Table 2.
Genetic variants identified in target genes in study subjects.
| Gene | Genomic coordinate | Nucleotide change* | Mutation type | Amino acid change (rs number in dbSNP) |
Allele frequency | Frequency in gnomAD database |
Affected patients (homo-/heterozygous) | Reported** | SIFT/Polyphen/Mutation- Taster prediction (Clinical significance based on clinVar) |
|---|---|---|---|---|---|---|---|---|---|
| CETP | Rare | ||||||||
| chr16: 57,017,292 | c.A1196G | nonsynonymous SNV |
p.D399G (rs2303790) |
12 (0.286) | 0.0000–0.03281 | 1/11 | Yes | Deleterious/possibly damaging/polymorphism | |
| chr16: 57,017,291 | c.G1195T | nonsynonymous SNV | p.D399Y | 1 (0.024) | NA | 0/1 | Yes | Deleterious/probably damaging/polymorphism | |
| Common | |||||||||
| chr16: 57,016,092 | c.G1084A | nonsynonymous SNV |
p.V362I (rs5882) |
38 (0.881) | 0.4194–0.6197 | 15/23 | Yes | Tolerated/benign/polymorphism_automatic | |
| Unknown frequency | |||||||||
| chr16: 57,015,077 | c.T974C | nonsynonymous SNV | p.V325A | 1 (0.024) | NA | 0/1 | No | Tolerated/benign/polymorphism | |
| chr16: 57,004,954 | c.G537A | stop-gain SNV | p.W179X | 1 (0.024) | NA | 0/1 | No | ||
| LIPC | Common | ||||||||
| chr15: 58,853,079 | c.C1068A | nonsynonymous SNV |
p.F356L (rs3829462) |
42 (1.000) | 0.8570–0.9969 | 32/10 | Yes | Tolerated/benign/polymorphism_automatic | |
| chr15: 58,838,010 | c.A644G | nonsynonymous SNV |
p.N215S (rs6083) |
42 (1.000) | 0.3260–0.8322 | 30/12 | Yes | Deleterious/benign/polymorphism_automatic | |
| chr15: 58,833,993 | c.G283A | nonsynonymous SNV |
p.V95M (rs6078) |
16 (0.381) | 0.01886–0.3325 | 0/16 | Yes | Tolerated/benign/polymorphism_automatic | |
| SCARB1 | Rare | ||||||||
| Chr12: 125,294,817 | c.G745A | nonsynonymous SNV |
p.D249N (rs201357313) |
1 (0.024) | NA | 0/1 | Yes | ||
SNV: single nucleotide variant, NA: not available, *Nucleotide location number was assigned according to the CETP (NM_001286085), LIPC (NM_000236), and SCARB1 (NM_005505) mRNA sequences. **Reported in gnomAD browser.