Table 3. . Inferred novel CYP2C19 haplotypes and unresolved diplotypes in African populations in this study.
| Resolved haplotypes | ||||||
|---|---|---|---|---|---|---|
| # | Background allele | Additional core variant(s) | Consequence(s) | Consensus VEP-based prediction | Count | Country/dataset |
| 1 | *1 | rs146991374∼95056∼A>T | Missense (K432I) | Deleterious | 4 | MSL/1000G |
| 2 | *1 | rs150152656∼ 17767∼C>T | Missense (T130M) | Deleterious | 1 | ESN/1000G |
| 3 | *1 | rs145328984∼17426∼C>T | Missense (R73C) | Deleterious | 1 | ESN/1000G |
| 4 | *1 | rs201306972∼17427∼G>A | Missense (R73H) | Benign | 1 | MSL/1000G |
| 5 | *39 | rs112197069∼17538∼T>A | Missense (F110Y) | Benign | 3 | SEB/AWI-Gen |
| 6 | *2 | rs145119820∼17715∼G>A | Missense (V113I) | Benign | 10 | MSL, LWK, GWD/1000G |
| Unresolved diplotypes with potentially novel star alleles | ||||||
|---|---|---|---|---|---|---|
| # | Background alleles | Additional core variant(s) | Consequence(s) | Consensus VEP-based prediction | Count | Country/dataset |
| 1 | [*1/*2] | rs183701923∼22893∼C>T | Missense (R186C) | Deleterious | 1 | LWK/1000G |
| 2 | [*17/*35] | rs192154563∼95085∼C>T | Missense (R442C) | Deleterious | 1 | LWK/1000G |
| 3 | [*2/*2] | rs201306972∼17427∼G>A+ rs537050749∼24271∼A>G |
Missense (R73H) Missense (N258S) |
Benign | 1 | ESN/1000G |
| 4 | [*1/*17] | rs375760063∼17856∼A>G | Missense (K160E) | Benign | 1 | MSL/1000G |
| 5 | [*1/*17] | rs545642100∼17526∼C>G | Missense (A106G) | Benign | 1 | ESN/1000G |
| 6 | [*2/*17] | rs527499296∼92332∼A>C | Missense (E415D) | Benign | 1 | LWK/1000G |
| 7 | [*1/*3] | rs144056033∼92303∼A>G | Missense (M406V) | Benign | 1 | LWK/1000G |
Note that CYP2C19*1 is defined by rs3758581 (I331V). Variant positions are according to the CYP2C19 RefSeq gene (NG_008384.3).
1000G: 1000 Genomes Project; AWI-Gen: Africa Wits-INDEPTH Partnership for Genomic Research; ESN: Esan in Nigeria; GWD: Mandinka in western divisions of The Gambia; LWK: Luhya in Webuye Kenya; MSL: Mende in Sierra Leone; SEB: Southeastern Bantu; VEP: Ensembl Variant Effect Predictor.