rs174546 — FADS1

3'UTR regulatory variant in FADS1 that disrupts a miR-149-5p binding site, reducing FADS1 desaturase expression by up to 30–60%; the T allele impairs conversion of linoleic acid to arachidonic acid and ALA to EPA, and is independently associated with elevated serum triglycerides.

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FADS1 rs174546 — 3'UTR Desaturase Control Switch

Most genetic variants in the FADS1 gene cluster affect expression through intronic regulatory elements, but rs174546 operates through a distinct mechanism: it sits in the 3' untranslated region11 3' untranslated region
3'UTR — the section of an mRNA transcript downstream of the protein-coding sequence, critical for mRNA stability, translation efficiency, and microRNA-mediated regulation of the FADS1 transcript, where it alters a binding site for the microRNA miR-149-5p. When the T allele is present, the miRNA binds more effectively and suppresses FADS1 translation — reducing the amount of delta-5 desaturase22 delta-5 desaturase
FADS1 — the enzyme responsible for the final step converting DGLA to arachidonic acid in the omega-6 pathway and ETA to EPA in the omega-3 pathway protein that reaches the cell. The functional and clinical consequences mirror the broader FADS1 impairment seen across the haplotype: elevated precursor fatty acids, lower long-chain PUFA products, and measurably higher serum triglycerides.

The Mechanism

rs174546 creates a quantifiable drop in FADS1 mRNA output through a two-layer miRNA mechanism. In a luciferase reporter study33 luciferase reporter study
Hermant et al. Identification of a functional FADS1 3'UTR variant associated with erythrocyte n-6 polyunsaturated fatty acids levels. J Clin Lipidol, 2018 of 540 subjects, the T allele haplotype reduced reporter gene activity by 30% at baseline. When miR-149-5p was co-expressed in the same system, the suppression deepened to 60% — and this amplified suppression was partially reversed when an miR-149-5p inhibitor was added, confirming that the miRNA is directly responsible for the allele-dependent effect.

Separately, the T allele interacts with miR-6728-3p in an in vivo Korean cohort44 in vivo Korean cohort
Lee et al. Functional Impact of the FADS1 rs174546 Single Nucleotide Polymorphism on Serum Lipid Levels. Mol Nutr Food Res, 2024 of 8,842 adults, confirming that the 3'UTR functional effect is not limited to a single miRNA species or a single cell line model. The downstream result of reduced FADS1 protein — regardless of which miRNA mediates it — is the same: the delta-5 desaturation step slows, DGLA accumulates in the omega-6 arm, and ETA-to-EPA conversion in the omega-3 arm is rate-limited.

What distinguishes rs174546 from other FADS1 variants on the platform is the mechanistic specificity: we know exactly which part of the gene is disrupted, which miRNA binds the disrupted site, and by how much transcription falls. This makes it the most directly characterized FADS1 3'UTR variant studied to date.

The Evidence

The triglyceride signal from rs174546 is independently documented in 8,842 Korean participants. Lee et al. 202455 Lee et al. 2024 found that each T allele increases fasting serum triglycerides by 6.48 ± 1.84 mg/dL — an additive effect consistent with reduced FADS1-mediated LC-PUFA production altering VLDL assembly and postprandial triglyceride clearance. The effect is detectable on a standard fasting lipid panel, not just on specialized fatty acid measurements, placing rs174546 in the same clinical-consequence tier as the more-studied rs174547.

The FADS1 locus-wide evidence anchors the population context. The landmark InCHIANTI GWAS66 landmark InCHIANTI GWAS
Tanaka et al. Genome-wide association study of plasma polyunsaturated fatty acids. PLoS Genet, 2009 demonstrated that the FADS1 haplotype (of which rs174546 is a member) accounts for 18.6% of all additive variance in circulating arachidonic acid — the largest explained variance for any common variant in PUFA metabolism. The CHARGE Consortium meta-analysis77 CHARGE Consortium meta-analysis
Lemaitre et al. Genetic loci associated with plasma phospholipid n-3 fatty acids. PLoS Genet, 2011 across 8,866 participants confirmed that FADS1 cluster minor alleles predict lower circulating EPA (p=5×10⁻⁵⁸) and higher plant-sourced ALA (p=3×10⁻⁶⁴), validated across European, African, Chinese, and Hispanic ancestry groups.

Practical Actions

The 3'UTR mechanism does not change the practical implication of carrying the T allele: FADS1 produces less delta-5 desaturase protein, and the conversion of ALA to EPA slows accordingly. For CT heterozygotes, 1–2 g preformed EPA+DHA daily from marine or algae-based sources supplements the partially impaired conversion step. For TT homozygotes, where both alleles carry the T variant, the suppression is more complete — 2–4 g daily becomes appropriate, and relying solely on plant- sourced ALA (flaxseed, chia, walnuts) is insufficient because that ALA requires the impaired FADS1 step to reach EPA.

