Table 4.
Commonly Tested Alleles and Available Reference Materials for CYP2C9, CYP2C19, VKORC1, CYP4F2, CYP2C Cluster Variant, and GGCX
| Gene | Allele | Allele function† | Coriell no. | Genotype | GeT-RM study | AMP tier |
|---|---|---|---|---|---|---|
| CYP2C9 | ∗2 | Decreased | HG00276 | ∗1/∗2 | 20166 | 1 |
| NA10854 | ∗2/∗2 | 2016 | ||||
| CYP2C9 | ∗3 | None | NA18524‡ | ∗1/∗3 | 2016 | 1 |
| CYP2C9 | ∗5 | Decreased | NA18519 | ∗1/∗5 | 2016 | 1 |
| NA23275 | ∗5/∗5 | 2016 | ||||
| CYP2C9 | ∗6 | None | NA19213 | ∗1/∗6 | 2016 | 1 |
| NA19143 | ∗1/∗6 | 2016 | ||||
| CYP2C9 | ∗8§ | Decreased | NA12815 | ∗1/∗8 | 2016 | 1 |
| NA17454 | ∗1/∗8 | 2016 | ||||
| CYP2C9 | ∗9 | Normal | NA19700 | ∗1/∗9 | 2016 | None |
| NA19178 | ∗5/∗9 | 2016 | ||||
| CYP2C9 | ∗10 | Uncertain | NA15245 | ∗10/∗12 | 2016 | None |
| CYP2C9 | ∗11 | Decreased | HG02861 | ∗1/∗11 | This study | 1 |
| HG02852 | ∗1/∗11 | This study | ||||
| NA19122 | ∗1/∗11 | 2016 | ||||
| CYP2C9 | ∗12 | Decreased | NA15245 | ∗10/∗12 | 2016 | 2 |
| CYP2C9 | ∗13 | None | HG01809 | ∗1/∗13 | This study | 2 |
| HG02087 | ∗1/∗13 | This study | ||||
| NA19075 | ∗1/∗13 | This study | ||||
| CYP2C9 | ∗15 | None | none | ND | 2 | |
| CYP2C19 | ∗2 | None | HG01190 | ∗1/∗2 | 2016 | 1 |
| NA12717 | ∗2/∗2 | 2016 | ||||
| CYP2C19 | ∗3 | None | NA18564 | ∗2/∗3 | 2016 | 1 |
| NA23246 | ∗3/∗17 | 2016 | ||||
| CYP2C19 | ∗4.001 | None | NA23881 | ∗1/∗4.001 | 2016 | 2 |
| NA18552 | ∗1/∗4.001 | 2016 | ||||
| CYP2C19 | ∗4.002 | None | NA23878 | ∗1/∗4.002 (∗4/∗17)¶ | 2016 | 2 |
| CYP2C19 | ∗5 | None | none | ND | 2 | |
| CYP2C19 | ∗6 | None | NA19178 | ∗1 (∗27)/∗6 | 2016 | 2 |
| NA23874 | ∗2/∗6 | 2016 | ||||
| CYP2C19 | ∗7 | None | none | ND | 2 | |
| CYP2C19 | ∗8 | None | NA23873 | ∗1/∗8 | 2016 | 2 |
| NA10865 | ∗8/∗17 | 2016 | ||||
| CYP2C19 | ∗9 | Decreased | NA24008 | ∗9/∗17 | 2016 | 2 |
| NA24009 | ∗2/∗9 | 2016 | ||||
| NA19466 | ∗1/∗9 | This study | ||||
| CYP2C19 | ∗10 | Decreased | NA07439 | ∗2/∗10 | 2016 | 2 |
| CYP2C19 | ∗12 | Uncertain | NA17074 | ∗1(∗12)/∗17 | 2016 | None |
| NA19700 | (∗12/∗27) | 2016 | ||||
| CYP2C19 | ∗13 | Normal | NA17448 | ∗1/∗13 | 2016 | None |
| NA19239 | ∗13/∗17 | 2016 | ||||
| CYP2C19 | ∗15 | Normal | NA19213 | ∗1/∗15 | 2016 | None |
| NA19143 | ∗1/∗15 | 2016 | ||||
| CYP2C19 | ∗17 | Increased | NA19035 | ∗17/∗17 | 2016 | 1 |
| NA17658 | ∗1/∗17 | 2016 | ||||
| CYP2C19 | ∗35 | None | HG02852 | ∗2/∗35 | This study | 2 |
| NA19327 | ∗2/∗35 | This study | ||||
| HG03370 | ∗2/∗35 | This study | ||||
| HG02861 | ∗2/∗35 | This study | ||||
| VKORC1 | c.-1639 G>A (rs9923231) | Decreased gene expression | HG00276 | G/A | 2016 | 1 |
| HG00589 | A/A | 2016 | ||||
| VKORC1 | rs61742245 | Warfarin resistance | HG01697 | G/T | This study | 2 |
| NA19395 | G/T | This study | ||||
| VKORC1 | rs72547529 | Warfarin resistance | HG01456 | G/A | This study | 2 |
| NA18877 | G/A | This study | ||||
| NA19466 | G/A | This study | ||||
| CYP4F2 | ∗3 | Possibly decreased | HG01190 | ∗1/∗3 | 2016 | 2 |
| NA07029 | ∗3/∗3 | 2016 | ||||
| CYP2C cluster variant | rs12777823 | Unknown | HG02087 | A/G | This study | 2 |
| HG01809 | A/A | This study | ||||
| GGCX | rs12714145 | Clotting factor activation | NA10854 | T/T | This study | None |
| NA12813 | T/C | This study | ||||
| GGCX | rs11676382 | Clotting factor activation | NA12873 | C/G | This study | None |
| NA23313 | C/G | This study |
Information about additional reference materials for these genes is available on the GeT-RM website (https://www.cdc.gov/labquality/get-rm/index.html, last accessed March 24, 2021).
AMP, Association for Molecular Pathology; GeT-RM, Genetic Testing Reference Material; ND, not detected.
Function shown for CYP2C9 and CYP2C19 corresponds to Clinical Pharmacogenetics Implementation Consortium clinical function as assigned by guideline authors. For all other alleles except GGCX, function information is according to PharmGKB (https://www.pharmgkb.org/page/pgxGeneRef, last accessed March 24, 2021) and Clinical Pharmacogenetics Implementation Consortium (https://cpicpgx.org/content/guideline/publication/warfarin/2017/28198005.pdf, last accessed March 24, 2021).
The CYP2C9∗3 tag variant (rs1057910) is present in both the ∗3 and ∗18 alleles and is present on multiple Coriell cell lines.
Samples were not genotyped for c.-1766T>C, a second core variant defining CYP2C9∗8.
Alleles in parentheses indicate that they were identified by only one laboratory.