| Allele Count: | 36 |
|---|---|
| Allele Number: | 5976 |
| Allele Frequency: | 6.0241e-3 |
| Number of Homozygotes: | 2 |
| Dataset | Population | Population abbr | Allele Frequency |
|---|---|---|---|
| 1KGP3 | East Asian | EAS | 2.0000e-3 |
| South Asian | SAS | 0.1094 | |
| African | AFR | 0.0605 | |
| Americas | AMR | 0.1297 | |
| European ancestry | EUR | 0.1859 | |
| total | 0.0931 | ||
| gnomAD v3 Genomes | East Asian | EAS | 6.7265e-3 |
| South Asian | SAS | 0.1092 | |
| Afican | AFR | 0.0776 | |
| Latino | AMR | 0.1312 | |
| Amish | AMI | 0.2381 | |
| European(Finnish) | FIN | 0.0963 | |
| European(non-Finnish) | NFE | 0.1994 | |
| Ashkenazi Jewish | ASJ | 0.1820 | |
| other | OTH | 0.1475 | |
| total | 0.1427 | ||
| Region | Gene ID | Gene Detail | Exonic function | Consequence | |
|---|---|---|---|---|---|
| Ensembl | splicing | CYP2D6 | ENST00000360608.9:exon4:c.506-1G>A;ENST00000389970.7:exon4:c.440-1G>A;ENST00000359033.4:exon3:c.353-1G>A | - | - |
| RefSeq | splicing | CYP2D6;CYP2D7 | NM_000106:exon4:c.506-1G>A;NM_001025161:exon3:c.353-1G>A;NM_001348386:exon4:c.506-1G>A | - | - |
| Method | Score | Rank Score | predicted consequence |
|---|---|---|---|
| SIFT | - | - | - |
| PolyPhen2_HDIV | - | - | - |
| PolyPhen2_HVAR | - | - | - |
| FATHMM | - | - | - |
| CADD | 3.457 | 0.473 | 23.0 |
| ClinVar Significance | ClinVar Disease Name | ClinVar Allele ID | Tag-value |
|---|---|---|---|
| drug_response | Debrisoquine,_poor_metabolism_of|not_specified|amitriptyline_response_-_Dosage,_Toxicity/ADR|antidepressants_response_-_Dosage,_Toxicity/ADR|clomipramine_response_-_Dosage,_Toxicity/ADR|desipramine_response_-_Dosage,_Toxicity/ADR|doxepin_response_-_Dosage,_Toxicity/ADR|imipramine_response_-_Dosage,_Toxicity/ADR|nortriptyline_response_-_Dosage,_Toxicity/ADR|trimipramine_response_-_Dosage,_Toxicity/ADR|tamoxifen_response_-_Efficacy,_Toxicity/ADR|not_provided | 31928 | MedGen:C1837156|MedGen:CN169374|MedGen:CN236466|MedGen:CN236477|MedGen:CN236505|MedGen:CN236523|MedGen:CN236529|MedGen:CN236532|MedGen:CN236538|MedGen:CN236546|MedGen:CN236584|MedGen:CN517202 |
Loss of Function (LoF) variants are indentified by package LOFTEE developed recently by gnomAD group to assess stop-gained, splice site disrupting and frameshift variants as “low-confidence” (LC) or “high-confidence” (HC) LoF variants.
