rs12266933 (NUDT9P1): Educational Attainment
Key takeaways
- rs12266933 is one of 3,952 genome-wide significant variants tied to educational attainment in a study of roughly 3 million people.
- Together, variants like this one explain 12 to 16% of the variation in years of schooling completed.
- Roughly half the genetic signal for educational attainment reflects direct biological effects rather than shared family environment.
- In testis tissue, the alternative allele at this locus is linked to sharply increased NUDT9P1 expression, while in arteries expression is reduced.
- The ANKRD1 gene nearby also shows increased expression in the colon in carriers of the alternative allele.
Key takeaways
- rs12266933 is one of 3,952 genome-wide significant variants tied to educational attainment in a study of roughly 3 million people.
- Together, variants like this one explain 12 to 16% of the variation in years of schooling completed.
- Roughly half the genetic signal for educational attainment reflects direct biological effects rather than shared family environment.
- In testis tissue, the alternative allele at this locus is linked to sharply increased NUDT9P1 expression, while in arteries expression is reduced.
- The ANKRD1 gene nearby also shows increased expression in the colon in carriers of the alternative allele.
What the research says rs12266933 is located near or within NUDT9P1 (a pseudogene, meaning a gene-like DNA sequence not known to produce a functional protein) and was among the 3,952 approximately uncorrelated single-nucleotide polymorphisms (SNPs, single-letter DNA variants) reaching genome-wide significance in a meta-analysis of educational attainment covering approximately 3,037,499 individuals. Together, all identified variants power a polygenic index (a score that sums thousands of small genetic contributions) that explains 12 to 16% of variance in educational attainment depending on the validation cohort. Analyses comparing the polygenic index in individuals with and without parental genetic data indicate that direct effects account for roughly half the overall association, suggesting family-environment contributions also play a substantial role.
Reported associations
- Educational attainment (years of schooling): rs12266933 is among 3,952 SNPs at genome-wide significance in a GWAS of approximately 3,037,499 individuals; the full polygenic index from this study explains 13.28% of variance using the LDpred method and contributes to risk prediction for ten diseases examined in the same analysis.
Evidence quality The association with educational attainment comes from a single large-scale meta-analysis (N approximately 3,037,499), representing a substantial increase over the prior largest study (N approximately 1,131,881). The mean chi-squared statistic across genome-wide markers was 4.90, consistent with a large true polygenic signal rather than artifactual inflation. Cohorts include 23andMe participants and the UK Biobank, providing multi-cohort coverage across different study designs. A parallel dominance GWAS (N approximately 2,574,253) found zero genome-wide significant SNPs, suggesting the effect of variants at this locus on educational attainment is likely additive rather than recessive or dominant. No replication studies or conflicting findings specific to rs12266933 are present in the provided sources, and evidence for any individual-level interpretation of this locus is therefore preliminary.
Tissue-specific expression effects
- NUDT9P1: The alternative allele is linked to strongly increased expression in testis tissue and reduced expression in subcutaneous adipose tissue, tibial artery, aorta, and thyroid gland. GTEx Portal
- ENSG00000294447: The alternative allele is associated with reduced expression in testis. GTEx Portal
- ENSG00000286981: The alternative allele is linked to increased expression in testis. GTEx Portal
- ANKRD1 (ankyrin repeat domain 1): The alternative allele is associated with increased expression in the transverse colon. GTEx Portal
Lifestyle considerations No lifestyle considerations on file for this variant.
Frequently asked questions
What is NUDT9P1?
NUDT9P1 is a pseudogene, meaning a gene-like DNA sequence that is not known to produce a functional protein. GTEx data show that rs12266933 is associated with changes in NUDT9P1 expression across multiple tissues, with the largest effect seen as increased expression in testis tissue and reduced expression in arteries, adipose tissue, and thyroid.
Is rs12266933 linked to educational attainment?
Yes. A genome-wide association study of approximately 3 million people identified rs12266933 as one of 3,952 variants reaching genome-wide significance for years of schooling completed. No individual variant, including this one, has a large effect on its own; the full set together explains 12 to 16% of variation in educational attainment.
What does rs12266933 do in the body?
GTEx data show that the alternative allele at rs12266933 is associated with increased NUDT9P1 expression in testis and decreased expression in adipose tissue, arteries, and thyroid, while also linking to expression changes in nearby genes ENSG00000294447, ENSG00000286981, and ANKRD1 in the colon. The functional significance of these expression shifts for educational attainment has not been established by the provided sources.
Does this variant have a large effect on educational attainment?
No single variant, including rs12266933, explains a large fraction of educational attainment on its own. The full set of 3,952 genome-wide significant variants together powers a polygenic score explaining 12 to 16% of variance; any individual variant's contribution is a small fraction of that total.
Is the genetic effect on education direct or driven by family environment?
Analyses controlling for parental genetics suggest direct biological effects account for roughly half the polygenic association with educational attainment, with the remainder potentially reflecting shared family environment and assortative mating (the tendency for people with similar genetic profiles to pair together).