Table 3. Rare variants detected in the study in infantile cholestasis-related genes.
| Sample no. | SNP ID | Gene | Nucleotide change (zygosity) | Amino acid change | Chr: position | MAF (dbSNP) | Effect prediction score | ||
|---|---|---|---|---|---|---|---|---|---|
| SIFT | PolyPhen-2 | MUTTASTER | |||||||
| B2 | rs200929472 | JAG1 | c.2048G > A (HET) | p.Arg683His | 20:10645421 | 0.0002 | 0.51 (T) | 0.037 (B) | 29, 0.99 (D) |
| rs370049107 | ABCC2 | c.3379G > A (HET) | p.Val1127Ile | 10:99834500 | 0.0002 | 1.00 (T) | 0.001 (B) | 29, 0.60 (P) | |
| B6 | rs35350960 | UGT1A1 | c.686C > A (HET) | p.Pro229Gln | 2:233760973 | 0.0030 | 0.13 (T) | 0.662 (P) | 76, 0.99 (P) |
| B7 | rs876660980 | JAG1 a | c.703G > A (HOM) | p.Arg235ST | 20:10656450 | < 0.0001 | N/A (D) | N/A (D) | N/A, 1.00 (D) |
| B8 | rs757769301 | MYO5B | c.3254G > A(HET) | p.Arg1085Gln | 18:49878967 | < 0.0001 | 0.30 (T) | 0.001 (B) | 43, 0.96 (D) |
| B52 | rs117920737 | MYO5B a | c.197A > C (HET) | p.Asp66Ala | 18:50040256 | 0.001 | 0.00 (D) | 0.019 (B) | 126, 1.00 (D) |
| B67 | rs527420845 | JAG1 | c.2884A > G (HET) | p.Thr962Ala | 20:10641492 | 0.0003 | 0.00 (D) | 0.881 (D) | 58, 1.00 (D) |
| B73 | rs775365826 | RFX6 | c.2021C > T (HET) | p.Ala674Val | 6:116927162 | < 0.0001 | 0.36 (T) | 0.00 (B) | 64, 1.00 (P) |
| B80 | rs3782356 | MLL2 a | c.15671G > A (HET) | p.Arg5224His | 12:4902695 | 0.002 | 0.00 (D) | 0.096 (B) | 29, 1.00 (D) |
| B86 | rs55761944 | ERCC4 a | c.241G > T (HET) | p.Val81Phe | 16:13922064 | 0.0003 | 0.04 (D) | 0.939 (D) | 50, 1.00 (D) |
| B95 | rs139318016 | KCNH1 | c.2372G > A (HET) | p.Arg791His | 1:210683879 | 0.0004 | 0.12 (T) | 0.977 (D) | 98, 1.00 (P) |
| rs183974372 | JAG1 a | c.133G > T (HET) | p.Val45Leu | 20:10672955 | 0.002 | 0.29 (T) | 0.038 (B) | 32, 0.95 (D) | |
| B101 | rs372939910 | ABCB11 | c.2135A > G (HET) | p.Leu712Ser | 2:168964249 | 0.0004 | 0.42 (T) | 0.001 (B) | 145, 1.00 (P) |
Abbreviations: HET, heterozygous; HOM, homozygous; MAF, minor allele frequency in 1,000 Genomes Project Phase 3; MUTTASTER, Mutation Taster–AA change score and probability value (D, disease causing; P, polymorphism); N/A, not applicable; PolyPhen, Polymorphism Phenotyping data collection (B, benign; P, possibly deleterious; D, deleterious); SIFT, scale-invariant feature transform (T, tolerated; D, damaging); SNP, single-nucleotide polymorphism.
Note: a The same position with prior reported to be pathogenic in other studies.