Table 3.
Category IIp (potential mutation).
| Gene | Position | dbSNP Code | cHGVS | Type | pHGVS | In Silico Prediction Programs | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| M.T. | SNAP2 | SIFT | PP2 | PhD-SNP | BDGP | NetGene2 | ASSP | C. Splice | ||||||
| ABCA1 | 9:107549242 | rs1230573600 | c.6220G>A | Missense | p.G2074S | PP (0.999) | PP (69) | PP (0.00) | PP (0.999) | PP (7) | ||||
| 9:107550232 | 9:107550232 | c.6173C>G | Missense | p.A2058G | PP (0.999) | PP (31) | PP (0.00) | PP (0.998) | PP (6) | |||||
| 9:107599296 | rs201586430 | c.1276T>C | Missense | p.F426L | PP (0.999) | PP (50) | PP (0.00) | PP (0.999) | PP (4) | |||||
| ABCG5 | 2:44040359 | rs137996263 | c.1852T>C | Missense | p.S618P | PP (0.998) | PP (51) | PP (0.00) | PP (0.945) | PP (8) | ||||
| 2:44051085 | 2:44051085 | c.1291C>G | Missense | p.P431A | PP (0.999) | PP (9) | NPP (0.94) | PP (1) | NPP (4) | |||||
| ANGPTL4 | 19:8435981 | rs866158597 | c.703G>A | Missense | p.V235M | PP (0.999) | PP (28) | NPP (0.14) | PP (0.999) | PP (7) | ||||
| APOB | 2:21225938 | 2:21225938 | c.12356C>A | Missense | p.A4119D | NPP (0.999) | PP (56) | PP (0.00) | PP (0.989) | PP (1) | ||||
| 2:21227295 | rs1458765902 | c.11933T>C | Missense | p.I3978T | PP (0.999) | PP (63) | PP (0.00) | PP (0.977) | PP (0) | |||||
| 2:21229970 | rs146178619 | c.9770A>G | Missense | p.N3257S | PP (0.984) | PP (4) | PP (0.00) | NPP (0.073) | PP (5) | |||||
| 2:21230600 | rs61742323 | c.9140C>T | Missense | p.T3047M | NPP (0.999) | PP (17) | PP (0.00) | PP (0.625) | NPP (6) | |||||
| 2:21233163 | 2:21233163 | c.6577G>T | Missense | p.D2193Y | NPP (0.999) | PP (42) | PP (0.00) | NPP (0.396) | PP (0) | |||||
| 2:21238007 | rs61736761 | c.3634C>A | Missense | p.L1212M | NPP (0.989) | PP (10) | PP (0.00) | PP (1) | NPP (7) | |||||
| 2:21246505 | rs773987185 | c.2496G>A | Missense | p.M832I | PP (0.738) | NPP (-55) | PP (0.03) | PP (0.592) | NPP (4) | |||||
| CD36 | 7:80276161 | rs754478799 | c.107del | Frameshift variant | p.K36Rfs*41 | PP (1) | - | - | - | - | ||||
| 7:80293767 | rs201715989 | c.655G>T | Missense | p.D219Y | PP (0.998) | PP (47) | PP (0.01) | NPP (0.139) | PP (9) | |||||
| 7:80299343 | rs748146857 | c.818+5G>A | Splicing variant | - | PP (1) | Diff. 24.24% | Diff. 34.04% | Diff. 11.06% | PP (21.3) | |||||
| CYP7A1 | CYP7A1/8:59405037 | rs149291486 | c.1090C>T | Missense | p.R364W | PP (0.999) | PP (93) | PP (0.00) | PP (1) | PP (9) | ||||
| LCAT | 16:67976376 | rs1186446170 | c.638A>G | Missense | p.Y213C | PP (0.989) | PP (29) | PP (0.01) | PP (1) | PP (6) | ||||
| LIPC | 15:58838165 | rs540524619 | c.799G>T | Missense | p.G267C | PP (0.999) | PP (60) | PP (0.01) | PP (1) | PP (8) | ||||
| LPA | 6:160966559 | rs139145675 | c.5311C>T | Missense | p.R1771C | PP (0.999) | PP (20) | PP (0.00) | PP (1) | PP (7) | ||||
| 6:160969591 | rs757921434 | c.5074C>T | Stop gained | p.R1692* | PP (1) | - | - | - | - | |||||
| 6:160998167 | rs200099994 | c.4631+1G>A | Splicing variant | - | PP (1) | Diff. >20% | - | Diff. >20% | PP (31) | |||||
