rs1934963 — CYP2C9

Deep intronic CYP2C9 variant associated with altered drug response

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CYP2C9 rs1934963 — Deep Intronic Variant Affecting Metabolizer Status

CYP2C9 is one of the most clinically important drug-metabolizing enzymes in the human body, responsible for clearing roughly 15-20% of all clinically used pharmaceuticals 11 CYP2C9 substrate drugs include warfarin, phenytoin, NSAIDs, and multiple sulfonylurea antidiabetics. The well-known functional variants CYP2C9*2 (rs1799853) and *3 (rs1057910) reduce enzyme activity by 50-90% and are the subject of CPIC and FDA pharmacogenomic guidance for warfarin and phenytoin. rs1934963 adds a deeper layer to this picture: a deep intronic variant sitting 2,674 nucleotides into intron 7 (NM_000771.4:c.961+2674T>C) that has emerged as an independent signal for variable drug response.

The Mechanism

Unlike CYP2C9*2 and *3, which directly alter the enzyme's active site through amino acid substitutions, rs1934963 lies within a non-coding intronic region and causes no protein change. Deep intronic variants can affect drug metabolism through several mechanisms: altered pre-mRNA splicing22 Cryptic splice sites in deep introns can be activated by single-nucleotide changes, diverting a fraction of transcripts toward aberrant mRNA isoforms, altered regulatory element binding affecting transcription factor access, or linkage disequilibrium with uncharacterized functional variants in the same genomic region. CYP2C9 is located on the minus strand of chromosome 10 (10q23.33); the plus-strand alleles T (reference) and C (alternate) correspond to the dbSNP-reported genotypes. The precise molecular mechanism by which the C allele influences CYP2C9 activity has not been established in functional biochemistry studies.

The Evidence

The primary pharmacogenomic evidence comes from a 2025 Indian cohort study of 144 type 2 diabetes mellitus patients stratified by HbA1c-defined drug response Mohanty et al. 202533 Mohanty et al. 2025
Mohanty IR et al. Association of CYP2C9, CYP2C19, CYP2C8, CYP2A6, and CYP3A4 gene polymorphism with drug response in an Indian cohort of T2DM. J Diabetes Metab Disord, 2025. The study found that rs1934963 polymorphism in CYP2C9 was significantly associated with drug response (P=0.001 across CYP2C9 genotypes), with wild-type T/T carriers demonstrating higher response rates to diabetes medications. The effect was observed alongside the established CYP2C9 variants rs2298037 and rs1057910 (*3).

This finding is promising but must be treated cautiously: the study was small (n=144), single-centre, and the abstract does not provide individual allele frequency data or effect sizes for rs1934963 alone. No replication study and no functional characterization study have yet been published for this specific variant. It has no entry in ClinVar and is not listed as part of any named CYP2C9 star allele in PharmVar, meaning it falls outside current CPIC/DPWG pharmacogenomic guidelines.

The C allele frequency is approximately 20% globally, with modest variation across ancestries (European ~20%, African ~22%, South Asian ~15%, East Asian ~11%).

Drug Interactions

glipizide dose_adjustment literature
glibenclamide dose_adjustment literature
tolbutamide dose_adjustment literature
warfarin dose_adjustment literature
ibuprofen increased_toxicity literature
celecoxib increased_toxicity literature

Genotype Interpretations

What each possible genotype means for this variant.

TT Normal Metabolizer Normal

Standard CYP2C9 activity at this intronic position

You carry two copies of the common T allele at rs1934963. About 65% of people globally share this genotype. Drug response for CYP2C9 substrates is governed primarily by other variants in this gene, particularly *2 (rs1799853) and *3 (rs1057910).

CT Intermediate Metabolizer Intermediate

One copy of the CYP2C9 intronic risk variant

rs1934963 sits 2,674 nucleotides into intron 7 of CYP2C9 (NM_000771.4:c.961+2674T>C), in a deep intronic position. Its mechanism of effect on enzyme activity is not established — possible routes include altered splicing, regulatory element effects, or tagging of a nearby functional variant. The C allele frequency (~20% globally) is consistent with a common modifier rather than a high-impact allele.

This variant does not appear in CPIC/DPWG guidelines and is not part of a named CYP2C9 star allele. Its clinical relevance is currently limited to the single published association study.

CC Poor Metabolizer Poor

Homozygous CYP2C9 intronic risk variant — potential for reduced enzyme activity

CC homozygosity at rs1934963 means both CYP2C9 alleles carry this intronic variant. If the C allele tags or causes reduced CYP2C9 expression or altered splicing in a codominant or additive pattern, CC carriers would have the greatest reduction in enzyme activity at this locus. Estimated genotype frequency is ~4% globally.

The available evidence (one study, n=144) is insufficient to quantify the specific effect size for homozygous carriers. This variant is not in CPIC/DPWG guidelines. CYP2C9 activity in CC carriers is still primarily determined by the *2 and *3 alleles; rs1934963 may represent an additional modifier. CYP2C9 phenotype testing (functional assays) or full gene sequencing could clarify the combined functional impact.