rs10798156 (SLC4A1APP2): COVID-19 vaccine antibody
Key takeaways
- This variant was flagged in a pilot genome-wide association study (GWAS) of only 168 people examining antibody levels after inactivated COVID-19 vaccination, so findings are early-stage.
- The study found 41 independent genomic regions linked to IgG, total antibody, or neutralizing antibody levels, using a suggestive significance threshold (p < 5e-7).
- A discrepancy between reported SNP counts in the abstract (177) and the main text (117) of the source study highlights its preliminary nature.
- GTEx data link the alternate allele here to reduced expression of a nearby gene in tibial nerve and testis tissue, hinting at a regulatory role.
Key takeaways
- This variant was flagged in a pilot genome-wide association study (GWAS) of only 168 people examining antibody levels after inactivated COVID-19 vaccination, so findings are early-stage.
- The study found 41 independent genomic regions linked to IgG, total antibody, or neutralizing antibody levels, using a suggestive significance threshold (p < 5e-7).
- A discrepancy between reported SNP counts in the abstract (177) and the main text (117) of the source study highlights its preliminary nature.
- GTEx data link the alternate allele here to reduced expression of a nearby gene (ENSG00000285894) in tibial nerve and testis tissue, hinting at a regulatory role.
What the research says rs10798156, at the SLC4A1APP2-RN7SKP156 locus, appeared in a pilot genome-wide association study (GWAS) of 168 Beijing residents that tested whether common genetic variants predict levels of IgG (a class of protective antibody), total antibodies, or neutralizing antibodies (antibodies that can block viral entry) after two doses of inactivated SARS-CoV-2 vaccine (BBIBP-CorV or CoronaVac); 41 independent genomic regions reached the study's suggestive threshold of p < 5e-7, though per-variant statistics for this specific locus were not provided in the available text, and no replication cohort is described. Separately, expression-quantitative trait locus (eQTL) analysis from GTEx v11 (which tests whether a genetic variant influences the activity of a nearby gene) across 953 donors shows the alternate allele is associated with reduced expression of ENSG00000285894 in tibial nerve and testis tissue GTEx Portal.
Reported associations
- Antibody response to inactivated SARS-CoV-2 vaccine (IgG, total antibody, or neutralizing antibody): one of 41 independent loci identified at p < 5e-7 in a 168-participant pilot GWAS; the specific antibody subtype and per-variant effect size for this locus are not reported in the available text.
- Gene expression of ENSG00000285894 in tibial nerve: the alternate allele is associated with reduced expression (effect size -0.45, p = 7.0e-10) GTEx Portal.
- Gene expression of ENSG00000285894 in testis: the alternate allele is associated with reduced expression (effect size -0.41, p = 7.2e-6) GTEx Portal.
Evidence quality The association of rs10798156 with vaccine antibody response is preliminary. The source GWAS is explicitly labeled a pilot, with only 168 participants after quality filtering - a very small sample for this type of genome-wide scan. The threshold used (p < 5e-7) is more permissive than the conventional genome-wide standard of p < 5e-8, meaning some of the 41 reported loci may be chance associations. No independent replication cohort is described. The study also contains an internal discrepancy: the abstract reports 177 significant SNPs while the introduction reports 117, which reduces confidence in the precision of published counts. Per-variant statistics for this locus specifically were not available in the provided text. The GTEx eQTL data are better-powered (953 donors, FDR < 0.05) and show a robust p-value in tibial nerve (p = 7.0e-10), but an expression change in a tissue is a regulatory mechanism, not a clinical outcome, and no provided study links this expression signal to any downstream disease or trait GTEx Portal.
Tissue-specific expression effects
- ENSG00000285894 (a gene at this locus): the alternate allele is associated with reduced expression in tibial nerve and in testis tissue, based on GTEx v11 eQTL analysis of 953 donors GTEx Portal.
Lifestyle considerations No lifestyle considerations on file for this variant.
Frequently asked questions
What is rs10798156 associated with?
rs10798156, at the SLC4A1APP2-RN7SKP156 locus, was identified in a small pilot genome-wide association study as one of 41 genomic regions potentially linked to IgG, total antibody, or neutralizing antibody levels after inactivated SARS-CoV-2 vaccination. The evidence is preliminary and no independent replication has been reported.
What are SLC4A1APP2 and RN7SKP156?
SLC4A1APP2 and RN7SKP156 are the two genetic elements that flank and name the locus where rs10798156 sits. Their specific functional roles in vaccine antibody response are not established by the studies available for this variant.
How reliable is the evidence linking rs10798156 to COVID-19 vaccine response?
The evidence is weak. The source study had only 168 participants, applied a below-standard significance threshold, contained an internal inconsistency in reported SNP counts, and included no replication cohort. These factors mean the association should be treated as a hypothesis-generating signal rather than a confirmed finding.
What do the GTEx expression data show for rs10798156?
GTEx v11 data across 953 donors show the alternate allele at rs10798156 is linked to reduced expression of a nearby gene (ENSG00000285894) in tibial nerve and testis tissue. This is an expression-level signal and does not directly indicate any disease risk or clinical outcome.
Was rs10798156 studied in a large population?
No. The only GWAS study available for this variant included 168 participants, which is very small for genome-wide research. Findings from studies this size routinely require confirmation in much larger independent cohorts before they are considered reliable.