rs11204828 (POGZ-CGN): Multi-tissue expression eQTL
Key takeaways
- The ALT allele reduces POGZ expression in six tissues including brain cerebellum, skeletal muscle, and whole blood.
- The same allele increases CGN (cingulin, a tight-junction protein) expression in esophageal muscle tissue.
- SELENBP1 expression in thyroid is reduced with a p-value of 1.4e-40, an exceptionally strong eQTL signal.
- This variant was studied in a metabolic GWAS of 490 elite athletes.
- These are gene expression effects from population-level data (953 donors), not direct disease associations.
Key takeaways
- The ALT allele reduces POGZ expression across six tissues: brain cerebellum, cerebellar hemisphere, skeletal muscle, esophagus, whole blood, and tibial nerve.
- The same allele increases CGN expression in esophageal muscularis - the opposite direction from the POGZ effect seen in a neighboring esophageal tissue site.
- SELENBP1 expression in thyroid is reduced with a very strong statistical signal (p=1.4e-40 in a 953-donor tissue expression dataset).
- This variant was examined in a metabolic genome-wide association study (mGWAS) of 490 elite athletes, but no specific metabolite association for this locus is confirmed in the available sources.
- All listed associations are gene expression effects (eQTLs), not direct links to disease or health outcomes.
What the research says A metabolic genome-wide association study (mGWAS) conducted in 490 elite athletes identified common genetic variants linked to serum metabolite levels, with the goal of finding genetically-influenced metabolites tied to athletic performance and endurance sports. Tissue-specific expression analysis from GTEx v11 (953 donors, cis-window, FDR<0.05) identifies rs11204828 as an expression quantitative trait locus (eQTL, meaning a variant that predicts how much of a nearby gene gets made) for three genes, POGZ, CGN, and SELENBP1, across eight statistically significant tissue-gene pairings GTEx Portal.
Reported associations
- POGZ expression (six tissues): The ALT allele is associated with reduced expression in brain cerebellum (slope -0.29, p=3.5e-7), cerebellar hemisphere (slope -0.24, p=1.7e-8), skeletal muscle (slope -0.20, p=2.0e-13), esophagus gastroesophageal junction (slope -0.17, p=1.2e-12), whole blood (slope -0.15, p=3.4e-13), and tibial nerve (slope -0.14, p=4.2e-19) GTEx Portal
- CGN expression (esophagus muscularis): The ALT allele is associated with increased expression (slope +0.27, p=8.1e-8) GTEx Portal
- SELENBP1 expression (thyroid): The ALT allele is associated with reduced expression (slope -0.46, p=1.4e-40) GTEx Portal
Evidence quality All eQTL associations come from GTEx v11, which profiled 953 donors across multiple tissues using a FDR-controlled cis-window mapping approach. P-values for the POGZ associations range from 3.5e-7 in brain cerebellum to 4.2e-19 in tibial nerve, and the SELENBP1 thyroid signal reaches p=1.4e-40, which is an unusually strong eQTL effect by any standard threshold. These findings indicate a consistent directional effect of the ALT allele on nearby gene expression, but eQTL associations measure gene regulatory effects and do not on their own establish links to disease or clinical outcomes. No PMID was provided for the elite athlete mGWAS referenced here, and the available study excerpt does not name rs11204828 or the POGZ-CGN locus explicitly in its text, so no specific metabolite association from that study can be attributed to this variant based on the materials provided. No independent replication of these eQTL associations appears in the provided materials.
Tissue-specific expression effects
- POGZ: Reduced expression in brain (cerebellum and cerebellar hemisphere), skeletal muscle, esophagus gastroesophageal junction, whole blood, and tibial nerve GTEx Portal
- CGN: Increased expression in esophagus muscularis GTEx Portal
- SELENBP1: Reduced expression in thyroid GTEx Portal
Lifestyle considerations No lifestyle considerations on file for this variant.
Frequently asked questions
What genes does rs11204828 affect?
rs11204828 is associated with reduced expression of POGZ in six tissues (brain, muscle, blood, esophagus, and nerve), reduced SELENBP1 expression in thyroid, and increased CGN expression in esophageal muscle. These are gene regulatory effects measured in population-scale expression data.
What does the POGZ gene do?
POGZ (Pogo transposable element-derived protein with ZNF domain) is a chromatin-associated protein involved in regulating gene activity in cells. It has been studied in contexts related to neurodevelopment and intellectual disability.
Is rs11204828 linked to athletic performance?
This variant was included in a metabolic genome-wide association study of 490 elite athletes searching for genetically-influenced metabolites. The available study text does not specify which metabolite, if any, rs11204828 was directly associated with, so any athletic performance link remains unconfirmed from the sources reviewed.
What is CGN (cingulin) and why does it appear here?
CGN encodes cingulin, a structural protein found at tight junctions - the molecular seals between adjacent cells that help control what substances pass between them. The ALT allele of rs11204828 is associated with increased CGN expression specifically in esophageal muscularis tissue.
How strong is the evidence for rs11204828 expression effects?
The eQTL data comes from GTEx v11 with 953 donors and rigorous FDR-controlled statistical thresholds. The strongest signal is for SELENBP1 in thyroid at p=1.4e-40. However, these are gene expression measurements, not disease risk estimates, and no independent replication is described in the available materials.