The triglyceride association adds a monitoring dimension. Because each T allele raises fasting triglycerides by approximately 6.5 mg/dL, TT homozygotes may carry a baseline elevation of ~13 mg/dL from this variant alone — detectable on a standard lipid panel when combined with dietary and metabolic factors.

Interactions

rs174546 is in high linkage disequilibrium with the established FADS1 haplotype that includes rs174541, rs174547, rs174548, rs174537, rs174553, and rs174561. Users carrying the T allele at rs174546 are likely to carry risk alleles at these linked sites on the same chromosomal segment. The variants tag the same underlying expression phenotype; their individual entries on the platform add resolution to different functional evidence layers — rs174546 provides the 3'UTR miRNA mechanism while rs174541 and rs174547 provide intronic regulatory and clinical lipid evidence.

The ELOVL2 variant rs17606561 encodes elongase 2, which converts EPA to DHA downstream of the FADS1 desaturation step. A user carrying both FADS1 T alleles (reduced ALA→EPA conversion) and an ELOVL2 impairment (reduced EPA→DHA conversion) faces sequential blocks in the omega-3 synthesis chain. For this combined genotype, DHA-targeted supplementation (≥500 mg DHA specifically, not just total EPA+DHA) addresses the downstream block that EPA supplementation alone would not reach.

Nutrient Interactions

linoleic acid (LA) impaired_conversion
alpha-linolenic acid (ALA) impaired_conversion
eicosapentaenoic acid (EPA) increased_need
docosahexaenoic acid (DHA) increased_need
arachidonic acid (AA) altered_metabolism

Genotype Interpretations

What each possible genotype means for this variant.

CC Efficient Converter Normal

Reference genotype — normal FADS1 3'UTR function and typical omega-3 conversion efficiency

The CC genotype preserves the miR-149-5p binding site in the FADS1 3'UTR in its reference configuration. Luciferase reporter data from Hermant et al. 2018 showed that C allele constructs maintained full reporter activity, confirming the absence of miRNA-mediated suppression at this site.

In population terms, CC genotype frequency is highest in African ancestry groups (>90% carry CC, corresponding to T allele frequency of ~9%), where diets historically higher in preformed AA from animal protein may have reduced evolutionary selection for maximal FADS1 activity. Among Europeans (~33% T allele frequency), roughly 45% carry CC. East Asian populations have the highest T allele frequency (~46%), meaning CC is a minority genotype there (~30% of individuals).

CT Intermediate Converter Intermediate

One T allele — partially reduced FADS1 3'UTR expression with modest omega-3 conversion impairment and mild triglyceride elevation

CT heterozygotes sit in the intermediate zone confirmed by the Hermant et al. 2018 luciferase reporter data: the T allele reduces FADS1 3'UTR reporter activity by 30% at baseline, and this amplifies to 60% suppression in the presence of miR-149-5p — a microRNA expressed in liver and adipose tissue. As a CT carrier, one of your two FADS1 alleles is subject to enhanced miRNA suppression while the other (C allele) maintains reference expression, producing an intermediate desaturase output.

The practical consequence is that plant-sourced omega-3 precursors (ALA from flaxseed, chia, canola) remain partially convertible to EPA, but at a rate meaningfully below CC carriers. Dietary circumstances amplify this: on a consistent low-fish diet, the CT genotype becomes more consequential because there is less dietary preformed EPA to compensate for the conversion shortfall.

TT Poor Converter Poor Converter

Two T alleles — substantially reduced FADS1 3'UTR expression, impaired omega-3 conversion, and measurably elevated triglycerides

TT homozygotes carry the maximum FADS1 3'UTR suppression conferred by this variant. The mechanism is dose-dependent: both alleles of the FADS1 transcript carry the T substitution, and both are subject to the miR-149-5p and miR-6728-3p binding-site disruption demonstrated in Hermant et al. 2018 and Lee et al. 2024. The result is a substantial reduction in delta-5 desaturase protein output, impairing two parallel metabolic pathways: the omega-6 arm (LA → GLA → DGLA → AA) stalls at the DGLA→AA step, causing DGLA accumulation; the omega-3 arm (ALA → stearidonic acid → ETA → EPA) stalls at the ETA→EPA step, limiting endogenous EPA synthesis.

The triglyceride consequence reflects downstream effects on hepatic lipid metabolism: reduced LC-PUFA production alters the phospholipid composition of VLDL particles, affecting hepatic lipase clearance and postprandial triglyceride disposal. In TT homozygotes, this effect is maximal, and when compounded by a high omega-6/omega-3 dietary ratio, fasting triglycerides can cross the borderline-elevated threshold (150–199 mg/dL) even in otherwise metabolically healthy individuals.

Because ALA-to-EPA conversion in unimpaired individuals is already only 5–15%, and rs174546 TT substantially reduces FADS1 throughput at this step, flaxseed oil or chia seeds provide negligible EPA benefit for this genotype. Only preformed EPA from marine fish oil or algae oil bypasses the impaired desaturation step entirely.