| 6:161006084 | rs76144756 | c.4283C>T | Missense | p.P1428L | NPP (0.996) | PP (33) | PP (0.02) | PP (1) | PP (5) | |||||
| LPL | 8:19819628 | rs116403115 | c.1325T>G | Missense, | p.V442G | PP (0.999) | PP (22) | PP (0.02) | PP (1) | NPP (3) | ||||
| LRP1 | 12:57549979 | rs750499142 | c.1330C>T | Missense | p.R444C | PP (0.999) | PP (44) | PP (0.00) | PP (1) | PP (8) | ||||
| 12:57577915 | rs141826184 | c.5977C>T | Missense | p.R1993W | PP (0.971) | PP (58) | PP (0.00) | PP (1) | PP (7) | |||||
| 12:57587039 | rs113379328 | c.7636G>A | Missense | p.G2546S | PP (0.996) | NPP (-19) | NPP (0.58) | PP (0.742) | PP (3) | |||||
| 12:57599365 | rs149488896 | c.11495G>C | Missense | p.G3832A | PP (0.997) | PP (26) | PP (0.04) | PP (0.999) | NPP (2) | |||||
| 12:57601936 | rs755903131 | c.11975G>A | Missense | p.R3992H | PP (0.999) | PP (6) | NPP (0.22) | PP (0.998) | PP (7) | |||||
| 12:57606021 | rs142605462 | c.13471G>C | Missense | p.D4491H | PP (0.999) | PP (25) | NPP (0.15) | PP (1) | NPP (4) | |||||
| LRP2 | 2:169997031 | rs746070288 | c.13133C>T | Missense | p.P4378L | PP (0.999) | PP (27) | NPP (0.17) | PP (1) | PP (1) | ||||
| 2:170034493 | rs145432614 | c.10213G>A | Missense | p.G3405R | PP (0.999) | PP (28) | NPP (0.48) | PP (0.907) | PP (4) | |||||
| 2:170037997 | rs1248351989 | c.10130A>C | Missense | p.D3377A | PP (0.999) | PP (38) | NPP (0.25) | PP (1) | PP (1) | |||||
| 2:170058335 | rs750566206 | c.8255G>A | Missense | p.R2752Q | PP (0.999) | PP (14) | PP (0.00) | PP (0.999) | PP (5) | |||||
| 2:170163815 | rs142594441 | c.403G>A | Missense | p.D135N | PP (0.999) | PP (2) | PP (0.00) | PP (1) | PP (7) | |||||
| LRPAP1 | 4:3519802 | rs760183295 | c.710G>A | Missense | p.R237H | PP (0.999) | PP (13) | - | PP (0.546) | NPP (3) | ||||
| 4:3521804 | rs141393177 | c.466C>T | Missense | p.H156Y | PP (0.996) | PP (10) | - | PP (0.934) | NPP (9) | |||||
| NPC1 | 18:21152041 | rs762610198 | c.284C>T | Missense | p.S95F | PP (0.999) | PP (23) | PP (0.01) | NPP (0.022) | PP (3) | ||||
| PCSK9 | 1:55521765 | 1:55521765 | c.899C>T | Missense | p.A300V | PP (0.999) | PP (66) | PP (0.01) | PP (1) | PP (7) | ||||
| PLTP | 20:44530943 | rs6065903 | c.1138C>T | Missense | p.R380W | NPP (0.551) | PP (68) | PP (0.00) | PP (1) | NPP (6) | ||||
| STAR | 8:38005810 | rs748942681 | c.214G>A | Missense | p.E72K | PP (0.999) | PP (65) | PP (0.02) | NPP (0.358) | PP (1) | ||||
| TSPO | 22:43557122 | rs746919529 | c.247G>C | Missense | p.G83R | PP (0.999) | PP (1) | NPP (0.28) | PP (1) | PP (4) | ||||
| 22:43557156 | rs142445069 | c.281C>T | Missense | p.A94V | PP (0.999) | PP (37) | NPP (0.36) | PP (0.805) | PP (5) | |||||
M.T.: Mutation taster; PP2: PolyPhen2; BDGP: splice site predictor; ASSP: alternative splice site predictor; C. Splice: combined annotation-dependent depletion splice; Diff: difference; PP: predicted pathogenic; NPP: non-predicted pathogenic; cHGVS: change in the gene-coding sequence; pHGVS: amino acid change in the protein.