rs117677995 (IGSF9B): Educational Attainment SNP

Key takeaways

• rs117677995 is one of 1,271 DNA variants linked to years of schooling in a genome-wide study of more than 1.1 million people
• Genes at this locus, including IGSF9B, are implicated in brain development and neuron-to-neuron communication
• Polygenic scores using all educational attainment variants explain 11-13% of variation in years of schooling
• The alternate allele is associated with higher expression of the nearby gene SPATA19 in esophageal tissue
• Individual-SNP effects on educational attainment are modest; across all 1,271 lead SNPs the median effect is about 1.7 weeks of schooling per allele

What the research says A genome-wide association study (GWAS, a scan of millions of DNA positions across the genome) of approximately 1.1 million individuals of European ancestry identified 1,271 independent genome-wide significant SNPs (single-nucleotide polymorphisms, meaning single-letter DNA differences) for educational attainment measured as years of schooling completed; the IGSF9B locus is among those implicated. Genes at the identified loci are enriched for functions in brain development and neuron-to-neuron communication. A joint analysis of educational attainment alongside cognitive test performance (n=257,841), self-reported math ability (n=564,698), and highest math class completed (n=430,445) produced polygenic scores (weighted sums of many variants) explaining 11-13% of variance in years of schooling and 7-10% of variance in cognitive performance.

Reported associations

• Educational attainment (years of schooling): rs117677995, at the IGSF9B locus, is among 1,271 genome-wide significant loci identified in a meta-analysis of over 1.1 million individuals; the median effect across all lead SNPs is approximately 1.7 weeks of schooling per allele, with the 5th-to-95th-percentile range spanning 1.1 to 2.6 weeks per allele
• Cognitive performance: The same study conducted joint GWAS with cognitive test performance (n=257,841), self-reported math ability (n=564,698), and highest math class completed (n=430,445); polygenic scores from the joint model explain 7-10% of variance in cognitive performance

Evidence quality The educational attainment GWAS reporting this locus is among the largest genetic studies of a behavioral trait to date, with a sample exceeding 1.1 million individuals. LD Score regression (a statistical method that separates genuine polygenic signal from confounded inflation) attributes approximately 5% of the observed test-statistic inflation to bias, with the remainder consistent with true polygenic signal; the LD Score intercept was 1.11. Within-family analyses across 22,135 sibling pairs in four cohorts were conducted to probe robustness against population stratification (a confound in which ancestry differences track with environmental differences). The genome-wide significance threshold applied was P < 5x10^-8; applying a stricter threshold of P < 1x10^-8 reduces the count to 995 loci. Individual-level effect-size estimates or replication data specific to rs117677995 are not provided in the available study text; this SNP is one of 1,271 collectively identified loci. Evidence for complex behavioral traits from GWAS, even at this scale, remains preliminary at the level of any single variant.

Tissue-specific expression effects

• SPATA19: The alternate allele at this locus is associated with increased expression of SPATA19 (Spermatogenesis-Associated Protein 19) in esophageal mucosa, the tissue lining the inner surface of the food pipe; the positive slope indicates the effect allele raises SPATA19 expression in this tissue; this is a cis-eQTL (a variant affecting a gene located nearby on the chromosome) and does not directly translate to a clinical or educational outcome GTEx Portal

Lifestyle considerations No lifestyle considerations on file for this variant.