rs35599367 — CYP3A4 *22

Intronic splice variant causing ~50% reduced CYP3A4 mRNA expression, affecting metabolism of ~50% of all prescription drugs

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CYP3A4*22 — The Splice Variant That Rewrites Drug Dosing

CYP3A4 is the single most important drug-metabolizing enzyme in the human body. Located primarily in the liver and intestinal wall, it processes approximately 50% of all prescription medications11 approximately 50% of all prescription medications
Including statins, immunosuppressants, benzodiazepines, calcium channel blockers, HIV protease inhibitors, many antidepressants, and chemotherapy agents, making it the workhorse of human pharmacology. The *22 allele (rs35599367) is an intronic variant that disrupts normal mRNA splicing, reducing functional CYP3A4 protein production by roughly half. Unlike the more common but controversial CYP3A4*1B promoter variant, *22 has a clear, well-characterized mechanism and established clinical consequences.

The Mechanism

The rs35599367 variant sits in intron 6 of the CYP3A4 gene, 191 base pairs upstream of exon 7. On the plus strand, this is a G-to-A change at chromosome 7 position 99,768,693; on the coding strand (CYP3A4 is on the minus strand), it reads as C>T — hence the HGVS notation c.522-191C>T. The substitution destroys a predicted SF2/ASF splicing factor binding site22 destroys a predicted SF2/ASF splicing factor binding site
SF2/ASF is a serine/arginine-rich protein essential for constitutive and alternative splicing, causing a twofold or greater increase in formation of a nonfunctional alternative splice variant with partial retention of intron 6. The resulting aberrant transcript produces a truncated protein lacking the heme-binding domain required for catalytic activity.

In liver tissue, Wang et al. (2011)33 Wang et al. (2011)
Intronic polymorphism in CYP3A4 affects hepatic expression and response to statin drugs found that CYP3A4 mRNA levels in CC livers (coding-strand notation; GG on the plus strand) were 1.7-fold higher than in carriers, and enzyme activity was 2.5-fold greater (P=0.037). This effect is tissue-specific — the splicing defect occurs in liver-derived HepG2 cells but not in intestine-derived LS-174T cells44 liver-derived HepG2 cells but not in intestine-derived LS-174T cells
Suggesting the variant primarily affects hepatic rather than intestinal first-pass metabolism, which has important implications for drug bioavailability.

The Evidence

The discovery study by Wang et al. (2011)55 Wang et al. (2011)
Intronic polymorphism in CYP3A4 affects hepatic expression and response to statin drugs examined 136 human liver samples and 235 patients on CYP3A4-metabolized statins. Carriers of the *22 allele required only 27% of the statin dose needed by non-carriers for equivalent lipid control (P=0.019). This dramatic dose reduction was the first clinical evidence that an intronic CYP3A4 variant could predict drug response.

For immunosuppressants, the evidence is particularly strong. Elens et al. (2011)66 Elens et al. (2011)
A new functional CYP3A4 intron 6 polymorphism significantly affects tacrolimus pharmacokinetics showed that *22 carriers required 33% lower daily tacrolimus doses to reach target trough concentrations. When combined with CYP3A5 non-expresser status (*3/*3), carriers had an 8.7-fold increased odds ratio for supratherapeutic tacrolimus levels and a 179% increase in dose-adjusted trough concentration.

A 2023 meta-analysis of 8 studies77 2023 meta-analysis of 8 studies
Effects of CYP3A4*22 polymorphism on trough concentration of tacrolimus in kidney transplantation encompassing 2,683 renal transplant recipients confirmed that *22 carriers exhibited 0.57 ng/mL/mg higher dose-adjusted trough concentrations (P=0.0001) and required 2.02 mg/day less tacrolimus (P<0.00001). For cyclosporine, Elens et al. (2012)88 Elens et al. (2012)
CYP3A4*22 and cyclosporine in kidney transplantation found dose-adjusted concentrations were 1.6-fold higher in carriers, with an increased risk of delayed graft function and worse renal outcomes.

Beyond transplant medicine, the *22 allele affects an expanding list of drug classes. Cancer patients carrying *22 showed 170% higher everolimus concentrations99 170% higher everolimus concentrations
Review of CYP3A4*22 effects across drug classes, 89% higher ticagrelor area under the curve, 40% reduced erythromycin clearance, and 21% lower midazolam metabolic ratio. For HIV treatment, patients with *22/*22 had 53% lower lopinavir clearance1010 patients with *22/*22 had 53% lower lopinavir clearance
CYP3A4*22 is associated with lopinavir pharmacokinetics in HIV-positive adults compared to non-carriers.

The Dutch Pharmacogenetics Working Group (DPWG)1111 Dutch Pharmacogenetics Working Group (DPWG)
DPWG guideline for CYP3A4 and antipsychotics now includes CYP3A4 in its guidelines for quetiapine, recommending that poor metabolizers use 30% of the standard dose for non-depression indications or switch to an alternative antipsychotic for depression.

