rs688 — LDLR Asn591Asn (c.1773C>T)

LDLR Exon 12 — A Silent Mutation With a Loud Effect on Cholesterol

The LDL receptor (LDLR) is the liver's primary tool for clearing low-density lipoprotein¹¹ low-density lipoprotein
LDL, the so-called "bad cholesterol," which ferries cholesterol through the bloodstream to tissues from the bloodstream. Mutations that disrupt LDLR function are the cause of familial hypercholesterolemia, one of the most common and dangerous inherited cardiovascular conditions. But you don't need a protein-changing mutation to impair LDLR function — rs688, a common polymorphism in exon 12, does it through a more subtle mechanism: altering how efficiently the LDLR gene's messenger RNA is spliced.

This variant — technically Asn591Asn (c.1773C>T) — causes no change to the protein sequence. The codon change (AAC→AAT) still encodes asparagine. Yet rs688 has measurable functional consequences on LDLR levels at the cell surface, LDL uptake, and ultimately plasma cholesterol. It represents a class of genetic variants increasingly recognized as important: synonymous variants that alter gene regulation rather than protein structure.

The Mechanism

LDLR pre-mRNA undergoes alternative splicing that can include or skip exon 12. When exon 12 is retained, the normal full-length LDLR receptor is produced. When it is skipped, a truncated, non-functional receptor is generated that is degraded by nonsense-mediated decay²² nonsense-mediated decay
NMD, a cellular quality-control mechanism that destroys mRNAs containing premature stop codons.

The rs688 C>T change neutralizes a putative exon splicing enhancer³³ putative exon splicing enhancer
ESE, a short sequence motif within the exon that recruits splicing factors to ensure the exon is included in the mature mRNA within exon 12. Without this enhancer signal, the splicing machinery is less likely to include exon 12 — reducing the fraction of LDLR mRNA that encodes functional receptor.

Gao et al. (2013)⁴⁴ Gao et al. (2013)
A common polymorphism in the LDL receptor gene has multiple effects on LDL receptor function, Human Molecular Genetics measured the downstream consequences in HepG2 liver cells: the minor (T) allele caused a 21.8% reduction in LDLR protein at the cell surface (P=0.012), a 25.7% increase in lysosomal mislocalization (P=0.037), and a 24.3% reduction in LDL uptake (P<0.01). The variant also impaired LDLR endosomal recycling and reduced binding to PCSK9, the regulator that controls LDLR degradation.

The splicing effect is quantified precisely: Lee et al. (2014)⁵⁵ Lee et al. (2014)
Mutual effect of rs688 and rs5925 in regulating low-density lipoprotein receptor splicing, DNA and Cell Biology showed that the T allele reduces exon 12 splicing efficiency by 9.36%±2.58% per allele. When combined with rs5925 (another LDLR polymorphism in the same haplotype block), the compound TT/TC haplotype produces the lowest splicing efficiency (68.54%±1.38%), compared to 79.60%±1.38% for the CC/CC haplotype.

This splicing reduction is also regulated by cellular sterol levels. Medina et al. (2011)⁶⁶ Medina et al. (2011)
Coordinately regulated alternative splicing of genes involved in cholesterol biosynthesis and uptake, PLoS One showed that cells normally increase LDLR exon 12 inclusion in response to low cholesterol — a feedback mechanism that boosts receptor production when cells need more cholesterol. In rs688 T allele carriers, this sterol-induced splicing regulation is blunted, impairing the body's ability to compensate for low-cholesterol states.

The Evidence

The clinical evidence connects splicing impairment to elevated LDL and cardiovascular risk. Zhu et al. (2007)⁷⁷ Zhu et al. (2007)
A common polymorphism decreases low-density lipoprotein receptor exon 12 splicing efficiency and associates with increased cholesterol, Human Molecular Genetics used the Framingham Offspring Study population to demonstrate that rs688 T allele carriers had approximately 10% higher total and LDL cholesterol than C allele homozygotes in pre-menopausal women. The effect was sex-dependent: it was absent or weak in men and post-menopausal women, suggesting that estrogen modulates the splicing mechanism or the downstream response to LDLR reduction.

