.0059 | 10 | Benign (0.002) | Tolerated (1) | 26 | C0 | – | ||
| c.1502 C > A | p.(Ala501Glu) [12] | rs141621969 | 0.0034 | 0.0038 | 17 | Benign (0.001) | Tolerated (1) | 107 | C0 | – | ||
| c.1982G > A | p.(Arg661Gln) | rs376672600 | 0 | 0.00003 | 0 | Benign (0.054) | Tolerated (0.4) | 43 | C0 | – | ||
| c.2108 T > C | p.(Ile703Thr) | novel | 0 | 0 | 0 | Benign (0.001) | Tolerated (0.37) | 89 | C0 | – | ||
| c.2268 C > T | p.(Ala756 = ) | rs143552557 | 0.0006 | 0.0017 | 1 | – | – | – | – | No difference | ||
| c.3231 C > A | p.(Phe1077Leu) | rs143240655 | 0 | 0.0003 | 0 | Benign (0.003) | Tolerated (0.34) | 22 | C0 | – | ||
| c.4122 C > G | p.(Asp1374Glu) | – | 0 | 0.00001 | 0 | Benign (0.001) | Tolerated (1) | 45 | C0 | – | ||
| c.4170 C > T | p.(Tyr1390 = ) | rs532847219 | 0.0002 | 0.00001 | 0 | – | – | – | – | IVS27-1 new donor | ||
| INTRONIC | c.613 + 11 C > T | p.? | rs370890203 | 0 | 0.00006 | 0 | – | – | – | – | No difference | |
| c.613 + 18 G > T | p.? | rs201364163 | 0 | 0.0019 | 2 | – | – | - | – | IVS7 + 12 new donor | ||
| c.991-94 G > C | p.? | Novel | 0 | 0 | 0 | – | – | – | – | No difference | ||
| c.2053-65 G > A | p.? | rs147395547 | 0.0034 | 0 | 0 | – | – | – | – | No difference | ||
| c.2513 + 23_2513 + 24insGT | p.? | Novel | 0 | 0 | 0 | – | – | – | – | No difference | ||
| c.2513 + 28 T > A | p.? | Novel | 0 | 0 | 0 | – | – | – | – | No difference | ||
| c.3279-39 G > A | p.? | rs374377819 | 0 | 0.00001 | 0 | – | – | – | – | No difference | ||
| c.3483 + 26 G > A | p.? | rs183047748 | 0.0002 | 0.00015 | 0 | – | – | – | – | No difference | ||
| c.3483 + 133 G > A | p.? | Novel | 0 | 0 | 0 | – | – | – | – | IVS23 + 135 new acceptor | ||
| c.3704-5 C > A | p.? | Novel | 0 | 0 | 0 | – | – | – | – | Affecting splice at exon 25 acceptor | ||
| c.3862 + 40 T > C | p.? | rs369424856 | 0.0006 | 0.003 | 5 | – | – | – | – | No difference | ||
| SFTPB | Coding | c.327 G > A | p.(Glu109 = ) | rs34682912 | 0.0028 | 0.0036 | 11 | – | – | - | – | No difference |
| c.394 T > C | p. (Phe132Leu) | rs138729391 | 0 | 0.00006 | 0 | Benign (0.018) | Tolerated (1) | 22 | C0 | – | ||
| c.541_552del12 | p.Pro181_Leu184del | – | 0 | 0.0004 | 0 | – | – | – | – | Affecting splice at exon 5 donor | ||
| c.883 G > A | p.(Ala295Thr) | rs36210375 | 0.0034 | 0.0016 | 1 | Benign (0.000) | Tolerated (0.43) | 58 | C0 | – | ||
| c.918 G > A | p.(Pro306 = ) | rs750280427 | 0 | 0.00002 | 0 | – | – | – | – | No difference | ||
| 3′-UTR | c*9 C > T | p.? | rs771704983 | 0 | 0.000017 | 0 | – | – | – | – | No difference | |
| SFTPC | INTRONIC | c.43-7 G > A [14] | p.? | rs79440568 | 0.0086 | 0.0027 | 12 | – | – | – | – | No difference |
| 3′-UTR | c*12 T > A | p.? | rs200469074 | 0.0004 | 0.00008 | 0 | – | – | – | – | No difference | |