How Our Genes Impact Our Cognitive Abilities in Childhood
New research shows that rare and common DNA variants influence cognitive ability differently across childhood.
Our genes influence many traits—from hair and eye color to disease risk and our personality.
New research from the Wellcome Sanger Institute, published in Nature Human Behaviour, has illustrated how genetic makeup can affect cognitive ability in early life.
The importance of studying genetics in cognition
Cognitive abilities include problem solving, pattern recognition, and memory, which influence educational, economic, and health outcomes. Deficits in cognitive ability define intellectual disabilities—conditions that limit intelligence and disrupt the ability to live independently.
Cognitive abilities, IQ, intellectual disability, and neurodevelopmental disorders
Intellectual disabilities are classed as a neurodevelopmental disorder, as they are caused by impaired brain development in utero or in early childhood. They are characterized by deficits in cognitive abilities—usually measured using an intelligence quotient (IQ) score—and adaptive functioning, which refers to the ability to carry out daily tasks. Many psychiatric, medical, and other neurodevelopmental disorders co-occur with intellectual disability.
Cognitive ability is shaped by genetic and environmental factors. Genetic effects can be direct, i.e., genetic variants in an individual’s genome that affect their phenotype, or indirect, where genetic effects are mediated by the environment.
For example, “genetic nurture” is an indirect genetic effect that refers to how a parent’s genotype changes the environment for their offspring, which can affect the child’s phenotype. If a parent carries genetic variants linked to higher cognitive ability, they may provide greater learning support, which boosts their child’s cognitive ability, even if the child did not inherit the genetic variants.
The contributions and roles of direct and indirect genetic effects on cognitive ability as a child develops are currently understudied.
Genetic variants linked to cognitive ability in adults are also associated with cognitive deficits in rare neurodevelopmental conditions in children, but how they are correlated with early-life cognition remains unclear.
Furthermore, in some instances, parents can carry but be unaffected by rare DNA mutations that cause intellectual disability in their child, which is a major puzzle in clinical genetics known as incomplete penetrance.
Understanding the link between genetics and cognition in childhood may help explain why some genetic variations increase the risk of neurodevelopmental disease, as well as why some children struggle in school.
In the new study, the researchers used genotype and newly generated exome sequence data from children and parents in British birth cohorts to examine how genetic differences relate to a child’s cognitive ability, how this changes over time, and how the influence of genetics compares to other early-life factors.
Rare and common DNA variants both have an impact
The researchers examined two broad categories of genetic differences: rare and common.
Common DNA variants are small differences that are frequently seen in a population and can influence gene activity without damaging the genes. Rare DNA variants, however, can disrupt or damage gene function.
Common DNA variants were analyzed using a polygenic index (PGI) for educational attainment, which was split into cognitive and non-cognitive components. A polygenic index represents an individual’s genetic predisposition for a specific trait, based on the effects of genetic variants.
The researchers used three cohorts in the study, with the Avon Longitudinal Study of Parents and Children serving as the primary cohort. In this group, IQ was used as a measure of cognitive ability and was assessed at ages 4, 8, and 16. The additional cohorts were used to support these findings using alternative measures of cognitive performance.
Rare variant burden was strongly associated with cognition in early childhood, but this association weakened over time. In contrast, the link between common variants and cognitive ability strengthened as children aged.
This finding indicates that rare genetic variants affecting cognition have a greater influence in early childhood, highlighting the importance of this period for understanding how genetic differences influence development.
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It could also help explain incomplete penetrance—people who carry a rare damaging variant in a cognition-linked gene may outgrow its early effects and therefore not manifest the phenotype later in life.
“Understanding when genetic differences matter most could transform how we study human development and help explain why the same genetic variant can have very different consequences from one person to another. In the future, these findings may inform genetic counseling for families of children with intellectual disability,” said Dr. Hilary Martin, a group leader and senior author of the study.
Genetic influence compared to other factors in cognition
Analyzing the PGIs for parents’ educational attainment separated the indirect and direct genetic effects on cognition, leading the researchers to conclude that genetic influences on cognitive ability during childhood are driven by direct genetic effects.
Additionally, the researchers compared the impact of rare mutational burden and PGIs of educational attainment on IQ with that of other factors previously associated with children’s cognitive abilities, namely parental educational attainment, maternal illness during pregnancy, and premature birth.
The contributions of rare mutations to cognitive ability were found to be broadly comparable to the perinatal factors, and the direct genetic effects on a child’s PGI of educational attainment were found to be similar to the effect of a parent’s educational status, emphasizing the importance of considering genetic data in studies on the factors affecting cognitive outcomes.
“Our findings suggest that the effects of genetic variation can change substantially across childhood. We hope the findings encourage future research linking the genetics of cognitive ability in population-based cohorts to studies of intellectual disability,” said Dr. Daniel Malawsky, the first author of the new paper and PhD student at the Wellcome Sanger Institute.
Reference: Malawsky DS, Koko M, Danacek P, et al. Common and rare genetic variant associations with cognitive performance across development in British birth cohorts. Nat Hum Behav. 2026. doi: 10.1038/s41562-026-02491-8
This article is a rework of a press release issued by The Wellcome Sanger Institute. Material has been edited for length and content.
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