Zou et al. (2008)⁸⁸ Zou et al. (2008)
Sex-dependent association of a common low-density lipoprotein receptor polymorphism with RNA splicing efficiency in the brain and Alzheimer's disease, Human Molecular Genetics found the opposite sex dependence in neural tissue: in brain samples from aged individuals, the T allele was associated with decreased LDLR exon 12 splicing efficiency specifically in males, not females. This tissue- and sex-dependent variation suggests the variant's effect depends on the splicing factor environment, which differs between liver and brain and varies with sex hormones.

At the cardiovascular disease level, a 2026 study from Bangladesh by Hossain et al.⁹⁹ Hossain et al.
Association of the rs688 Polymorphism in LDLR with Coronary Artery Disease, Genetics Research examined 225 participants (150 CAD patients, 75 controls) and found TT genotype carriers had 3.6-fold higher odds of coronary artery disease (OR=3.617, 95% CI: 1.089–10.05, P=0.035), with significantly elevated LDL cholesterol in TT and CT genotypes compared to CC. This study is limited by its small sample size and single-population design, but the direction of effect is consistent with the mechanistic evidence.

The GWAS Catalog records multiple genome-wide significant associations between rs688 and LDL and total cholesterol levels across large multi-ancestry studies (P=5×10⁻³⁰ for LDL, P=4×10⁻²⁸ for total cholesterol), confirming at population scale what the mechanistic studies show at the molecular level.

Practical Implications

The rs688 T allele is common — about 43% globally in European populations — so TT homozygosity (roughly 18% of Europeans) is not a rare finding. Unlike the rare LDLR mutations causing classical familial hypercholesterolemia, rs688 produces a modest per-allele effect. However, the magnitude of LDL elevation (~10% in susceptible individuals) is clinically relevant: a 10% LDL increase corresponds roughly to a 10-15% increase in cardiovascular event risk over a lifetime.

For TT homozygotes, the practical implications are earlier attention to lipid panels and consideration of lifestyle and pharmacological interventions at lower LDL thresholds than might be applied to the general population. The sex-dependent effects suggest pre-menopausal women carrying TT may be disproportionately affected and should be the highest-priority group for monitoring.

rs688 does not cause familial hypercholesterolemia and is classified as benign in ClinVar for that specific condition — meaning it is not a high-penetrance mutation that guarantees disease. It is best understood as a common functional variant that modestly shifts the LDL distribution upward and, at the population level, contributes meaningfully to cardiovascular risk.

Interactions

rs688 interacts with rs5925, another LDLR exon 12 polymorphism. The two variants regulate splicing cooperatively: the compound haplotype carrying both T alleles (rs688-T / rs5925-T) produces the lowest splicing efficiency (68.54%), while the C/C haplotype produces the highest (79.60%). When both variants are present in the same individual, the splicing deficit is additive.

LDLR splicing variants interact broadly with other cholesterol metabolism genes. Carriers of APOE ε4 (rs429358/rs7412) already face impaired LDL clearance due to apolipoprotein E binding differences; rs688-driven LDLR surface reduction compounds this deficit. PCSK9 gain-of-function variants (rs11590235) further reduce LDLR survival on the cell surface — rs688 TT homozygotes carrying a PCSK9 gain-of-function mutation face LDL reduction from two independent mechanisms simultaneously.

In individuals on statins: statins increase LDLR expression by inhibiting cholesterol synthesis and activating SREBP-mediated transcription. However, if rs688 simultaneously reduces the efficiency of LDLR pre-mRNA splicing, the net LDLR surface increase from statin therapy may be blunted relative to individuals with the CC genotype — an interaction worth exploring in pharmacogenomics research.