rs115440539 (ALX1): Liver Protein Expression pQTL
Key takeaways
- rs115440539 near the ALX1 gene was identified as a protein quantitative trait locus (pQTL) in human liver tissue
- A pQTL variant influences how much of a specific protein a cell produces, distinct from effects measured at the RNA level
- The study used 287 human liver samples and found nearly 5,000 pQTL variants; over 2,000 were undetected by prior RNA-level studies
- Specific effect sizes and p-values for rs115440539 are not available from the provided study text, so findings should be treated as preliminary
Key takeaways
- rs115440539 near the ALX1 gene was identified as a protein quantitative trait locus (pQTL) in human liver tissue
- A pQTL variant influences how much of a specific protein a cell produces, which is distinct from effects on RNA levels
- The study used 287 human liver samples and found nearly 5,000 pQTL variants total; over 2,000 of them had not been detected by prior RNA-level studies
- Specific effect sizes and statistical data for rs115440539 are not present in the provided study excerpt
What the research says A genome-wide pQTL study in 287 normal human liver samples (He B et al., BMC Biology, 2021) identified thousands of genetic variants influencing protein expression levels in liver tissue. The authors found that mRNA and protein expression correlate poorly for many genes, indicating that post-transcriptional mechanisms (such as differences in protein translation or protein degradation) are partly under genetic control. Across all samples, 1,508 liver proteins were absolutely quantified, and 900 local and 4,026 distant pQTL variants were identified; rs115440539 was among the variants reported, but no variant-specific statistics appear in the provided study text.
Reported associations
- Liver protein expression (pQTL): rs115440539 was identified in a genome-wide pQTL analysis of 287 human liver samples as part of a set of 4,926 total pQTL variants (900 local, 4,026 distant); whether it is a local or distant pQTL and which specific protein it affects are not specified in the provided text (He B et al., BMC Biology, 2021)
Evidence quality The study by He B et al. (BMC Biology, 2021) quantified 1,508 proteins across 287 normal human liver samples using data-independent acquisition mass spectrometry, a relatively small sample size compared to large genome-wide association studies that typically include tens of thousands of participants. The study identified a total of 4,926 pQTL variants and noted that over 2,000 of them had not been detected in prior mRNA-level eQTL studies, pointing to a distinct post-transcriptional layer of genetic regulation. No variant-specific p-values, odds ratios, or effect sizes for rs115440539 are available from the provided study text, and no independent replication of this variant in a separate cohort is described. Evidence for this variant should be considered preliminary pending confirmation in larger datasets.
Lifestyle considerations No lifestyle considerations on file for this variant.
Frequently asked questions
What is rs115440539?
rs115440539 is a single-nucleotide polymorphism, meaning a position in the human genome where one DNA letter varies between people, located near the ALX1 gene. It was identified in a genome-wide protein quantitative trait locus (pQTL) study of human liver tissue.
What is a pQTL and how is it different from an eQTL?
A protein quantitative trait locus (pQTL) is a genetic variant associated with the amount of a specific protein produced in a cell. An expression quantitative trait locus (eQTL) is associated with RNA levels. Because protein and RNA levels often diverge, pQTL studies can capture genetic regulation that RNA-only studies miss.
How was rs115440539 discovered?
It was identified in a genome-wide pQTL study that absolutely quantified 1,508 proteins across 287 normal human liver samples using mass spectrometry-based proteomics. The study reported 4,926 pQTL variants in total across the genome.
How strong is the evidence for rs115440539?
The evidence is preliminary. It comes from a single study of 287 liver samples with no described independent replication. Variant-specific effect sizes and p-values are not available from the provided study text.
Is rs115440539 linked to any liver disease?
The broader pQTL study noted potential connections between pQTL variants as a group and liver diseases including alcohol dependence, but no direct link between rs115440539 specifically and any disease is reported in the available study text.