rs10057670 (RAB9BP1): Educational Attainment Variant

Key takeaways

• rs10057670 is located in the RAB9BP1 - RNA5SP189 genomic region and was among 1,271 genome-wide-significant variants associated with years of schooling in a study of over 1.1 million individuals.
• The study is one of the largest genetic analyses of educational attainment conducted, using a meta-analysis across European-ancestry cohorts.
• Across all 1,271 identified variants, the typical (median) effect per allele corresponds to approximately 1.7 weeks of additional schooling, ranging from 1.1 to 2.6 weeks (5th to 95th percentile).
• The identified variants as a group implicate genes involved in brain development and neuron-to-neuron communication.
• Polygenic scores derived from this study explain approximately 11% of variance in educational attainment and 7-10% of variance in cognitive performance.

What the research says A genome-wide association study (GWAS, a method that scans millions of genetic positions across the genome simultaneously) of educational attainment, measured as years of schooling completed, enrolled approximately 1.1 million individuals and identified 1,271 approximately independent genome-wide-significant single-nucleotide polymorphisms (SNPs, variants at a single genomic position), including rs10057670 at the RAB9BP1 - RNA5SP189 locus. The median effect size for lead SNPs (the most statistically significant representative from each associated region) corresponds to 1.7 weeks of schooling per allele, with a 5th-to-95th percentile range of 1.1 to 2.6 weeks. Polygenic scores (composite scores that sum effects across many variants genome-wide) derived from this analysis explain approximately 11% of variance in educational attainment and 7-10% of variance in cognitive performance in held-out test samples.

Reported associations

• Educational attainment (years of schooling completed): Identified as genome-wide significant in a meta-analysis of approximately 1.1 million European-ancestry individuals; the median effect per allele across all 1,271 identified variants corresponds to approximately 1.7 weeks of additional schooling, ranging from 1.1 to 2.6 weeks (5th to 95th percentile). Evidence of heterogeneous effects across environments was observed for the identified variants as a group. Polygenic scores built from these variants explain approximately 11% of educational attainment variance.

Evidence quality The discovery sample comprised approximately 1.1 million European-ancestry individuals in a sample-size-weighted meta-analysis across multiple cohorts, making this one of the largest GWAS of a behavioral trait at the time of publication. Genome-wide significance was set at P < 5x10^-8; 995 of the 1,271 lead SNPs also survived the stricter threshold of P < 1x10^-8. LD Score regression (a statistical method used to separate genuine polygenic signal from inflation due to population stratification bias) estimated that approximately 5% of test statistic inflation was attributable to bias, indicating that most inflation reflects true polygenic effects. Within-family sibling analyses in 22,135 sibling pairs were conducted as an additional robustness check. Previously reported SNP associations from a smaller study (N = 405,073) replicated in the non-overlapping portion of this dataset (N = 726,808) at rates consistent with theoretical expectations. The study was restricted to European-ancestry individuals, which limits generalizability to other populations. No independent replication specific to this locus is described in the provided source.

Lifestyle considerations No lifestyle considerations on file for this variant.