Practical Implications

The *22 allele is most common in Europeans (~5% allele frequency), moderately frequent in Latino populations (~2.6%), and rare in African (~0.9%), South Asian (~0.9%), and East Asian (<0.1%) populations. Because it follows codominant inheritance, heterozygous carriers (AG) show intermediate enzyme reduction while rare homozygotes (AA) have severely impaired CYP3A4.

The clinical impact is greatest for drugs with narrow therapeutic indices — where small changes in blood levels can mean the difference between efficacy and toxicity. Tacrolimus and cyclosporine in transplant medicine are the prime examples: too little leads to organ rejection, too much causes nephrotoxicity. Statins present a different concern: carriers may achieve target lipid levels on lower doses, but standard doses increase risk of myopathy and rhabdomyolysis.

For carriers who learn about their status, the key action is sharing this information with prescribers before starting any CYP3A4-metabolized medication. The variant is not yet included in routine pre-prescribing panels at most institutions, making patient-initiated disclosure especially valuable.

Interactions

The most clinically important interaction is between CYP3A4*22 and CYP3A5*3 (rs776746). CYP3A5 is a closely related enzyme that can partially compensate for reduced CYP3A4 activity. CYP3A5*3/*3 individuals (CYP3A5 non-expressers, roughly 80-90% of Europeans) lose this compensatory pathway. When a patient carries both CYP3A4*22 and CYP3A5*3/*3, total CYP3A activity drops dramatically — Elens et al. demonstrated an 8.7-fold increased odds of supratherapeutic tacrolimus levels in this combination. CPIC tacrolimus guidelines already incorporate CYP3A5 genotype; adding CYP3A4*22 refines the prediction substantially for CYP3A5 non-expressers.

CYP3A4*22 also interacts with the *1B promoter variant (rs2740574). If someone carries both *1B (uncertain effect on expression) and *22 (established decreased function), the *22 allele dominates the phenotype. Clinical guidance should follow *22 recommendations regardless of *1B status.

Drug-drug interactions compound the genetic effect. Strong CYP3A4 inhibitors (clarithromycin, ketoconazole, itraconazole, ritonavir, grapefruit juice) further reduce already-impaired enzyme activity in *22 carriers, creating potentially dangerous drug level spikes. Conversely, CYP3A4 inducers (rifampin, carbamazepine, St. John's wort) may partially overcome the genetic deficiency but make dosing unpredictable.

Drug Interactions

tacrolimus increased_toxicity CPIC
cyclosporine increased_toxicity literature
atorvastatin dose_adjustment literature
simvastatin dose_adjustment literature
lovastatin dose_adjustment literature
quetiapine increased_toxicity DPWG
ticagrelor increased_toxicity literature
everolimus increased_toxicity literature
sirolimus increased_toxicity literature
midazolam dose_adjustment literature
fentanyl dose_adjustment literature
lopinavir dose_adjustment literature

Genotype Interpretations

What each possible genotype means for this variant.

GG Normal Metabolizer Normal

Standard CYP3A4 enzyme activity from fully functional splicing

You have two copies of the normal CYP3A4 intron 6 sequence. Your CYP3A4 mRNA undergoes proper splicing, producing full-length functional enzyme at typical levels. This is the most common genotype globally, found in approximately 91% of people overall, including ~90% of Europeans, >99% of East Asians, and ~98% of Africans. Standard drug dosing protocols are designed for individuals with this genotype.

AG Intermediate Metabolizer Intermediate

Reduced CYP3A4 activity from one copy of the *22 splice variant

The single *22 allele disrupts an SF2/ASF splicing factor binding site in intron 6, causing approximately twofold higher production of an aberrant splice variant that retains part of intron 6 and produces a truncated, catalytically inactive protein. This effect is liver-specific — intestinal CYP3A4 appears unaffected, meaning first-pass hepatic metabolism is reduced while intestinal metabolism remains intact. The clinical consequence is a codominant intermediate phenotype: drug clearance is modestly to moderately reduced depending on the specific substrate, with effects ranging from 21% lower midazolam metabolism to 89% higher ticagrelor exposure.

The interaction with CYP3A5 status is critical. If you are also a CYP3A5 non-expresser (CYP3A5*3/*3, which is the case for ~85% of Europeans), your total CYP3A enzyme capacity is substantially reduced because you lack the compensatory CYP3A5 pathway.

AA Poor Metabolizer Poor

Severely reduced CYP3A4 activity from two copies of the *22 splice variant

With two *22 alleles, both copies of the CYP3A4 gene produce predominantly aberrant mRNA with intron 6 retention. Residual functional enzyme activity comes from the small fraction of correctly spliced transcripts. In the lopinavir study, *22/*22 patients showed 53% lower drug clearance compared to non-carriers. For tacrolimus, this genotype in combination with CYP3A5*3/*3 creates a metabolic bottleneck where the two major CYP3A enzymes are both severely impaired — the functional equivalent of a CYP3A ultra-poor metabolizer.

The DPWG has issued specific guidance for this metabolizer status: for quetiapine, use only 30% of the standard dose for non-depression indications, or choose an alternative drug entirely for depression. While formal guidelines for other CYP3A4 substrates are still being developed, the pharmacokinetic evidence consistently shows that standard doses produce dangerously elevated drug levels in this genotype.