| LoF | LoF_filter | LoF_flags | LoF_info |
|---|---|---|---|
| HC | - | NON_CAN_SPLICE | ACCEPTOR_MES_DIFF:8.75037930371984,BRANCHPOINT_DISTANCE:21,INTRON_START:42128945,MUTANT_ACCEPTOR_MES:1.48609484940874,EXON_END:42128944,ACCEPTOR_GERP_DIFF:0,ACCEPTOR_ESS:4,ACCEPTOR_ISE:6,ACCEPTOR_DISRUPTION_PROB:0.999447669579739,ACCEPTOR_ESE:32,INTRON_END:42129737,ACCEPTOR_ISS:6,EXON_START:42128784,ACCEPTOR_DISRUPTING,CRYPTIC_ACCEPTOR_MES:2.33167869079523,RESCUE_ACCEPTOR_MES:1.48609484940874,CRYPTIC_ACCEPTOR_POS:1,RESCUE_ACCEPTOR_POS:0,INTRON_SIZE:793 |
| HC | - | - | ACCEPTOR_ESS:4,ACCEPTOR_ISE:6,EXON_END:42128944,MUTANT_ACCEPTOR_MES:1.48609484940874,ACCEPTOR_GERP_DIFF:0,INTRON_START:42128945,BRANCHPOINT_DISTANCE:21,ACCEPTOR_MES_DIFF:8.75037930371984,ACCEPTOR_ISS:6,EXON_START:42128784,INTRON_END:42129032,ACCEPTOR_ESE:32,ACCEPTOR_DISRUPTION_PROB:0.999447669579739,ACCEPTOR_DISRUPTING,CRYPTIC_ACCEPTOR_MES:2.33167869079523,RESCUE_ACCEPTOR_MES:1.48609484940874,CRYPTIC_ACCEPTOR_POS:1,RESCUE_ACCEPTOR_POS:0,INTRON_SIZE:88 |
| HC | - | - | EXON_END:42128944,MUTANT_ACCEPTOR_MES:1.48609484940874,ACCEPTOR_GERP_DIFF:0,ACCEPTOR_ISE:6,ACCEPTOR_ESS:4,ACCEPTOR_MES_DIFF:8.75037930371984,BRANCHPOINT_DISTANCE:21,INTRON_START:42128945,EXON_START:42128784,ACCEPTOR_ISS:6,ACCEPTOR_DISRUPTION_PROB:0.999447669579739,ACCEPTOR_ESE:32,INTRON_END:42129032,ACCEPTOR_DISRUPTING,CRYPTIC_ACCEPTOR_MES:2.33167869079523,RESCUE_ACCEPTOR_MES:1.48609484940874,CRYPTIC_ACCEPTOR_POS:1,RESCUE_ACCEPTOR_POS:0,INTRON_SIZE:88 |
| Belong to Haplotype | Drug | Guideine | URL | CPIC_Level | PharmGKB_Level_of_Evidence | PGx_on_ FDA_Label | CPIC_Publications _PMID |
|---|---|---|---|---|---|---|---|
| CYP2D6*4 | atomoxetine | CYP2D6 and Atomoxetine | https://cpicpgx.org/cpic-guideline-for-atomoxetine-based-on-cyp2d6-genotype/ | A | 1A | Actionable PGx | 30801677 |
| CYP2D6*4 | codeine | CYP2D6 and Codeine | https://cpicpgx.org/guidelines/guideline-for-codeine-and-cyp2d6/ | A | 1A | Actionable PGx | 22205192;24458010 |
| CYP2D6*4 | ondansetron | CYP2D6 and Ondansetron and Tropisetron | https://cpicpgx.org/guidelines/guideline-for-ondansetron-and-tropisetron-and-cyp2d6-genotype/ | A | 1A | Informative PGx | 28002639 |
| CYP2D6*4 | tamoxifen | CYP2D6 and Tamoxifen | https://cpicpgx.org/guidelines/cpic-guideline-for-tamoxifen-based-on-cyp2d6-genotype/ | A | 1A | Actionable PGx | 29385237 |
| CYP2D6*4 | fluvoxamine | CYP2D6, CYP2C19 and Selective Serotonin Reuptake Inhibitors | https://cpicpgx.org/guidelines/guideline-for-selective-serotonin-reuptake-inhibitors-and-cyp2d6-and-cyp2c19/ | A | 1A | Actionable PGx | 25974703 |
| CYP2D6*4 | clomipramine | CYP2D6, CYP2C19 and Tricyclic Antidepressants | https://cpicpgx.org/guidelines/guideline-for-tricyclic-antidepressants-and-cyp2d6-and-cyp2c19/ | B | 1A | Actionable PGx | 23486447;27997040 |
